A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks.

PubMed

Park, HoSung; Kim, Beom-Su; Kim, Kyong Hoon; Shah, Babar; Kim, Ki-Il

2017-11-09

Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new ( m , k )-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the ( m , k )-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured ( m , k )-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption.

Environmental impacts of forest road construction on mountainous terrain.

PubMed

Caliskan, Erhan

2013-03-15

Forest roads are the base infrastructure foundation of forestry operations. These roads entail a complex engineering effort because they can cause substantial environmental damage to forests and include a high-cost construction. This study was carried out in four sample sites of Giresun, Trabzon(2) and Artvin Forest Directorate, which is in the Black Sea region of Turkey. The areas have both steep terrain (30-50% gradient) and very steep terrain (51-80% gradient). Bulldozers and hydraulic excavators were determined to be the main machines for forest road construction, causing environmental damage and cross sections in mountainous areas.As a result of this study, the percent damage to forests was determined as follows: on steep terrain, 21% of trees were damaged by excavators and 33% of trees were damaged by bulldozers during forest road construction, and on very steep terrain, 27% of trees were damaged by excavators and 44% of trees were damaged by bulldozers during forest road construction. It was also determined that on steep terrain, when excavators were used, 12.23% less forest area was destroyed compared with when bulldozers were used and 16.13% less area was destroyed by excavators on very steep terrain. In order to reduce the environmental damage on the forest ecosystem, especially in steep terrains, hydraulic excavators should replace bulldozers in forest road construction activities.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

PubMed Central

Chesters, Douglas

2017-01-01

Abstract Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. PMID:27798407

OCTGRAV: Sparse Octree Gravitational N-body Code on Graphics Processing Units

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-10-01

Octgrav is a very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The algorithms are based on parallel-scan and sort methods. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way, a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s is achieved. It takes about a second to compute forces on a million particles with an opening angle of heta approx 0.5. To test the performance and feasibility, we implemented the algorithms in CUDA in the form of a gravitational tree-code which completely runs on the GPU. The tree construction and traverse algorithms are portable to many-core devices which have support for CUDA or OpenCL programming languages. The gravitational tree-code outperforms tuned CPU code during the tree-construction and shows a performance improvement of more than a factor 20 overall, resulting in a processing rate of more than 2.8 million particles per second. The code has a convenient user interface and is freely available for use.

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

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

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

Towards organ printing: engineering an intra-organ branched vascular tree.

PubMed

Visconti, Richard P; Kasyanov, Vladimir; Gentile, Carmine; Zhang, Jing; Markwald, Roger R; Mironov, Vladimir

2010-03-01

Effective vascularization of thick three-dimensional engineered tissue constructs is a problem in tissue engineering. As in native organs, a tissue-engineered intra-organ vascular tree must be comprised of a network of hierarchically branched vascular segments. Despite this requirement, current tissue-engineering efforts are still focused predominantly on engineering either large-diameter macrovessels or microvascular networks. We present the emerging concept of organ printing or robotic additive biofabrication of an intra-organ branched vascular tree, based on the ability of vascular tissue spheroids to undergo self-assembly. The feasibility and challenges of this robotic biofabrication approach to intra-organ vascularization for tissue engineering based on organ-printing technology using self-assembling vascular tissue spheroids including clinically relevantly vascular cell sources are analyzed. It is not possible to engineer 3D thick tissue or organ constructs without effective vascularization. An effective intra-organ vascular system cannot be built by the simple connection of large-diameter vessels and microvessels. Successful engineering of functional human organs suitable for surgical implantation will require concomitant engineering of a 'built in' intra-organ branched vascular system. Organ printing enables biofabrication of human organ constructs with a 'built in' intra-organ branched vascular tree.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

USDA-ARS?s Scientific Manuscript database

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

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

PubMed

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

2014-05-06

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

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

PubMed

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

2012-01-01

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

A Tree Based Broadcast Scheme for (m, k)-firm Real-Time Stream in Wireless Sensor Networks

PubMed Central

Park, HoSung; Kim, Beom-Su; Kim, Kyong Hoon; Shah, Babar; Kim, Ki-Il

2017-01-01

Recently, various unicast routing protocols have been proposed to deliver measured data from the sensor node to the sink node within the predetermined deadline in wireless sensor networks. In parallel with their approaches, some applications demand the specific service, which is based on broadcast to all nodes within the deadline, the feasible real-time traffic model and improvements in energy efficiency. However, current protocols based on either flooding or one-to-one unicast cannot meet the above requirements entirely. Moreover, as far as the authors know, there is no study for the real-time broadcast protocol to support the application-specific traffic model in WSN yet. Based on the above analysis, in this paper, we propose a new (m, k)-firm-based Real-time Broadcast Protocol (FRBP) by constructing a broadcast tree to satisfy the (m, k)-firm, which is applicable to the real-time model in resource-constrained WSNs. The broadcast tree in FRBP is constructed by the distance-based priority scheme, whereas energy efficiency is improved by selecting as few as nodes on a tree possible. To overcome the unstable network environment, the recovery scheme invokes rapid partial tree reconstruction in order to designate another node as the parent on a tree according to the measured (m, k)-firm real-time condition and local states monitoring. Finally, simulation results are given to demonstrate the superiority of FRBP compared to the existing schemes in terms of average deadline missing ratio, average throughput and energy consumption. PMID:29120404

Further Effects of Phylogenetic Tree Style on Student Comprehension in an Introductory Biology Course.

PubMed

Dees, Jonathan; Bussard, Caitlin; Momsen, Jennifer L

2018-06-01

Phylogenetic trees have become increasingly important across the life sciences, and as a result, learning to interpret and reason from these diagrams is now an essential component of biology education. Unfortunately, students often struggle to understand phylogenetic trees. Style (i.e., diagonal or bracket) is one factor that has been observed to impact how students interpret phylogenetic trees, and one goal of this research was to investigate these style effects across an introductory biology course. In addition, we investigated the impact of instruction that integrated diagonal and bracket phylogenetic trees equally. Before instruction, students were significantly more accurate with the bracket style for a variety of interpretation and construction tasks. After instruction, however, students were significantly more accurate only for construction tasks and interpretations involving taxa relatedness when using the bracket style. Thus, instruction that used both styles equally mitigated some, but not all, style effects. These results inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

An Extension of CART's Pruning Algorithm. Program Statistics Research Technical Report No. 91-11.

ERIC Educational Resources Information Center

Kim, Sung-Ho

Among the computer-based methods used for the construction of trees such as AID, THAID, CART, and FACT, the only one that uses an algorithm that first grows a tree and then prunes the tree is CART. The pruning component of CART is analogous in spirit to the backward elimination approach in regression analysis. This idea provides a tool in…

Using traveling salesman problem algorithms for evolutionary tree construction.

PubMed

Korostensky, C; Gonnet, G H

2000-07-01

The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity. We present a new tree construction method that constructs a tree with minimum score for a given set of sequences, where the score is the amount of evolution measured in PAM distances. To do this, the problem of tree construction is reduced to the Traveling Salesman Problem (TSP). The input for the TSP algorithm are the pairwise distances of the sequences and the output is a circular tour through the optimal, unknown tree plus the minimum score of the tree. The circular order and the score can be used to construct the topology of the optimal tree. Our method can be used for any scoring function that correlates to the amount of changes along the branches of an evolutionary tree, for instance it could also be used for parsimony scores, but it cannot be used for least squares fit of distances. A TSP solution reduces the space of all possible trees to 2n. Using this order, we can guarantee that we reconstruct a correct evolutionary tree if the absolute value of the error for each distance measurement is smaller than f2.gif" BORDER="0">, where f3.gif" BORDER="0">is the length of the shortest edge in the tree. For data sets with large errors, a dynamic programming approach is used to reconstruct the tree. Finally simulations and experiments with real data are shown.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

PubMed

Chesters, Douglas

2017-05-01

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Environmental impacts of forest road construction on mountainous terrain

PubMed Central

2013-01-01

Forest roads are the base infrastructure foundation of forestry operations. These roads entail a complex engineering effort because they can cause substantial environmental damage to forests and include a high-cost construction. This study was carried out in four sample sites of Giresun, Trabzon(2) and Artvin Forest Directorate, which is in the Black Sea region of Turkey. The areas have both steep terrain (30-50% gradient) and very steep terrain (51-80% gradient). Bulldozers and hydraulic excavators were determined to be the main machines for forest road construction, causing environmental damage and cross sections in mountainous areas. As a result of this study, the percent damage to forests was determined as follows: on steep terrain, 21% of trees were damaged by excavators and 33% of trees were damaged by bulldozers during forest road construction, and on very steep terrain, 27% of trees were damaged by excavators and 44% of trees were damaged by bulldozers during forest road construction. It was also determined that on steep terrain, when excavators were used, 12.23% less forest area was destroyed compared with when bulldozers were used and 16.13% less area was destroyed by excavators on very steep terrain. In order to reduce the environmental damage on the forest ecosystem, especially in steep terrains, hydraulic excavators should replace bulldozers in forest road construction activities. PMID:23497078

Investigating Tree Thinking & Ancestry with Cladograms

ERIC Educational Resources Information Center

Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

2015-01-01

Interpreting cladograms is a key skill for biological literacy. In this lesson, students interpret cladograms based on familial relationships and language relationships to build their understanding of tree thinking and to construct a definition of "common ancestor." These skills can then be applied to a true biological cladogram.

Improving estimation of tree carbon stocks by harvesting aboveground woody biomass within airborne LiDAR flight areas

NASA Astrophysics Data System (ADS)

Colgan, M.; Asner, G. P.; Swemmer, A. M.

2011-12-01

The accurate estimation of carbon stored in a tree is essential to accounting for the carbon emissions due to deforestation and degradation. Airborne LiDAR (Light Detection and Ranging) has been successful in estimating aboveground carbon density (ACD) by correlating airborne metrics, such as canopy height, to field-estimated biomass. This latter step is reliant on field allometry which is applied to forest inventory quantities, such as stem diameter and height, to predict the biomass of a given tree stem. Constructing such allometry is expensive, time consuming, and requires destructive sampling. Consequently, the sample sizes used to construct such allometry are often small, and the largest tree sampled is often much smaller than the largest in the forest population. The uncertainty resulting from these sampling errors can lead to severe biases when the allometry is applied to stems larger than those harvested to construct the allometry, which is then subsequently propagated to airborne ACD estimates. The Kruger National Park (KNP) mission of maintaining biodiversity coincides with preserving ecosystem carbon stocks. However, one hurdle to accurately quantifying carbon density in savannas is that small stems are typically harvested to construct woody biomass allometry, yet they are not representative of Kruger's distribution of biomass. Consequently, these equations inadequately capture large tree variation in sapwood/hardwood composition, root/shoot/leaf allocation, branch fall, and stem rot. This study eliminates the "middleman" of field allometry by directly measuring, or harvesting, tree biomass within the extent of airborne LiDAR. This enables comparisons of field and airborne ACD estimates, and also enables creation of new airborne algorithms to estimate biomass at the scale of individual trees. A field campaign was conducted at Pompey Silica Mine 5km outside Kruger National Park, South Africa, in Mar-Aug 2010 to harvest and weigh tree mass. Since harvesting of trees is not possible within KNP, this was a unique opportunity to fell trees already scheduled to be cleared for mining operations. The area was first flown by the Carnegie Airborne Observatory in early May, prior to harvest, to enable correlation of LiDAR-measured tree height and crown diameter to harvested tree mass. Results include over 4,000 harvested stems and 13 species-specific biomass equations, including seven Kruger woody species previously without allometry. We found existing biomass stem allometry over-estimates ACD in the field, whereas airborne estimates based on harvest data avoid this bias while maintaining similar precision to field-based estimates. Lastly, a new airborne algorithm estimating biomass at the tree-level reduced error from tree canopies "leaning" into field plots but whose stems are outside plot boundaries. These advances pave the way to better understanding of savanna and forest carbon density at landscape and regional scales.

Towards organ printing: engineering an intra-organ branched vascular tree

PubMed Central

Visconti, Richard P; Kasyanov, Vladimir; Gentile, Carmine; Zhang, Jing; Markwald, Roger R; Mironov, Vladimir

2013-01-01

Importance of the field Effective vascularization of thick three-dimensional engineered tissue constructs is a problem in tissue engineering. As in native organs, a tissue-engineered intra-organ vascular tree must be comprised of a network of hierarchically branched vascular segments. Despite this requirement, current tissue-engineering efforts are still focused predominantly on engineering either large-diameter macrovessels or microvascular networks. Areas covered in this review We present the emerging concept of organ printing or robotic additive biofabrication of an intra-organ branched vascular tree, based on the ability of vascular tissue spheroids to undergo self-assembly. What the reader will gain The feasibility and challenges of this robotic biofabrication approach to intra-organ vascularization for tissue engineering based on organ-printing technology using self-assembling vascular tissue spheroids including clinically relevantly vascular cell sources are analyzed. Take home message It is not possible to engineer 3D thick tissue or organ constructs without effective vascularization. An effective intra-organ vascular system cannot be built by the simple connection of large-diameter vessels and microvessels. Successful engineering of functional human organs suitable for surgical implantation will require concomitant engineering of a ‘built in’ intra-organ branched vascular system. Organ printing enables biofabrication of human organ constructs with a ‘built in’ intra-organ branched vascular tree. PMID:20132061

A new serial pooling method of shifted tree ring blocks to construct millennia long tree ring isotope chronologies with annual resolution.

PubMed

Boettger, Tatjana; Friedrich, Michael

2009-03-01

The study presents a new serial pooling method of shifted tree ring blocks for the building of isotope chronologies. This method combines the advantages of traditional 'serial' and 'intertree' pooling, and can be recommended for the construction of sub-regional long isotope chronologies with sufficient replication, and on annual resolution, especially for the case of extremely narrow tree rings. For Scots pines (Pinus sylvestris L., Khibiny Low Mountains, NW Russia) and Silver firs (Abies alba Mill., Franconia, Southern Germany), serial pooling of five consecutive tree rings seems appropriate because the species- and site-specific particularities lead to blurs of climate linkages in their tree rings for the period up to ca. five years back. An equivalent to a five-year running means that curve gained on the base annual data sets of single trees can be derived from the analysis of yearly shifted five-year blocks of consecutive tree rings, and therefore, with approximately 20% of the expense. Good coherence of delta(13)C- and delta(18)O-values between calculated means of annual total rings or late wood data and means of five-year blocks of consecutive total tree rings analysed experimentally on most similar material confirms this assumption.

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

PubMed

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

2018-01-01

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

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

PubMed

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

PubMed

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.

PubMed

Lyu, Ming-Ju Amy; Gowik, Udo; Kelly, Steve; Covshoff, Sarah; Mallmann, Julia; Westhoff, Peter; Hibberd, Julian M; Stata, Matt; Sage, Rowan F; Lu, Haorong; Wei, Xiaofeng; Wong, Gane Ka-Shu; Zhu, Xin-Guang

2015-06-18

The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a "F. pringlei" genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4). We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.

Genetic linkage maps of white birches (Betula platyphylla Suk. and B. pendula Roth) based on RAPD and AFLP markers

USDA-ARS?s Scientific Manuscript database

Genetic linkage maps in plants are usually constructed using segregating populations obtained from crosses between two inbred lines such as rice, maize, or soybean. Such populations are generally not available for forest trees because of time constraints. But tree species have the property of outcro...

Volume tables for red alder.

Treesearch

Floyd A. Johnson; R. M. Kallander; Paul G. Lauterbach

1949-01-01

The increasing importance of red alder as a commercial species in the Pacific Northwest has prompted the three agencies listed above to pool their tree measurement data for the construction of standard regional red alder volume tables. The tables included here were based on trees from a variety of sites and form classes. Approximately one quarter of the total number of...

Tree-Based Unrooted Phylogenetic Networks.

PubMed

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

A construction scheme of web page comment information extraction system based on frequent subtree mining

NASA Astrophysics Data System (ADS)

Zhang, Xiaowen; Chen, Bingfeng

2017-08-01

Based on the frequent sub-tree mining algorithm, this paper proposes a construction scheme of web page comment information extraction system based on frequent subtree mining, referred to as FSM system. The entire system architecture and the various modules to do a brief introduction, and then the core of the system to do a detailed description, and finally give the system prototype.

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

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

Reachability analysis of real-time systems using time Petri nets.

PubMed

Wang, J; Deng, Y; Xu, G

2000-01-01

Time Petri nets (TPNs) are a popular Petri net model for specification and verification of real-time systems. A fundamental and most widely applied method for analyzing Petri nets is reachability analysis. The existing technique for reachability analysis of TPNs, however, is not suitable for timing property verification because one cannot derive end-to-end delay in task execution, an important issue for time-critical systems, from the reachability tree constructed using the technique. In this paper, we present a new reachability based analysis technique for TPNs for timing property analysis and verification that effectively addresses the problem. Our technique is based on a concept called clock-stamped state class (CS-class). With the reachability tree generated based on CS-classes, we can directly compute the end-to-end time delay in task execution. Moreover, a CS-class can be uniquely mapped to a traditional state class based on which the conventional reachability tree is constructed. Therefore, our CS-class-based analysis technique is more general than the existing technique. We show how to apply this technique to timing property verification of the TPN model of a command and control (C2) system.

[Construction of information management-based virtual forest landscape and its application].

PubMed

Chen, Chongcheng; Tang, Liyu; Quan, Bing; Li, Jianwei; Shi, Song

2005-11-01

Based on the analysis of the contents and technical characteristics of different scale forest visualization modeling, this paper brought forward the principles and technical systems of constructing an information management-based virtual forest landscape. With the combination of process modeling and tree geometric structure description, a software method of interactively and parameterized tree modeling was developed, and the corresponding renderings and geometrical elements simplification algorithms were delineated to speed up rendering run-timely. As a pilot study, the geometrical model bases associated with the typical tree categories in Zhangpu County of Fujian Province, southeast China were established as template files. A Virtual Forest Management System prototype was developed with GIS component (ArcObject), OpenGL graphics environment, and Visual C++ language, based on forest inventory and remote sensing data. The prototype could be used for roaming between 2D and 3D, information query and analysis, and virtual and interactive forest growth simulation, and its reality and accuracy could meet the needs of forest resource management. Some typical interfaces of the system and the illustrative scene cross-sections of simulated masson pine growth under conditions of competition and thinning were listed.

A fully resolved consensus between fully resolved phylogenetic trees.

PubMed

Quitzau, José Augusto Amgarten; Meidanis, João

2006-03-31

Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunately, there is also a taboo concerning consensus methods, because most biologists see them mainly as comparators and not as phylogenetic tree constructors. We challenged this taboo by defining a consensus method that builds a fully resolved phylogenetic tree based on the most common parts of fully resolved trees in a given collection. We also generated results showing that this consensus is in a way a kind of "median" of the input trees; as such it can be closer to the correct tree in many situations.

A Model of Desired Performance in Phylogenetic Tree Construction for Teaching Evolution.

ERIC Educational Resources Information Center

Brewer, Steven D.

This research paper examines phylogenetic tree construction-a form of problem solving in biology-by studying the strategies and heuristics used by experts. One result of the research is the development of a model of desired performance for phylogenetic tree construction. A detailed description of the model and the sample problems which illustrate…

Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars

PubMed Central

Shahin, Arwa; Smulders, Marinus J. M.; van Tuyl, Jaap M.; Arens, Paul; Bakker, Freek T.

2014-01-01

Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium. PMID:25368628

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach.

PubMed

Ghadie, Mohamed A; Japkowicz, Nathalie; Perkins, Theodore J

2015-08-15

Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. tperkins@ohri.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Supertrees Based on the Subtree Prune-and-Regraft Distance

PubMed Central

Whidden, Christopher; Zeh, Norbert; Beiko, Robert G.

2014-01-01

Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying processes, have known biases, and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and > 50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of benchmark datasets simulated under plausible rates of LGT, we show that SPR supertrees are more similar to correct species histories than supertrees based on parsimony or Robinson–Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera. A Small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT. [Lateral gene transfer; matrix representation with parsimony; phylogenomics; prokaryotic phylogeny; Robinson–Foulds; subtree prune-and-regraft; supertrees.] PMID:24695589

Contact Trees: Network Visualization beyond Nodes and Edges

PubMed Central

Sallaberry, Arnaud; Fu, Yang-chih; Ho, Hwai-Chung; Ma, Kwan-Liu

2016-01-01

Node-Link diagrams make it possible to take a quick glance at how nodes (or actors) in a network are connected by edges (or ties). A conventional network diagram of a “contact tree” maps out a root and branches that represent the structure of nodes and edges, often without further specifying leaves or fruits that would have grown from small branches. By furnishing such a network structure with leaves and fruits, we reveal details about “contacts” in our ContactTrees upon which ties and relationships are constructed. Our elegant design employs a bottom-up approach that resembles a recent attempt to understand subjective well-being by means of a series of emotions. Such a bottom-up approach to social-network studies decomposes each tie into a series of interactions or contacts, which can help deepen our understanding of the complexity embedded in a network structure. Unlike previous network visualizations, ContactTrees highlight how relationships form and change based upon interactions among actors, as well as how relationships and networks vary by contact attributes. Based on a botanical tree metaphor, the design is easy to construct and the resulting tree-like visualization can display many properties at both tie and contact levels, thus recapturing a key ingredient missing from conventional techniques of network visualization. We demonstrate ContactTrees using data sets consisting of up to three waves of 3-month contact diaries over the 2004-2012 period, and discuss how this design can be applied to other types of datasets. PMID:26784350

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Rare itemsets mining algorithm based on RP-Tree and spark framework

NASA Astrophysics Data System (ADS)

Liu, Sainan; Pan, Haoan

2018-05-01

For the issues of the rare itemsets mining in big data, this paper proposed a rare itemsets mining algorithm based on RP-Tree and Spark framework. Firstly, it arranged the data vertically according to the transaction identifier, in order to solve the defects of scan the entire data set, the vertical datasets are divided into frequent vertical datasets and rare vertical datasets. Then, it adopted the RP-Tree algorithm to construct the frequent pattern tree that contains rare items and generate rare 1-itemsets. After that, it calculated the support of the itemsets by scanning the two vertical data sets, finally, it used the iterative process to generate rare itemsets. The experimental show that the algorithm can effectively excavate rare itemsets and have great superiority in execution time.

[RS estimation of inventory parameters and carbon storage of moso bamboo forest based on synergistic use of object-based image analysis and decision tree].

PubMed

Du, Hua Qiang; Sun, Xiao Yan; Han, Ning; Mao, Fang Jie

2017-10-01

By synergistically using the object-based image analysis (OBIA) and the classification and regression tree (CART) methods, the distribution information, the indexes (including diameter at breast, tree height, and crown closure), and the aboveground carbon storage (AGC) of moso bamboo forest in Shanchuan Town, Anji County, Zhejiang Province were investigated. The results showed that the moso bamboo forest could be accurately delineated by integrating the multi-scale ima ge segmentation in OBIA technique and CART, which connected the image objects at various scales, with a pretty good producer's accuracy of 89.1%. The investigation of indexes estimated by regression tree model that was constructed based on the features extracted from the image objects reached normal or better accuracy, in which the crown closure model archived the best estimating accuracy of 67.9%. The estimating accuracy of diameter at breast and tree height was relatively low, which was consistent with conclusion that estimating diameter at breast and tree height using optical remote sensing could not achieve satisfactory results. Estimation of AGC reached relatively high accuracy, and accuracy of the region of high value achieved above 80%.

A Voronoi interior adjacency-based approach for generating a contour tree

NASA Astrophysics Data System (ADS)

Chen, Jun; Qiao, Chaofei; Zhao, Renliang

2004-05-01

A contour tree is a good graphical tool for representing the spatial relations of contour lines and has found many applications in map generalization, map annotation, terrain analysis, etc. A new approach for generating contour trees by introducing a Voronoi-based interior adjacency set concept is proposed in this paper. The immediate interior adjacency set is employed to identify all of the children contours of each contour without contour elevations. It has advantages over existing methods such as the point-in-polygon method and the region growing-based method. This new approach can be used for spatial data mining and knowledge discovering, such as the automatic extraction of terrain features and construction of multi-resolution digital elevation model.

A Metric on Phylogenetic Tree Shapes.

PubMed

Colijn, C; Plazzotta, G

2018-01-01

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

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

PubMed Central

Ji, Zhicheng; Ji, Hongkai

2016-01-01

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. PMID:27179027

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.

PubMed

Ji, Zhicheng; Ji, Hongkai

2016-07-27

When analyzing single-cell RNA-seq data, constructing a pseudo-temporal path to order cells based on the gradual transition of their transcriptomes is a useful way to study gene expression dynamics in a heterogeneous cell population. Currently, a limited number of computational tools are available for this task, and quantitative methods for comparing different tools are lacking. Tools for Single Cell Analysis (TSCAN) is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. TSCAN uses a cluster-based minimum spanning tree (MST) approach to order cells. Cells are first grouped into clusters and an MST is then constructed to connect cluster centers. Pseudo-time is obtained by projecting each cell onto the tree, and the ordered sequence of cells can be used to study dynamic changes of gene expression along the pseudo-time. Clustering cells before MST construction reduces the complexity of the tree space. This often leads to improved cell ordering. It also allows users to conveniently adjust the ordering based on prior knowledge. TSCAN has a graphical user interface (GUI) to support data visualization and user interaction. Furthermore, quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods. TSCAN is available at https://github.com/zji90/TSCAN and as a Bioconductor package. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genomewide Function Conservation and Phylogeny in the Herpesviridae

PubMed Central

Albà, M. Mar; Das, Rhiju; Orengo, Christine A.; Kellam, Paul

2001-01-01

The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all predicted open reading frames of 19 herpesvirus genomes. Sequence comparison and protein sequence clustering methods have been used to construct herpesvirus protein homologous families. This resulted in 1692 proteins being clustered into 243 multiprotein families and 196 singleton proteins. Predicted functions were assigned to each homologous family based on genome annotation and published data and each family classified into seven broad functional groups. Phylogenetic profiles were constructed for each herpesvirus from the homologous protein families and used to determine conserved functions and genomewide phylogenetic trees. These trees agreed with molecular-sequence-derived trees and allowed greater insight into the phylogeny of ungulate and murine gammaherpesviruses. PMID:11156614

Memory-Scalable GPU Spatial Hierarchy Construction.

PubMed

Qiming Hou; Xin Sun; Kun Zhou; Lauterbach, C; Manocha, D

2011-04-01

Recent GPU algorithms for constructing spatial hierarchies have achieved promising performance for moderately complex models by using the breadth-first search (BFS) construction order. While being able to exploit the massive parallelism on the GPU, the BFS order also consumes excessive GPU memory, which becomes a serious issue for interactive applications involving very complex models with more than a few million triangles. In this paper, we propose to use the partial breadth-first search (PBFS) construction order to control memory consumption while maximizing performance. We apply the PBFS order to two hierarchy construction algorithms. The first algorithm is for kd-trees that automatically balances between the level of parallelism and intermediate memory usage. With PBFS, peak memory consumption during construction can be efficiently controlled without costly CPU-GPU data transfer. We also develop memory allocation strategies to effectively limit memory fragmentation. The resulting algorithm scales well with GPU memory and constructs kd-trees of models with millions of triangles at interactive rates on GPUs with 1 GB memory. Compared with existing algorithms, our algorithm is an order of magnitude more scalable for a given GPU memory bound. The second algorithm is for out-of-core bounding volume hierarchy (BVH) construction for very large scenes based on the PBFS construction order. At each iteration, all constructed nodes are dumped to the CPU memory, and the GPU memory is freed for the next iteration's use. In this way, the algorithm is able to build trees that are too large to be stored in the GPU memory. Experiments show that our algorithm can construct BVHs for scenes with up to 20 M triangles, several times larger than previous GPU algorithms.

Snakes and Eels and Dogs! Oh, My! Evaluating High School Students' Tree-Thinking Skills: An Entry Point to Understanding Evolution

ERIC Educational Resources Information Center

Catley, Kefyn M.; Phillips, Brenda C.; Novick, Laura R.

2013-01-01

The biological community is currently undertaking one its greatest scientific endeavours, that of constructing the Tree of Life, a phylogeny intended to be an evidenced-based, predictive road map of evolutionary relationships among Earth's biota. Unfortunately, we know very little about how such diagrams are understood, interpreted, or used…

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

PubMed

Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

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

2008-04-01

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

Analytical simulation and PROFAT II: a new methodology and a computer automated tool for fault tree analysis in chemical process industries.

PubMed

Khan, F I; Abbasi, S A

2000-07-10

Fault tree analysis (FTA) is based on constructing a hypothetical tree of base events (initiating events) branching into numerous other sub-events, propagating the fault and eventually leading to the top event (accident). It has been a powerful technique used traditionally in identifying hazards in nuclear installations and power industries. As the systematic articulation of the fault tree is associated with assigning probabilities to each fault, the exercise is also sometimes called probabilistic risk assessment. But powerful as this technique is, it is also very cumbersome and costly, limiting its area of application. We have developed a new algorithm based on analytical simulation (named as AS-II), which makes the application of FTA simpler, quicker, and cheaper; thus opening up the possibility of its wider use in risk assessment in chemical process industries. Based on the methodology we have developed a computer-automated tool. The details are presented in this paper.

An improved spatial contour tree constructed method

NASA Astrophysics Data System (ADS)

Zheng, Yi; Zhang, Ling; Guilbert, Eric; Long, Yi

2018-05-01

Contours are important data to delineate the landform on a map. A contour tree provides an object-oriented description of landforms and can be used to enrich the topological information. The traditional contour tree is used to store topological relationships between contours in a hierarchical structure and allows for the identification of eminences and depressions as sets of nested contours. This research proposes an improved contour tree so-called spatial contour tree that contains not only the topological but also the geometric information. It can be regarded as a terrain skeleton in 3-dimention, and it is established based on the spatial nodes of contours which have the latitude, longitude and elevation information. The spatial contour tree is built by connecting spatial nodes from low to high elevation for a positive landform, and from high to low elevation for a negative landform to form a hierarchical structure. The connection between two spatial nodes can provide the real distance and direction as a Euclidean vector in 3-dimention. In this paper, the construction method is tested in the experiment, and the results are discussed. The proposed hierarchical structure is in 3-demintion and can show the skeleton inside a terrain. The structure, where all nodes have geo-information, can be used to distinguish different landforms and applied for contour generalization with consideration of geographic characteristics.

Complexity of major UK companies between 2006 and 2010: Hierarchical structure method approach

NASA Astrophysics Data System (ADS)

Ulusoy, Tolga; Keskin, Mustafa; Shirvani, Ayoub; Deviren, Bayram; Kantar, Ersin; Çaǧrı Dönmez, Cem

2012-11-01

This study reports on topology of the top 40 UK companies that have been analysed for predictive verification of markets for the period 2006-2010, applying the concept of minimal spanning tree and hierarchical tree (HT) analysis. Construction of the minimal spanning tree (MST) and the hierarchical tree (HT) is confined to a brief description of the methodology and a definition of the correlation function between a pair of companies based on the London Stock Exchange (LSE) index in order to quantify synchronization between the companies. A derivation of hierarchical organization and the construction of minimal-spanning and hierarchical trees for the 2006-2008 and 2008-2010 periods have been used and the results validate the predictive verification of applied semantics. The trees are known as useful tools to perceive and detect the global structure, taxonomy and hierarchy in financial data. From these trees, two different clusters of companies in 2006 were detected. They also show three clusters in 2008 and two between 2008 and 2010, according to their proximity. The clusters match each other as regards their common production activities or their strong interrelationship. The key companies are generally given by major economic activities as expected. This work gives a comparative approach between MST and HT methods from statistical physics and information theory with analysis of financial markets that may give new valuable and useful information of the financial market dynamics.

Dendrometer bands made easy: using modified cable ties to measure incremental growth of trees

USGS Publications Warehouse

Anemaet, Evelyn R.; Middleton, Beth A.

2013-01-01

Dendrometer bands are a useful way to make sequential repeated measurements of tree growth, but traditional dendrometer bands can be expensive, time consuming, and difficult to construct in the field. An alternative to the traditional method of band construction is to adapt commercially available materials. This paper describes how to construct and install dendrometer bands using smooth-edged, stainless steel, cable tie banding and attachable rollerball heads. As a performance comparison, both traditional and cable tie dendrometer bands were installed on baldcypress trees at the National Wetlands Research Center in Lafayette, Louisiana, by both an experienced and a novice worker. Band installation times were recorded, and growth of the trees as estimated by the two band types was measured after approximately one year, demonstrating equivalence of the two methods. This efficient approach to dendrometer band construction can help advance the knowledge of long-term tree growth in ecological studies.

Decision tree methods: applications for classification and prediction.

PubMed

Song, Yan-Yan; Lu, Ying

2015-04-25

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

Predictive mapping of soil organic carbon in wet cultivated lands using classification-tree based models: the case study of Denmark.

PubMed

Bou Kheir, Rania; Greve, Mogens H; Bøcher, Peder K; Greve, Mette B; Larsen, René; McCloy, Keith

2010-05-01

Soil organic carbon (SOC) is one of the most important carbon stocks globally and has large potential to affect global climate. Distribution patterns of SOC in Denmark constitute a nation-wide baseline for studies on soil carbon changes (with respect to Kyoto protocol). This paper predicts and maps the geographic distribution of SOC across Denmark using remote sensing (RS), geographic information systems (GISs) and decision-tree modeling (un-pruned and pruned classification trees). Seventeen parameters, i.e. parent material, soil type, landscape type, elevation, slope gradient, slope aspect, mean curvature, plan curvature, profile curvature, flow accumulation, specific catchment area, tangent slope, tangent curvature, steady-state wetness index, Normalized Difference Vegetation Index (NDVI), Normalized Difference Wetness Index (NDWI) and Soil Color Index (SCI) were generated to statistically explain SOC field measurements in the area of interest (Denmark). A large number of tree-based classification models (588) were developed using (i) all of the parameters, (ii) all Digital Elevation Model (DEM) parameters only, (iii) the primary DEM parameters only, (iv), the remote sensing (RS) indices only, (v) selected pairs of parameters, (vi) soil type, parent material and landscape type only, and (vii) the parameters having a high impact on SOC distribution in built pruned trees. The best constructed classification tree models (in the number of three) with the lowest misclassification error (ME) and the lowest number of nodes (N) as well are: (i) the tree (T1) combining all of the parameters (ME=29.5%; N=54); (ii) the tree (T2) based on the parent material, soil type and landscape type (ME=31.5%; N=14); and (iii) the tree (T3) constructed using parent material, soil type, landscape type, elevation, tangent slope and SCI (ME=30%; N=39). The produced SOC maps at 1:50,000 cartographic scale using these trees are highly matching with coincidence values equal to 90.5% (Map T1/Map T2), 95% (Map T1/Map T3) and 91% (Map T2/Map T3). The overall accuracies of these maps once compared with field observations were estimated to be 69.54% (Map T1), 68.87% (Map T2) and 69.41% (Map T3). The proposed tree models are relatively simple, and may be also applied to other areas. Copyright 2010 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-04-01

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

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.

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

PubMed Central

2013-01-01

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

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.

A new algorithm to construct phylogenetic networks from trees.

PubMed

Wang, J

2014-03-06

Developing appropriate methods for constructing phylogenetic networks from tree sets is an important problem, and much research is currently being undertaken in this area. BIMLR is an algorithm that constructs phylogenetic networks from tree sets. The algorithm can construct a much simpler network than other available methods. Here, we introduce an improved version of the BIMLR algorithm, QuickCass. QuickCass changes the selection strategy of the labels of leaves below the reticulate nodes, i.e., the nodes with an indegree of at least 2 in BIMLR. We show that QuickCass can construct simpler phylogenetic networks than BIMLR. Furthermore, we show that QuickCass is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary.

75 FR 5941 - Umatilla National Forest, Walla Walla Ranger District, Walla Walla, WA; Cobbler II Timber Sale...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-05

... construction (that will be decommissioned after project use), new road construction, danger tree removal along... increasing population. Late seral tree species have become dominant after long periods without disturbance... and vigor. Timber stands of seral tree species such as western larch and ponderosa pine are infilling...

A stable RNA virus-based vector for citrus trees

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

Folimonov, Alexey S.; Folimonova, Svetlana Y.; Bar-Joseph, Moshe

Virus-based vectors are important tools in plant molecular biology and plant genomics. A number of vectors based on viruses that infect herbaceous plants are in use for expression or silencing of genes in plants as well as screening unknown sequences for function. Yet there is a need for useful virus-based vectors for woody plants, which demand much greater stability because of the longer time required for systemic infection and analysis. We examined several strategies to develop a Citrus tristeza virus (CTV)-based vector for transient expression of foreign genes in citrus trees using a green fluorescent protein (GFP) as a reporter.more » These strategies included substitution of the p13 open reading frame (ORF) by the ORF of GFP, construction of a self-processing fusion of GFP in-frame with the major coat protein (CP), or expression of the GFP ORF as an extra gene from a subgenomic (sg) mRNA controlled either by a duplicated CTV CP sgRNA controller element (CE) or an introduced heterologous CE of Beet yellows virus. Engineered vector constructs were examined for replication, encapsidation, GFP expression during multiple passages in protoplasts, and for their ability to infect, move, express GFP, and be maintained in citrus plants. The most successful vectors based on the 'add-a-gene' strategy have been unusually stable, continuing to produce GFP fluorescence after more than 4 years in citrus trees.« less

Alternative construction of graceful symmetric trees

NASA Astrophysics Data System (ADS)

Sandy, I. P.; Rizal, A.; Manurung, E. N.; Sugeng, K. A.

2018-04-01

Graceful labeling is one of the interesting topics in graph theory. Let G = (V, E) be a tree. The injective mapping f:V\\to \\{0,1,\\ldots,|E|\\} is called graceful if the weight of edge w(xy)=|f(x)-f(y)| are all different for every edge xy. The famous conjecture in this area is all trees are graceful. In this paper we give alternative construction of graceful labeling on symmetric tree using adjacency matrix.

Evolving optimised decision rules for intrusion detection using particle swarm paradigm

NASA Astrophysics Data System (ADS)

Sivatha Sindhu, Siva S.; Geetha, S.; Kannan, A.

2012-12-01

The aim of this article is to construct a practical intrusion detection system (IDS) that properly analyses the statistics of network traffic pattern and classify them as normal or anomalous class. The objective of this article is to prove that the choice of effective network traffic features and a proficient machine-learning paradigm enhances the detection accuracy of IDS. In this article, a rule-based approach with a family of six decision tree classifiers, namely Decision Stump, C4.5, Naive Baye's Tree, Random Forest, Random Tree and Representative Tree model to perform the detection of anomalous network pattern is introduced. In particular, the proposed swarm optimisation-based approach selects instances that compose training set and optimised decision tree operate over this trained set producing classification rules with improved coverage, classification capability and generalisation ability. Experiment with the Knowledge Discovery and Data mining (KDD) data set which have information on traffic pattern, during normal and intrusive behaviour shows that the proposed algorithm produces optimised decision rules and outperforms other machine-learning algorithm.

Data Clustering and Evolving Fuzzy Decision Tree for Data Base Classification Problems

NASA Astrophysics Data System (ADS)

Chang, Pei-Chann; Fan, Chin-Yuan; Wang, Yen-Wen

Data base classification suffers from two well known difficulties, i.e., the high dimensionality and non-stationary variations within the large historic data. This paper presents a hybrid classification model by integrating a case based reasoning technique, a Fuzzy Decision Tree (FDT), and Genetic Algorithms (GA) to construct a decision-making system for data classification in various data base applications. The model is major based on the idea that the historic data base can be transformed into a smaller case-base together with a group of fuzzy decision rules. As a result, the model can be more accurately respond to the current data under classifying from the inductions by these smaller cases based fuzzy decision trees. Hit rate is applied as a performance measure and the effectiveness of our proposed model is demonstrated by experimentally compared with other approaches on different data base classification applications. The average hit rate of our proposed model is the highest among others.

Fragment-based prediction of skin sensitization using recursive partitioning

NASA Astrophysics Data System (ADS)

Lu, Jing; Zheng, Mingyue; Wang, Yong; Shen, Qiancheng; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

2011-09-01

Skin sensitization is an important toxic endpoint in the risk assessment of chemicals. In this paper, structure-activity relationships analysis was performed on the skin sensitization potential of 357 compounds with local lymph node assay data. Structural fragments were extracted by GASTON (GrAph/Sequence/Tree extractiON) from the training set. Eight fragments with accuracy significantly higher than 0.73 ( p < 0.1) were retained to make up an indicator descriptor fragment. The fragment descriptor and eight other physicochemical descriptors closely related to the endpoint were calculated to construct the recursive partitioning tree (RP tree) for classification. The balanced accuracy of the training set, test set I, and test set II in the leave-one-out model were 0.846, 0.800, and 0.809, respectively. The results highlight that fragment-based RP tree is a preferable method for identifying skin sensitizers. Moreover, the selected fragments provide useful structural information for exploring sensitization mechanisms, and RP tree creates a graphic tree to identify the most important properties associated with skin sensitization. They can provide some guidance for designing of drugs with lower sensitization level.

Growth response of conifers in Adirondack plantations to changing environment: Model approaches based on stem-analysis

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

Pan, Y.

1993-01-01

Based on model approaches, three conifer species, red pine, Norway spruce and Scots pine grown in plantations at Pack Demonstration Forest, in the southeastern Adirondack mountains of New York, were chosen to study growth response to different environmental changes, including silvicultural treatments and changes in climate and chemical environment. Detailed stem analysis data provided a basis for constructing tree growth models. These models were organized into three groups: morphological, dynamic and predictive. The morphological model was designed to evaluate relationship between tree attributes and interactive influences of intrinsic and extrinsic factors on the annual increments. Three types of morphological patternsmore » have been characterized: space-time patterns of whole-stem rings, intrinsic wood deposition pattern along the tree-stem, and bolewood allocation ratio patterns along the tree-stem. The dynamic model reflects the growth process as a system which responds to extrinsic signal inputs, including fertilization pulses, spacing effects and climatic disturbance, as well as intrinsic feedback. Growth signals indicative of climatic effects were used to construct growth-climate models using both multivariate analysis and Kalman filter methods. The predictive model utilized GCMs and growth-climate relationships to forecast tree growth responses in relation to future scenarios of CO[sub 2]-induced climate change. Prediction results indicate that different conifer species have individualistic growth response to future climatic change and suggest possible changes in future growth and distribution of naturally occurring conifers in this region.« less

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

PubMed Central

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

2004-01-01

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

Dendrometer bands made easy: Using modified cable ties to measure incremental growth of trees1

PubMed Central

Anemaet, Evelyn R.; Middleton, Beth A.

2013-01-01

• Premise of the study: Dendrometer bands are a useful way to make sequential repeated measurements of tree growth, but traditional dendrometer bands can be expensive, time consuming, and difficult to construct in the field. An alternative to the traditional method of band construction is to adapt commercially available materials. This paper describes how to construct and install dendrometer bands using smooth-edged, stainless steel, cable tie banding and attachable rollerball heads. • Methods and Results: As a performance comparison, both traditional and cable tie dendrometer bands were installed on baldcypress trees at the National Wetlands Research Center in Lafayette, Louisiana, by both an experienced and a novice worker. Band installation times were recorded, and growth of the trees as estimated by the two band types was measured after approximately one year, demonstrating equivalence of the two methods. • Conclusions: This efficient approach to dendrometer band construction can help advance the knowledge of long-term tree growth in ecological studies. PMID:25202589

Constructing Student Problems in Phylogenetic Tree Construction.

ERIC Educational Resources Information Center

Brewer, Steven D.

Evolution is often equated with natural selection and is taught from a primarily functional perspective while comparative and historical approaches, which are critical for developing an appreciation of the power of evolutionary theory, are often neglected. This report describes a study of expert problem-solving in phylogenetic tree construction.…

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.

PubMed

Xu, Duo; Jaber, Yousef; Pavlidis, Pavlos; Gokcumen, Omer

2017-09-26

Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies. Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format. VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .

Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks.

PubMed

Wei, Fangping; Chen, Bowen

2012-03-01

To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.

Automatic creation of object hierarchies for ray tracing

NASA Technical Reports Server (NTRS)

Goldsmith, Jeffrey; Salmon, John

1987-01-01

Various methods for evaluating generated trees are proposed. The use of the hierarchical extent method of Rubin and Whitted (1980) to find the objects that will be hit by a ray is examined. This method employs tree searching; the construction of a tree of bounding volumes in order to determine the number of objects that will be hit by a ray is discussed. A tree generation algorithm, which uses a heuristic tree search strategy, is described. The effects of shuffling and sorting on the input data are investigated. The cost of inserting an object into the hierarchy during the construction of a tree algorithm is estimated. The steps involved in estimating the number of intersection calculations are presented.

An Isometric Mapping Based Co-Location Decision Tree Algorithm

NASA Astrophysics Data System (ADS)

Zhou, G.; Wei, J.; Zhou, X.; Zhang, R.; Huang, W.; Sha, H.; Chen, J.

2018-05-01

Decision tree (DT) induction has been widely used in different pattern classification. However, most traditional DTs have the disadvantage that they consider only non-spatial attributes (ie, spectral information) as a result of classifying pixels, which can result in objects being misclassified. Therefore, some researchers have proposed a co-location decision tree (Cl-DT) method, which combines co-location and decision tree to solve the above the above-mentioned traditional decision tree problems. Cl-DT overcomes the shortcomings of the existing DT algorithms, which create a node for each value of a given attribute, which has a higher accuracy than the existing decision tree approach. However, for non-linearly distributed data instances, the euclidean distance between instances does not reflect the true positional relationship between them. In order to overcome these shortcomings, this paper proposes an isometric mapping method based on Cl-DT (called, (Isomap-based Cl-DT), which is a method that combines heterogeneous and Cl-DT together. Because isometric mapping methods use geodetic distances instead of Euclidean distances between non-linearly distributed instances, the true distance between instances can be reflected. The experimental results and several comparative analyzes show that: (1) The extraction method of exposed carbonate rocks is of high accuracy. (2) The proposed method has many advantages, because the total number of nodes, the number of leaf nodes and the number of nodes are greatly reduced compared to Cl-DT. Therefore, the Isomap -based Cl-DT algorithm can construct a more accurate and faster decision tree.

Carbon Sequestration Estimation of Street Trees Based on Point Cloud from Vehicle-Borne Laser Scanning System

NASA Astrophysics Data System (ADS)

Zhao, Y.; Hu, Q.

2017-09-01

Continuous development of urban road traffic system requests higher standards of road ecological environment. Ecological benefits of street trees are getting more attention. Carbon sequestration of street trees refers to the carbon stocks of street trees, which can be a measurement for ecological benefits of street trees. Estimating carbon sequestration in a traditional way is costly and inefficient. In order to solve above problems, a carbon sequestration estimation approach for street trees based on 3D point cloud from vehicle-borne laser scanning system is proposed in this paper. The method can measure the geometric parameters of a street tree, including tree height, crown width, diameter at breast height (DBH), by processing and analyzing point cloud data of an individual tree. Four Chinese scholartree trees and four camphor trees are selected for experiment. The root mean square error (RMSE) of tree height is 0.11m for Chinese scholartree and 0.02m for camphor. Crown widths in X direction and Y direction, as well as the average crown width are calculated. And the RMSE of average crown width is 0.22m for Chinese scholartree and 0.10m for camphor. The last calculated parameter is DBH, the RMSE of DBH is 0.5cm for both Chinese scholartree and camphor. Combining the measured geometric parameters and an appropriate carbon sequestration calculation model, the individual tree's carbon sequestration will be estimated. The proposed method can help enlarge application range of vehicle-borne laser point cloud data, improve the efficiency of estimating carbon sequestration, construct urban ecological environment and manage landscape.

Base structure consisting of an endothelialized vascular-tree network and hepatocytes for whole liver engineering.

PubMed

Shirakigawa, Nana; Takei, Takayuki; Ijima, Hiroyuki

2013-12-01

Reconstructed liver has been desired as a liver substitute for transplantation. However, reconstruction of a whole liver has not been achieved because construction of a vascular network at an organ scale is very difficult. We focused on decellularized liver (DC-liver) as an artificial scaffold for the construction of a hierarchical vascular network. In this study, we obtained DC-liver and the tubular network structure in which both portal vein and hepatic vein systems remained intact. Furthermore, endothelialization of the tubular structure in DC-liver was achieved, which prevented blood leakage from the tubular structure. In addition, hepatocytes suspended in a collagen sol were injected from the surroundings using a syringe as a suitable procedure for liver cell inoculation. In summary, we developed a base structure consisting of an endothelialized vascular-tree network and hepatocytes for whole liver engineering. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Phylogenomic analyses data of the avian phylogenomics project.

PubMed

Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y W; Faircloth, Brant C; Nabholz, Benoit; Howard, Jason T; Suh, Alexander; Weber, Claudia C; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Narula, Nitish; Liu, Liang; Burt, Dave; Ellegren, Hans; Edwards, Scott V; Stamatakis, Alexandros; Mindell, David P; Cracraft, Joel; Braun, Edward L; Warnow, Tandy; Jun, Wang; Gilbert, M Thomas Pius; Zhang, Guojie

2015-01-01

Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides, amino acids, indels, and transposable elements, as well as tree files containing gene trees and species trees. Inferring an accurate phylogeny required generating: 1) A well annotated data set across species based on genome synteny; 2) Alignments with unaligned or incorrectly overaligned sequences filtered out; and 3) Diverse data sets, including genes and their inferred trees, indels, and transposable elements. Our total evidence nucleotide tree (TENT) data set (consisting of exons, introns, and UCEs) gave what we consider our most reliable species tree when using the concatenation-based ExaML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. The Avian Phylogenomics Project is the largest vertebrate phylogenomics project to date that we are aware of. The sequence, alignment, and tree data are expected to accelerate analyses in phylogenomics and other related areas.

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

NASA Astrophysics Data System (ADS)

Muntean, Ionuţ; Ionescu, Clara; Naşcu, Ioan

2009-04-01

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

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

Parallel Continuous Flow: A Parallel Suffix Tree Construction Tool for Whole Genomes

PubMed Central

Farreras, Montse

2014-01-01

Abstract The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes. PMID:24597675

On the Effective Construction of Compactly Supported Wavelets Satisfying Homogenous Boundary Conditions on the Interval

NASA Technical Reports Server (NTRS)

Chiavassa, G.; Liandrat, J.

1996-01-01

We construct compactly supported wavelet bases satisfying homogeneous boundary conditions on the interval (0,1). The maximum features of multiresolution analysis on the line are retained, including polynomial approximation and tree algorithms. The case of H(sub 0)(sup 1)(0, 1)is detailed, and numerical values, required for the implementation, are provided for the Neumann and Dirichlet boundary conditions.

Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees.

PubMed

Mirzaei, Sajad; Wu, Yufeng

2016-01-01

Hybridization networks represent plausible evolutionary histories of species that are affected by reticulate evolutionary processes. An established computational problem on hybridization networks is constructing the most parsimonious hybridization network such that each of the given phylogenetic trees (called gene trees) is "displayed" in the network. There have been several previous approaches, including an exact method and several heuristics, for this NP-hard problem. However, the exact method is only applicable to a limited range of data, and heuristic methods can be less accurate and also slow sometimes. In this paper, we develop a new algorithm for constructing near parsimonious networks for multiple binary gene trees. This method is more efficient for large numbers of gene trees than previous heuristics. This new method also produces more parsimonious results on many simulated datasets as well as a real biological dataset than a previous method. We also show that our method produces topologically more accurate networks for many datasets.

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

PubMed

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

2014-11-01

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

Bayesian additive decision trees of biomarker by treatment interactions for predictive biomarker detection and subgroup identification.

PubMed

Zhao, Yang; Zheng, Wei; Zhuo, Daisy Y; Lu, Yuefeng; Ma, Xiwen; Liu, Hengchang; Zeng, Zhen; Laird, Glen

2017-10-11

Personalized medicine, or tailored therapy, has been an active and important topic in recent medical research. Many methods have been proposed in the literature for predictive biomarker detection and subgroup identification. In this article, we propose a novel decision tree-based approach applicable in randomized clinical trials. We model the prognostic effects of the biomarkers using additive regression trees and the biomarker-by-treatment effect using a single regression tree. Bayesian approach is utilized to periodically revise the split variables and the split rules of the decision trees, which provides a better overall fitting. Gibbs sampler is implemented in the MCMC procedure, which updates the prognostic trees and the interaction tree separately. We use the posterior distribution of the interaction tree to construct the predictive scores of the biomarkers and to identify the subgroup where the treatment is superior to the control. Numerical simulations show that our proposed method performs well under various settings comparing to existing methods. We also demonstrate an application of our method in a real clinical trial.

Application of the Feynman-tree theorem together with BCFW recursion relations

NASA Astrophysics Data System (ADS)

Maniatis, M.

2018-03-01

Recently, it has been shown that on-shell scattering amplitudes can be constructed by the Feynman-tree theorem combined with the BCFW recursion relations. Since the BCFW relations are restricted to tree diagrams, the preceding application of the Feynman-tree theorem is essential. In this way, amplitudes can be constructed by on-shell and gauge-invariant tree amplitudes. Here, we want to apply this method to the electron-photon vertex correction. We present all the single, double, and triple phase-space tensor integrals explicitly and show that the sum of amplitudes coincides with the result of the conventional calculation of a virtual loop correction.

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

PubMed Central

Nasr Esfahani, Bahram; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Moghoofei, Mohsen; Sedighi, Mansour; Hadifar, Shima

2016-01-01

Background Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study. Conclusions The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity. PMID:27284397

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.

The scientific dating of standing buildings.

PubMed

Alcock, Nathaniel W

2017-11-17

The techniques of dendrochronology (tree-ring dating) and radiocarbon (14C) dating are described, as they are applied to historic buildings. Both rely on determining the felling dates of the trees used in their construction. For dendrochronology, the construction of master chronologies and the matching of individual ring-width sequences to them is described and, for radiocarbon dating, the use of tree-ring results in calibration. Results of dating are discussed, ranging from the cathedrals of Peterborough and Beauvais and the development of crown-post roof structures, to the dating and identification of standing medieval peasant houses, particularly those built using cruck construction.

A Deliberate Practice Approach to Teaching Phylogenetic Analysis

PubMed Central

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

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

Jamil, Akhtar; Bayram, Bulent

2018-05-01

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

ANTLR Tree Grammar Generator and Extensions

NASA Technical Reports Server (NTRS)

Craymer, Loring

2005-01-01

A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

NASA Astrophysics Data System (ADS)

Hosoi, F.

2014-12-01

Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of consecutive voxels that filled the outer surface and the interior of the stem and large branches. From the model, the woody material volume of any part of the target tree can be directly calculated easily by counting the number of corresponding voxels and multiplying the result by the per-voxel volume.

Binary tree eigen solver in finite element analysis

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

PubMed Central

2014-01-01

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

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

PubMed

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

2014-03-29

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

Big cat phylogenies, consensus trees, and computational thinking.

PubMed

Sul, Seung-Jin; Williams, Tiffani L

2011-07-01

Phylogenetics seeks to deduce the pattern of relatedness between organisms by using a phylogeny or evolutionary tree. For a given set of organisms or taxa, there may be many evolutionary trees depicting how these organisms evolved from a common ancestor. As a result, consensus trees are a popular approach for summarizing the shared evolutionary relationships in a group of trees. We examine these consensus techniques by studying how the pantherine lineage of cats (clouded leopard, jaguar, leopard, lion, snow leopard, and tiger) evolved, which is hotly debated. While there are many phylogenetic resources that describe consensus trees, there is very little information, written for biologists, regarding the underlying computational techniques for building them. The pantherine cats provide us with a small, relevant example to explore the computational techniques (such as sorting numbers, hashing functions, and traversing trees) for constructing consensus trees. Our hope is that life scientists enjoy peeking under the computational hood of consensus tree construction and share their positive experiences with others in their community.

Rapid Leaf Deployment Strategies in a Deciduous Savanna

PubMed Central

2016-01-01

Deciduous plants avoid the costs of maintaining leaves in the unfavourable season, but carry the costs of constructing new leaves every year. Deciduousness is therefore expected in ecological situations with pronounced seasonality and low costs of leaf construction. In our study system, a seasonally dry tropical savanna, many trees are deciduous, suggesting that leaf construction costs must be low. Previous studies have, however, shown that nitrogen is limiting in this system, suggesting that leaf construction costs are high. Here we examine this conundrum using a time series of soil moisture availability, leaf phenology and nitrogen distribution in the tree canopy to illustrate how trees resorb nitrogen before leaf abscission and use stored reserves of nitrogen and carbon to construct new leaves at the onset of the growing season. Our results show that trees deployed leaves shortly before and in anticipation of the first rains with its associated pulse of nitrogen mineralisation. Our results also show that trees rapidly constructed a full canopy of leaves within two weeks of the first rains. We detected an increase in leaf nitrogen content that corresponded with the first rains and with the movement of nitrogen to more distal branches, suggesting that stored nitrogen reserves are used to construct leaves. Furthermore the stable carbon isotope ratios (δ13C) of these leaves suggest the use of stored carbon for leaf construction. Our findings suggest that the early deployment of leaves using stored nitrogen and carbon reserves is a strategy that is integrally linked with the onset of the first rains. This strategy may confer a competitive advantage over species that deploy leaves at or after the onset of the rains. PMID:27310398

Multipoint to multipoint routing and wavelength assignment in multi-domain optical networks

NASA Astrophysics Data System (ADS)

Qin, Panke; Wu, Jingru; Li, Xudong; Tang, Yongli

2018-01-01

In multi-point to multi-point (MP2MP) routing and wavelength assignment (RWA) problems, researchers usually assume the optical networks to be a single domain. However, the optical networks develop toward to multi-domain and larger scale in practice. In this context, multi-core shared tree (MST)-based MP2MP RWA are introduced problems including optimal multicast domain sequence selection, core nodes belonging in which domains and so on. In this letter, we focus on MST-based MP2MP RWA problems in multi-domain optical networks, mixed integer linear programming (MILP) formulations to optimally construct MP2MP multicast trees is presented. A heuristic algorithm base on network virtualization and weighted clustering algorithm (NV-WCA) is proposed. Simulation results show that, under different traffic patterns, the proposed algorithm achieves significant improvement on network resources occupation and multicast trees setup latency in contrast with the conventional algorithms which were proposed base on a single domain network environment.

Outdoor Illegal Construction Identification Algorithm Based on 3D Point Cloud Segmentation

NASA Astrophysics Data System (ADS)

An, Lu; Guo, Baolong

2018-03-01

Recently, various illegal constructions occur significantly in our surroundings, which seriously restrict the orderly development of urban modernization. The 3D point cloud data technology is used to identify the illegal buildings, which could address the problem above effectively. This paper proposes an outdoor illegal construction identification algorithm based on 3D point cloud segmentation. Initially, in order to save memory space and reduce processing time, a lossless point cloud compression method based on minimum spanning tree is proposed. Then, a ground point removing method based on the multi-scale filtering is introduced to increase accuracy. Finally, building clusters on the ground can be obtained using a region growing method, as a result, the illegal construction can be marked. The effectiveness of the proposed algorithm is verified using a publicly data set collected from the International Society for Photogrammetry and Remote Sensing (ISPRS).

Modeling Tree Growth Taking into Account Carbon Source and Sink Limitations.

PubMed

Hayat, Amaury; Hacket-Pain, Andrew J; Pretzsch, Hans; Rademacher, Tim T; Friend, Andrew D

2017-01-01

Increasing CO 2 concentrations are strongly controlled by the behavior of established forests, which are believed to be a major current sink of atmospheric CO 2 . There are many models which predict forest responses to environmental changes but they are almost exclusively carbon source (i.e., photosynthesis) driven. Here we present a model for an individual tree that takes into account the intrinsic limits of meristems and cellular growth rates, as well as control mechanisms within the tree that influence its diameter and height growth over time. This new framework is built on process-based understanding combined with differential equations solved by numerical method. Our aim is to construct a model framework of tree growth for replacing current formulations in Dynamic Global Vegetation Models, and so address the issue of the terrestrial carbon sink. Our approach was successfully tested for stands of beech trees in two different sites representing part of a long-term forest yield experiment in Germany. This model provides new insights into tree growth and limits to tree height, and addresses limitations of previous models with respect to sink-limited growth.

Indexing Volumetric Shapes with Matching and Packing

PubMed Central

Koes, David Ryan; Camacho, Carlos J.

2014-01-01

We describe a novel algorithm for bulk-loading an index with high-dimensional data and apply it to the problem of volumetric shape matching. Our matching and packing algorithm is a general approach for packing data according to a similarity metric. First an approximate k-nearest neighbor graph is constructed using vantage-point initialization, an improvement to previous work that decreases construction time while improving the quality of approximation. Then graph matching is iteratively performed to pack related items closely together. The end result is a dense index with good performance. We define a new query specification for shape matching that uses minimum and maximum shape constraints to explicitly specify the spatial requirements of the desired shape. This specification provides a natural language for performing volumetric shape matching and is readily supported by the geometry-based similarity search (GSS) tree, an indexing structure that maintains explicit representations of volumetric shape. We describe our implementation of a GSS tree for volumetric shape matching and provide a comprehensive evaluation of parameter sensitivity, performance, and scalability. Compared to previous bulk-loading algorithms, we find that matching and packing can construct a GSS-tree index in the same amount of time that is denser, flatter, and better performing, with an observed average performance improvement of 2X. PMID:26085707

Association between split selection instability and predictive error in survival trees.

PubMed

Radespiel-Tröger, M; Gefeller, O; Rabenstein, T; Hothorn, T

2006-01-01

To evaluate split selection instability in six survival tree algorithms and its relationship with predictive error by means of a bootstrap study. We study the following algorithms: logrank statistic with multivariate p-value adjustment without pruning (LR), Kaplan-Meier distance of survival curves (KM), martingale residuals (MR), Poisson regression for censored data (PR), within-node impurity (WI), and exponential log-likelihood loss (XL). With the exception of LR, initial trees are pruned by using split-complexity, and final trees are selected by means of cross-validation. We employ a real dataset from a clinical study of patients with gallbladder stones. The predictive error is evaluated using the integrated Brier score for censored data. The relationship between split selection instability and predictive error is evaluated by means of box-percentile plots, covariate and cutpoint selection entropy, and cutpoint selection coefficients of variation, respectively, in the root node. We found a positive association between covariate selection instability and predictive error in the root node. LR yields the lowest predictive error, while KM and MR yield the highest predictive error. The predictive error of survival trees is related to split selection instability. Based on the low predictive error of LR, we recommend the use of this algorithm for the construction of survival trees. Unpruned survival trees with multivariate p-value adjustment can perform equally well compared to pruned trees. The analysis of split selection instability can be used to communicate the results of tree-based analyses to clinicians and to support the application of survival trees.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences.

PubMed

Zheng, Xiaoyan; Cai, Danying; Potter, Daniel; Postman, Joseph; Liu, Jing; Teng, Yuanwen

2014-11-01

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence datasets. Phylogenetic trees based on both cpDNA and nuclear LFY2int2-N (LN) data resulted in poor resolution, especially, only five primary species were monophyletic in the LN tree. A phylogenetic network of LN suggested that reticulation caused by hybridization is one of the major evolutionary processes for Pyrus species. Polytomies of the gene trees and star-like structure of cpDNA networks suggested rapid radiation is another major evolutionary process, especially for the occidental species. Pyrus calleryana and P. regelii were the earliest diverged Pyrus species. Two North African species, P. cordata, P. spinosa and P. betulaefolia were descendent of primitive stock Pyrus species and still share some common molecular characters. Southwestern China, where a large number of P. pashia populations are found, is probably the most important diversification center of Pyrus. More accessions and nuclear genes are needed for further understanding the evolutionary histories of Pyrus. Copyright © 2014 Elsevier Inc. All rights reserved.

An Intelligent Decision Support System for Workforce Forecast

DTIC Science & Technology

2011-01-01

ARIMA ) model to forecast the demand for construction skills in Hong Kong. This model was based...Decision Trees ARIMA Rule Based Forecasting Segmentation Forecasting Regression Analysis Simulation Modeling Input-Output Models LP and NLP Markovian...data • When results are needed as a set of easily interpretable rules 4.1.4 ARIMA Auto-regressive, integrated, moving-average ( ARIMA ) models

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

PubMed Central

2013-01-01

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

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

PubMed

Heled, Joseph; Bouckaert, Remco R

2013-10-04

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

Minimum spanning tree filtering of correlations for varying time scales and size of fluctuations

NASA Astrophysics Data System (ADS)

Kwapień, Jarosław; Oświecimka, Paweł; Forczek, Marcin; DroŻdŻ, Stanisław

2017-05-01

Based on a recently proposed q -dependent detrended cross-correlation coefficient, ρq [J. Kwapień, P. Oświęcimka, and S. Drożdż, Phys. Rev. E 92, 052815 (2015), 10.1103/PhysRevE.92.052815], we generalize the concept of the minimum spanning tree (MST) by introducing a family of q -dependent minimum spanning trees (q MST s ) that are selective to cross-correlations between different fluctuation amplitudes and different time scales of multivariate data. They inherit this ability directly from the coefficients ρq, which are processed here to construct a distance matrix being the input to the MST-constructing Kruskal's algorithm. The conventional MST with detrending corresponds in this context to q =2 . In order to illustrate their performance, we apply the q MSTs to sample empirical data from the American stock market and discuss the results. We show that the q MST graphs can complement ρq in disentangling "hidden" correlations that cannot be observed in the MST graphs based on ρDCCA, and therefore, they can be useful in many areas where the multivariate cross-correlations are of interest. As an example, we apply this method to empirical data from the stock market and show that by constructing the q MSTs for a spectrum of q values we obtain more information about the correlation structure of the data than by using q =2 only. More specifically, we show that two sets of signals that differ from each other statistically can give comparable trees for q =2 , while only by using the trees for q ≠2 do we become able to distinguish between these sets. We also show that a family of q MSTs for a range of q expresses the diversity of correlations in a manner resembling the multifractal analysis, where one computes a spectrum of the generalized fractal dimensions, the generalized Hurst exponents, or the multifractal singularity spectra: the more diverse the correlations are, the more variable the tree topology is for different q 's. As regards the correlation structure of the stock market, our analysis exhibits that the stocks belonging to the same or similar industrial sectors are correlated via the fluctuations of moderate amplitudes, while the largest fluctuations often happen to synchronize in those stocks that do not necessarily belong to the same industry.

A resource-saving collective approach to biomedical semantic role labeling

PubMed Central

2014-01-01

Background Biomedical semantic role labeling (BioSRL) is a natural language processing technique that identifies the semantic roles of the words or phrases in sentences describing biological processes and expresses them as predicate-argument structures (PAS’s). Currently, a major problem of BioSRL is that most systems label every node in a full parse tree independently; however, some nodes always exhibit dependency. In general SRL, collective approaches based on the Markov logic network (MLN) model have been successful in dealing with this problem. However, in BioSRL such an approach has not been attempted because it would require more training data to recognize the more specialized and diverse terms found in biomedical literature, increasing training time and computational complexity. Results We first constructed a collective BioSRL system based on MLN. This system, called collective BIOSMILE (CBIOSMILE), is trained on the BioProp corpus. To reduce the resources used in BioSRL training, we employ a tree-pruning filter to remove unlikely nodes from the parse tree and four argument candidate identifiers to retain candidate nodes in the tree. Nodes not recognized by any candidate identifier are discarded. The pruned annotated parse trees are used to train a resource-saving MLN-based system, which is referred to as resource-saving collective BIOSMILE (RCBIOSMILE). Our experimental results show that our proposed CBIOSMILE system outperforms BIOSMILE, which is the top BioSRL system. Furthermore, our proposed RCBIOSMILE maintains the same level of accuracy as CBIOSMILE using 92% less memory and 57% less training time. Conclusions This greatly improved efficiency makes RCBIOSMILE potentially suitable for training on much larger BioSRL corpora over more biomedical domains. Compared to real-world biomedical corpora, BioProp is relatively small, containing only 445 MEDLINE abstracts and 30 event triggers. It is not large enough for practical applications, such as pathway construction. We consider it of primary importance to pursue SRL training on large corpora in the future. PMID:24884358

Cloud Detection from Satellite Imagery: A Comparison of Expert-Generated and Automatically-Generated Decision Trees

NASA Technical Reports Server (NTRS)

Shiffman, Smadar

2004-01-01

Automated cloud detection and tracking is an important step in assessing global climate change via remote sensing. Cloud masks, which indicate whether individual pixels depict clouds, are included in many of the data products that are based on data acquired on- board earth satellites. Many cloud-mask algorithms have the form of decision trees, which employ sequential tests that scientists designed based on empirical astrophysics studies and astrophysics simulations. Limitations of existing cloud masks restrict our ability to accurately track changes in cloud patterns over time. In this study we explored the potential benefits of automatically-learned decision trees for detecting clouds from images acquired using the Advanced Very High Resolution Radiometer (AVHRR) instrument on board the NOAA-14 weather satellite of the National Oceanic and Atmospheric Administration. We constructed three decision trees for a sample of 8km-daily AVHRR data from 2000 using a decision-tree learning procedure provided within MATLAB(R), and compared the accuracy of the decision trees to the accuracy of the cloud mask. We used ground observations collected by the National Aeronautics and Space Administration Clouds and the Earth s Radiant Energy Systems S COOL project as the gold standard. For the sample data, the accuracy of automatically learned decision trees was greater than the accuracy of the cloud masks included in the AVHRR data product.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

Gao, Connie W.; Allen, Joshua W.; Green, William H.; ...

2016-02-24

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involvingmore » carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.« less

A New Minimum Trees-Based Approach for Shape Matching with Improved Time Computing: Application to Graphical Symbols Recognition

NASA Astrophysics Data System (ADS)

Franco, Patrick; Ogier, Jean-Marc; Loonis, Pierre; Mullot, Rémy

Recently we have developed a model for shape description and matching. Based on minimum spanning trees construction and specifics stages like the mixture, it seems to have many desirable properties. Recognition invariance in front shift, rotated and noisy shape was checked through median scale tests related to GREC symbol reference database. Even if extracting the topology of a shape by mapping the shortest path connecting all the pixels seems to be powerful, the construction of graph induces an expensive algorithmic cost. In this article we discuss on the ways to reduce time computing. An alternative solution based on image compression concepts is provided and evaluated. The model no longer operates in the image space but in a compact space, namely the Discrete Cosine space. The use of block discrete cosine transform is discussed and justified. The experimental results led on the GREC2003 database show that the proposed method is characterized by a good discrimination power, a real robustness to noise with an acceptable time computing.

Development of Gis Tool for the Solution of Minimum Spanning Tree Problem using Prim's Algorithm

NASA Astrophysics Data System (ADS)

Dutta, S.; Patra, D.; Shankar, H.; Alok Verma, P.

2014-11-01

minimum spanning tree (MST) of a connected, undirected and weighted network is a tree of that network consisting of all its nodes and the sum of weights of all its edges is minimum among all such possible spanning trees of the same network. In this study, we have developed a new GIS tool using most commonly known rudimentary algorithm called Prim's algorithm to construct the minimum spanning tree of a connected, undirected and weighted road network. This algorithm is based on the weight (adjacency) matrix of a weighted network and helps to solve complex network MST problem easily, efficiently and effectively. The selection of the appropriate algorithm is very essential otherwise it will be very hard to get an optimal result. In case of Road Transportation Network, it is very essential to find the optimal results by considering all the necessary points based on cost factor (time or distance). This paper is based on solving the Minimum Spanning Tree (MST) problem of a road network by finding it's minimum span by considering all the important network junction point. GIS technology is usually used to solve the network related problems like the optimal path problem, travelling salesman problem, vehicle routing problems, location-allocation problems etc. Therefore, in this study we have developed a customized GIS tool using Python script in ArcGIS software for the solution of MST problem for a Road Transportation Network of Dehradun city by considering distance and time as the impedance (cost) factors. It has a number of advantages like the users do not need a greater knowledge of the subject as the tool is user-friendly and that allows to access information varied and adapted the needs of the users. This GIS tool for MST can be applied for a nationwide plan called Prime Minister Gram Sadak Yojana in India to provide optimal all weather road connectivity to unconnected villages (points). This tool is also useful for constructing highways or railways spanning several cities optimally or connecting all cities with minimum total road length.

Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm.

PubMed

Seo, Joo-Hyun; Park, Jihyang; Kim, Eun-Mi; Kim, Juhan; Joo, Keehyoung; Lee, Jooyoung; Kim, Byung-Gee

2014-02-01

Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named 'Subgrouping Automata' was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and 'Subgrouping Automata' searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping. Copyright © 2013. Published by Elsevier Ltd.

Developing techniques for cause-responsibility analysis of occupational accidents.

PubMed

Jabbari, Mousa; Ghorbani, Roghayeh

2016-11-01

The aim of this study was to specify the causes of occupational accidents, determine social responsibility and the role of groups involved in work-related accidents. This study develops occupational accidents causes tree, occupational accidents responsibility tree, and occupational accidents component-responsibility analysis worksheet; based on these methods, it develops cause-responsibility analysis (CRA) techniques, and for testing them, analyzes 100 fatal/disabling occupational accidents in the construction setting that were randomly selected from all the work-related accidents in Tehran, Iran, over a 5-year period (2010-2014). The main result of this study involves two techniques for CRA: occupational accidents tree analysis (OATA) and occupational accidents components analysis (OACA), used in parallel for determination of responsible groups and responsibilities rate. From the results, we find that the management group of construction projects has 74.65% responsibility of work-related accidents. The developed techniques are purposeful for occupational accidents investigation/analysis, especially for the determination of detailed list of tasks, responsibilities, and their rates. Therefore, it is useful for preventing work-related accidents by focusing on the responsible group's duties. Copyright © 2016 Elsevier Ltd. All rights reserved.

Historic Landscape Survey, Randolph AFB, Texas

DTIC Science & Technology

2013-09-01

listed men. Throughout 1930 and 1931, construction at the base was steady in spite of the nation’s depressed economy.22 Figure 3. The road... centennial year of 1932, during which patriotic societies planted trees throughout the country in honor of the first president. During the next year, the

Phylogenetic classification and the universal tree.

PubMed

Doolittle, W F

1999-06-25

From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

Effect of historical land-use and climate change on tree-climate relationships in the upper Midwestern United States.

PubMed

Goring, Simon J; Williams, John W

2017-04-01

Contemporary forest inventory data are widely used to understand environmental controls on tree species distributions and to construct models to project forest responses to climate change, but the stability and representativeness of contemporary tree-climate relationships are poorly understood. We show that tree-climate relationships for 15 tree genera in the upper Midwestern US have significantly altered over the last two centuries due to historical land-use and climate change. Realised niches have shifted towards higher minimum temperatures and higher rainfall. A new attribution method implicates both historical climate change and land-use in these shifts, with the relative importance varying among genera and climate variables. Most climate/land-use interactions are compounding, in which historical land-use reinforces shifts in species-climate relationships toward wetter distributions, or confounding, in which land-use complicates shifts towards warmer distributions. Compounding interactions imply that contemporary-based models of species distributions may underestimate species resilience to climate change. © 2017 John Wiley & Sons Ltd/CNRS.

A method to study response of large trees to different amounts of available soil water

Treesearch

D.H. Marx; Shi-Jean S. Sung; J.S. Cunningham; M.D. Thompson; L.M. White

1995-01-01

A method was developed to manipulate available soil water on large trees by intercepting thrufall with gutters placed under tree canopies and irrigating the intercepted thrufall onto other trees. With this design, trees were exposed for 2 years to either 25% less thrufall, normal thrufall, or 25% additional thrufall.Undercanopy construction in these plots moderately...

A Method to Study Response of Large Trees to Different Amounts of Available Soil Water

Treesearch

Donald H. Marx; Shi-jean S. Sung; James S. Cunningham; Michael D. Thompson; Linda M. White

1995-01-01

A method was developed to manipulate available soil water on large trees by intercepting thrufall with gutters placed under tree canopies and irrigating the intercepted thrufall onto other trees. With this design, trees were exposed for 2 years to either 25 percent less thrufall, normal tbrufall,or 25 percent additional thrufall. Undercanopy construction in these plots...

Finding of No Significant Impact and Finding of No Practicable Alternative: Construction of Visiting Quarters - Phase One and Phase Two MacDill Air Force Base, Florida

DTIC Science & Technology

2011-07-13

the Munitions Storage Area . Although the tree has since succumb to pine beetles, Affected Environment Environmental Assessment for Construction...from Environmental Health Risks and Safety Risks requires Federal agencies, to the extent permitted by law and mission, to identify and assess ...pose a risk to workers or installation personnel. Industrial hygiene programs address Affected Environment Environmental Assessment for

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

Statistical analysis of texture in trunk images for biometric identification of tree species.

PubMed

Bressane, Adriano; Roveda, José A F; Martins, Antônio C G

2015-04-01

The identification of tree species is a key step for sustainable management plans of forest resources, as well as for several other applications that are based on such surveys. However, the present available techniques are dependent on the presence of tree structures, such as flowers, fruits, and leaves, limiting the identification process to certain periods of the year. Therefore, this article introduces a study on the application of statistical parameters for texture classification of tree trunk images. For that, 540 samples from five Brazilian native deciduous species were acquired and measures of entropy, uniformity, smoothness, asymmetry (third moment), mean, and standard deviation were obtained from the presented textures. Using a decision tree, a biometric species identification system was constructed and resulted to a 0.84 average precision rate for species classification with 0.83accuracy and 0.79 agreement. Thus, it can be considered that the use of texture presented in trunk images can represent an important advance in tree identification, since the limitations of the current techniques can be overcome.

Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

PubMed Central

Naushad, Sohail; Barkema, Herman W.; Luby, Christopher; Condas, Larissa A. Z.; Nobrega, Diego B.; Carson, Domonique A.; De Buck, Jeroen

2016-01-01

Non-aureus staphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA, hsp60, rpoB, sodA, and tuf genes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity. PMID:28066335

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

PubMed

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

2018-03-01

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

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

PubMed Central

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

2018-01-01

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

The application of remote sensing image sea ice monitoring method in Bohai Bay based on C4.5 decision tree algorithm

NASA Astrophysics Data System (ADS)

Ye, Wei; Song, Wei

2018-02-01

In The Paper, the remote sensing monitoring of sea ice problem was turned into a classification problem in data mining. Based on the statistic of the related band data of HJ1B remote sensing images, the main bands of HJ1B images related with the reflectance of seawater and sea ice were found. On the basis, the decision tree rules for sea ice monitoring were constructed by the related bands found above, and then the rules were applied to Liaodong Bay area seriously covered by sea ice for sea ice monitoring. The result proved that the method is effective.

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

PubMed Central

Redelings, Benjamin D.

2017-01-01

We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project’s “synthetic tree” starting at version 5. This software pipeline is called “propinquity”. It relies heavily on “otcetera”—a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub. PMID:28265520

Niche construction within riparian corridors. Part II: The unexplored role of positive intraspecific interactions in Salicaceae species

NASA Astrophysics Data System (ADS)

Corenblit, Dov; Garófano-Gómez, Virginia; González, Eduardo; Hortobágyi, Borbála; Julien, Frédéric; Lambs, Luc; Otto, Thierry; Roussel, Erwan; Steiger, Johannes; Tabacchi, Eric; Till-Bottraud, Irène

2018-03-01

Within riparian corridors, Salicaceae trees and shrubs affect hydrogeomorphic processes and lead to the formation of wooded fluvial landforms. These trees form dense stands and enhance plant anchorage, as grouped plants are less prone to be uprooted than free-standing individuals. This also enhances their role as ecosystem engineers through the trapping of sediment, organic matter, and nutrients. The landform formation caused by these wooded biogeomorphic landforms probably represents a positive niche construction, which ultimately leads, through facilitative processes, to an improved capacity of the individual trees to survive, exploit resources, and reach sexual maturity in the interval between destructive floods. The facilitative effects of riparian vegetation are well established; however, the nature and intensity of biotic interactions among trees of the same species forming dense woody stands and constructing the niche remain unclear. Our hypothesis is that the niche construction process also comprises more direct intraspecific interactions, such as cooperation or altruism. Our aim in this paper is to propose an original theoretical framework for positive intraspecific interactions among riparian Salicaceae species operating from establishment to sexual maturity. Within this framework, we speculate that (i) positive intraspecific interactions among trees are maximized in dynamic river reaches; (ii) during establishment, intraspecific facilitation (or helping) occurs among trees and this leads to the maintenance of a dense stand that improves survival and growth because saplings protect each other from shear stress and scour; (iii) in addition to the improved capacity to trap mineral and organic matter, individuals that constitute the dense stand can cooperate to mutually support a mycorrhizal network that will connect plants, soil, and groundwater and influence nutrient transfer, cycling, and storage within the shared constructed niche; (iv) during post-establishment, roots form functional grafts between neighbouring trees to increase biomechanical and physiological anchorage as well as nutrient acquisition and exchange; and (v) these stands remain dense on alluvial bars until a threshold of landform construction and hydrogeomorphic disconnection is reached. At this last stage, intraspecific competition for resources (light and nutrients) increases, inducing a density reduction in the aerial stand (i.e., self-thinning), but root systems of altruistic individuals could remain functional via root grafting. Finally, we suggest new methodological perspectives for testing our hypotheses related to the occurrence of positive intraspecific interactions among Salicaceae trees in fluvial landform and niche construction through in situ and ex situ experiments.

Toward an optimal design principle in symmetric and asymmetric tree flow networks.

PubMed

Miguel, Antonio F

2016-01-21

Fluid flow in tree-shaped networks plays an important role in both natural and engineered systems. This paper focuses on laminar flows of Newtonian and non-Newtonian power law fluids in symmetric and asymmetric bifurcating trees. Based on the constructal law, we predict the tree-shaped architecture that provides greater access to the flow subjected to the total network volume constraint. The relationships between the sizes of parent and daughter tubes are presented both for symmetric and asymmetric branching tubes. We also approach the wall-shear stresses and the flow resistance in terms of first tube size, degree of asymmetry between daughter branches, and rheological behavior of the fluid. The influence of tubes obstructing the fluid flow is also accounted for. The predictions obtained by our theory-driven approach find clear support in the findings of previous experimental studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Binary Decision Trees for Preoperative Periapical Cyst Screening Using Cone-beam Computed Tomography.

PubMed

Pitcher, Brandon; Alaqla, Ali; Noujeim, Marcel; Wealleans, James A; Kotsakis, Georgios; Chrepa, Vanessa

2017-03-01

Cone-beam computed tomographic (CBCT) analysis allows for 3-dimensional assessment of periradicular lesions and may facilitate preoperative periapical cyst screening. The purpose of this study was to develop and assess the predictive validity of a cyst screening method based on CBCT volumetric analysis alone or combined with designated radiologic criteria. Three independent examiners evaluated 118 presurgical CBCT scans from cases that underwent apicoectomies and had an accompanying gold standard histopathological diagnosis of either a cyst or granuloma. Lesion volume, density, and specific radiologic characteristics were assessed using specialized software. Logistic regression models with histopathological diagnosis as the dependent variable were constructed for cyst prediction, and receiver operating characteristic curves were used to assess the predictive validity of the models. A conditional inference binary decision tree based on a recursive partitioning algorithm was constructed to facilitate preoperative screening. Interobserver agreement was excellent for volume and density, but it varied from poor to good for the radiologic criteria. Volume and root displacement were strong predictors for cyst screening in all analyses. The binary decision tree classifier determined that if the volume of the lesion was >247 mm 3 , there was 80% probability of a cyst. If volume was <247 mm 3 and root displacement was present, cyst probability was 60% (78% accuracy). The good accuracy and high specificity of the decision tree classifier renders it a useful preoperative cyst screening tool that can aid in clinical decision making but not a substitute for definitive histopathological diagnosis after biopsy. Confirmatory studies are required to validate the present findings. Published by Elsevier Inc.

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Kramer, Christian; Liedl, Klaus R.

2013-01-01

Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available. PMID:24244149

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.

Supersonic air jets preserve tree roots in underground pipeline installation

Treesearch

Rob Gross; Michelle Julene

2002-01-01

Tree roots are often damaged during construction projects, particularly during trenching operations for pipeline installation. Although mechanical soil excavation using heavy equipment, such as an excavator or backhoe is considered the fastest the most economical method, it damages and destroys tree roots and can lead to unintentional tree loss, poor public relations,...

A review of tree root conflicts with sidewalks, curbs, and roads

Treesearch

T.B. Randrup; E.G. McPherson; L.R. Costello

2003-01-01

Literature relevant to tree root and urban infrastructure conflicts is reviewed. Although tree roots can conflict with many infrastructure elements, sidewalk and curb conflicts are the focus of this review. Construction protocols, urban soils, root growth, and causal factors (soil conditions, limited planting space, tree size, variation in root architecture, management...

Reconciliation of Gene and Species Trees

PubMed Central

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

2014-01-01

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

The Academic Roots of Forestry Programs: A Case Study from Virginia Tech

ERIC Educational Resources Information Center

Copenheaver, Carolyn A.; Nelson, Katie L.; Goldbeck, Kryrille

2009-01-01

Constructing academic genealogies involves the practice of creating family trees based on doctoral advisors, that is, the advisor-graduate student relationship replaces the father-son relationship. Forestry academic genealogies document the historical development of forestry and quantify the contributions of other disciplines. In this study, the…

Perturbative Quantum Gravity from Gauge Theory

NASA Astrophysics Data System (ADS)

Carrasco, John Joseph

In this dissertation we present the graphical techniques recently developed in the construction of multi-loop scattering amplitudes using the method of generalized unitarity. We construct the three-loop and four-loop four-point amplitudes of N = 8 supergravity using these methods and the Kawaii, Lewellen and Tye tree-level relations which map tree-level gauge theory amplitudes to tree-level gravity theory amplitudes. We conclude by extending a tree-level duality between color and kinematics, generic to gauge theories, to a loop level conjecture, allowing the easy relation between loop-level gauge and gravity kinematics. We provide non-trivial evidence for this conjecture at three-loops in the particular case of maximal supersymmetry.

Set-Based Discrete Particle Swarm Optimization Based on Decomposition for Permutation-Based Multiobjective Combinatorial Optimization Problems.

PubMed

Yu, Xue; Chen, Wei-Neng; Gu, Tianlong; Zhang, Huaxiang; Yuan, Huaqiang; Kwong, Sam; Zhang, Jun

2018-07-01

This paper studies a specific class of multiobjective combinatorial optimization problems (MOCOPs), namely the permutation-based MOCOPs. Many commonly seen MOCOPs, e.g., multiobjective traveling salesman problem (MOTSP), multiobjective project scheduling problem (MOPSP), belong to this problem class and they can be very different. However, as the permutation-based MOCOPs share the inherent similarity that the structure of their search space is usually in the shape of a permutation tree, this paper proposes a generic multiobjective set-based particle swarm optimization methodology based on decomposition, termed MS-PSO/D. In order to coordinate with the property of permutation-based MOCOPs, MS-PSO/D utilizes an element-based representation and a constructive approach. Through this, feasible solutions under constraints can be generated step by step following the permutation-tree-shaped structure. And problem-related heuristic information is introduced in the constructive approach for efficiency. In order to address the multiobjective optimization issues, the decomposition strategy is employed, in which the problem is converted into multiple single-objective subproblems according to a set of weight vectors. Besides, a flexible mechanism for diversity control is provided in MS-PSO/D. Extensive experiments have been conducted to study MS-PSO/D on two permutation-based MOCOPs, namely the MOTSP and the MOPSP. Experimental results validate that the proposed methodology is promising.

A novel knowledge-based system for interpreting complex engineering drawings: theory, representation, and implementation.

PubMed

Lu, Tong; Tai, Chiew-Lan; Yang, Huafei; Cai, Shijie

2009-08-01

We present a novel knowledge-based system to automatically convert real-life engineering drawings to content-oriented high-level descriptions. The proposed method essentially turns the complex interpretation process into two parts: knowledge representation and knowledge-based interpretation. We propose a new hierarchical descriptor-based knowledge representation method to organize the various types of engineering objects and their complex high-level relations. The descriptors are defined using an Extended Backus Naur Form (EBNF), facilitating modification and maintenance. When interpreting a set of related engineering drawings, the knowledge-based interpretation system first constructs an EBNF-tree from the knowledge representation file, then searches for potential engineering objects guided by a depth-first order of the nodes in the EBNF-tree. Experimental results and comparisons with other interpretation systems demonstrate that our knowledge-based system is accurate and robust for high-level interpretation of complex real-life engineering projects.

Integrative modeling of gene and genome evolution roots the archaeal tree of life

PubMed Central

Szöllősi, Gergely J.; Spang, Anja; Foster, Peter G.; Heaps, Sarah E.; Boussau, Bastien; Ettema, Thijs J. G.; Embley, T. Martin

2017-01-01

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer. PMID:28533395

Integrative modeling of gene and genome evolution roots the archaeal tree of life.

PubMed

Williams, Tom A; Szöllősi, Gergely J; Spang, Anja; Foster, Peter G; Heaps, Sarah E; Boussau, Bastien; Ettema, Thijs J G; Embley, T Martin

2017-06-06

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum , which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO 2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

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

PubMed

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

2017-04-01

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

Object-based methods for individual tree identification and tree species classification from high-spatial resolution imagery

NASA Astrophysics Data System (ADS)

Wang, Le

2003-10-01

Modern forest management poses an increasing need for detailed knowledge of forest information at different spatial scales. At the forest level, the information for tree species assemblage is desired whereas at or below the stand level, individual tree related information is preferred. Remote Sensing provides an effective tool to extract the above information at multiple spatial scales in the continuous time domain. To date, the increasing volume and readily availability of high-spatial-resolution data have lead to a much wider application of remotely sensed products. Nevertheless, to make effective use of the improving spatial resolution, conventional pixel-based classification methods are far from satisfactory. Correspondingly, developing object-based methods becomes a central challenge for researchers in the field of Remote Sensing. This thesis focuses on the development of methods for accurate individual tree identification and tree species classification. We develop a method in which individual tree crown boundaries and treetop locations are derived under a unified framework. We apply a two-stage approach with edge detection followed by marker-controlled watershed segmentation. Treetops are modeled from radiometry and geometry aspects. Specifically, treetops are assumed to be represented by local radiation maxima and to be located near the center of the tree-crown. As a result, a marker image was created from the derived treetop to guide a watershed segmentation to further differentiate overlapping trees and to produce a segmented image comprised of individual tree crowns. The image segmentation method developed achieves a promising result for a 256 x 256 CASI image. Then further effort is made to extend our methods to the multiscales which are constructed from a wavelet decomposition. A scale consistency and geometric consistency are designed to examine the gradients along the scale-space for the purpose of separating true crown boundary from unwanted textures occurring due to branches and twigs. As a result from the inverse wavelet transform, the tree crown boundary is enhanced while the unwanted textures are suppressed. Based on the enhanced image, an improvement is achieved when applying the two-stage methods to a high resolution aerial photograph. To improve tree species classification, we develop a new method to choose the optimal scale parameter with the aid of Bhattacharya Distance (BD), a well-known index of class separability in traditional pixel-based classification. The optimal scale parameter is then fed in the process of a region-growing-based segmentation as a break-off value. Our object classification achieves a better accuracy in separating tree species when compared to the conventional Maximum Likelihood Classification (MLC). In summary, we develop two object-based methods for identifying individual trees and classifying tree species from high-spatial resolution imagery. Both methods achieve promising results and will promote integration of Remote Sensing and GIS in forest applications.

Graph-associated entanglement cost of a multipartite state in exact and finite-block-length approximate constructions

NASA Astrophysics Data System (ADS)

Yamasaki, Hayata; Soeda, Akihito; Murao, Mio

2017-09-01

We introduce and analyze graph-associated entanglement cost, a generalization of the entanglement cost of quantum states to multipartite settings. We identify a necessary and sufficient condition for any multipartite entangled state to be constructible when quantum communication between the multiple parties is restricted to a quantum network represented by a tree. The condition for exact state construction is expressed in terms of the Schmidt ranks of the state defined with respect to edges of the tree. We also study approximate state construction and provide a second-order asymptotic analysis.

Evaluation of acoustic tomography for tree decay detection

Treesearch

Shanquing Liang; Xiping Wang; Janice Wiedenbeck; Zhiyong Cai; Feng Fu

2008-01-01

In this study, the acoustic tomography technique was used to detect internal decay in high value black cherry (Prunus seratina) trees. Two-dimensional images of the cross sections of the tree samples were constructed using PiCUS Q70 software. The trees were felled following the field test, and a disc from each testing elevation was subsequently cut...

The balance of planting and mortality in a street tree population

Treesearch

Lara A. Roman; John J. Battles; Joe R. McBride

2013-01-01

Street trees have aesthetic, environmental, human health, and economic benefits in urban ecosystems. Street tree populations are constructed by cycles of planting, growth, death, removal and replacement. The goals of this study were to understand how tree mortality and planting rates affect net population growth, evaluate the shape of the mortality curve, and assess...

Blood oxygen level dependent magnetic resonance imaging for detecting pathological patterns in lupus nephritis patients: a preliminary study using a decision tree model.

PubMed

Shi, Huilan; Jia, Junya; Li, Dong; Wei, Li; Shang, Wenya; Zheng, Zhenfeng

2018-02-09

Precise renal histopathological diagnosis will guide therapy strategy in patients with lupus nephritis. Blood oxygen level dependent (BOLD) magnetic resonance imaging (MRI) has been applicable noninvasive technique in renal disease. This current study was performed to explore whether BOLD MRI could contribute to diagnose renal pathological pattern. Adult patients with lupus nephritis renal pathological diagnosis were recruited for this study. Renal biopsy tissues were assessed based on the lupus nephritis ISN/RPS 2003 classification. The Blood oxygen level dependent magnetic resonance imaging (BOLD-MRI) was used to obtain functional magnetic resonance parameter, R2* values. Several functions of R2* values were calculated and used to construct algorithmic models for renal pathological patterns. In addition, the algorithmic models were compared as to their diagnostic capability. Both Histopathology and BOLD MRI were used to examine a total of twelve patients. Renal pathological patterns included five classes III (including 3 as class III + V) and seven classes IV (including 4 as class IV + V). Three algorithmic models, including decision tree, line discriminant, and logistic regression, were constructed to distinguish the renal pathological pattern of class III and class IV. The sensitivity of the decision tree model was better than that of the line discriminant model (71.87% vs 59.48%, P < 0.001) and inferior to that of the Logistic regression model (71.87% vs 78.71%, P < 0.001). The specificity of decision tree model was equivalent to that of the line discriminant model (63.87% vs 63.73%, P = 0.939) and higher than that of the logistic regression model (63.87% vs 38.0%, P < 0.001). The Area under the ROC curve (AUROCC) of the decision tree model was greater than that of the line discriminant model (0.765 vs 0.629, P < 0.001) and logistic regression model (0.765 vs 0.662, P < 0.001). BOLD MRI is a useful non-invasive imaging technique for the evaluation of lupus nephritis. Decision tree models constructed using functions of R2* values may facilitate the prediction of renal pathological patterns.

A population 'consensus', partial linkage map of Picea abies Karst. based on RAPD markers

Treesearch

G. Bucci; Thomas L. Kubisiak; W.L. Nance; P. Menozzi

1997-01-01

The authors built a "consensus" partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight...

Bayesian-network-based safety risk assessment for steel construction projects.

PubMed

Leu, Sou-Sen; Chang, Ching-Miao

2013-05-01

There are four primary accident types at steel building construction (SC) projects: falls (tumbles), object falls, object collapse, and electrocution. Several systematic safety risk assessment approaches, such as fault tree analysis (FTA) and failure mode and effect criticality analysis (FMECA), have been used to evaluate safety risks at SC projects. However, these traditional methods ineffectively address dependencies among safety factors at various levels that fail to provide early warnings to prevent occupational accidents. To overcome the limitations of traditional approaches, this study addresses the development of a safety risk-assessment model for SC projects by establishing the Bayesian networks (BN) based on fault tree (FT) transformation. The BN-based safety risk-assessment model was validated against the safety inspection records of six SC building projects and nine projects in which site accidents occurred. The ranks of posterior probabilities from the BN model were highly consistent with the accidents that occurred at each project site. The model accurately provides site safety-management abilities by calculating the probabilities of safety risks and further analyzing the causes of accidents based on their relationships in BNs. In practice, based on the analysis of accident risks and significant safety factors, proper preventive safety management strategies can be established to reduce the occurrence of accidents on SC sites. Copyright © 2013 Elsevier Ltd. All rights reserved.

dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees.

PubMed

Wise, Michael J

2016-01-01

Biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. However, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. In addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. A decision must therefore be made about which gene, or gene combinations, should be used to compute a tree. Deflated Cladistic Information based on Total Entropy (dCITE) is proposed as an easily computed metric for measuring the cladistic information in multiple sequence alignments representing a range of taxa, without the need to first compute the corresponding trees. dCITE scores can be used to rank candidate genes or decide whether input sequences provide insufficient cladistic information, making artefactual polytomies more likely. The dCITE method can be applied to protein, nucleotide or encoded phenotypic data, so can be used to select which data-type is most appropriate, given the choice. In a series of experiments the dCITE method was compared with related measures. Then, as a practical demonstration, the ideas developed in the paper were applied to a dataset representing species from the order Campylobacterales; trees based on sequence combinations, selected on the basis of their dCITE scores, were compared with a tree constructed to mimic Multi-Locus Sequence Typing (MLST) combinations of fragments. We see that the greater the dCITE score the more likely it is that the computed phylogenetic tree will be free of artefactual polytomies. Secondly, cladistic information saturates, beyond which little additional cladistic information can be obtained by adding additional sequences. Finally, sequences with high cladistic information produce more consistent trees for the same taxa.

dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees

PubMed Central

2016-01-01

Biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. However, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. In addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. A decision must therefore be made about which gene, or gene combinations, should be used to compute a tree. Deflated Cladistic Information based on Total Entropy (dCITE) is proposed as an easily computed metric for measuring the cladistic information in multiple sequence alignments representing a range of taxa, without the need to first compute the corresponding trees. dCITE scores can be used to rank candidate genes or decide whether input sequences provide insufficient cladistic information, making artefactual polytomies more likely. The dCITE method can be applied to protein, nucleotide or encoded phenotypic data, so can be used to select which data-type is most appropriate, given the choice. In a series of experiments the dCITE method was compared with related measures. Then, as a practical demonstration, the ideas developed in the paper were applied to a dataset representing species from the order Campylobacterales; trees based on sequence combinations, selected on the basis of their dCITE scores, were compared with a tree constructed to mimic Multi-Locus Sequence Typing (MLST) combinations of fragments. We see that the greater the dCITE score the more likely it is that the computed phylogenetic tree will be free of artefactual polytomies. Secondly, cladistic information saturates, beyond which little additional cladistic information can be obtained by adding additional sequences. Finally, sequences with high cladistic information produce more consistent trees for the same taxa. PMID:27898695

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

NASA Astrophysics Data System (ADS)

Giguère, Claudie; Boucher, Étienne; Bergeron, Yves

2016-04-01

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

Statistical indicators of collective behavior and functional clusters in gene networks of yeast

NASA Astrophysics Data System (ADS)

Živković, J.; Tadić, B.; Wick, N.; Thurner, S.

2006-03-01

We analyze gene expression time-series data of yeast (S. cerevisiae) measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene interaction networks based on correlation coefficients and study the formation of the corresponding giant components and minimum spanning trees. By coloring genes according to their cell function we find functional clusters in the correlation networks and functional branches in the associated trees. Our results suggest that a percolation point of functional clusters can be identified on these gene expression correlation networks.

A tree island approach to inferring phylogeny in the ant subfamily Formicinae, with especial reference to the evolution of weaving.

PubMed

Johnson, Rebecca N; Agapow, Paul-Michael; Crozier, Ross H

2003-11-01

The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been lost once. A maximum likelihood analysis showed that loss of the metapleural gland is significantly associated with the weaver life-pattern. The graph of the frequencies with which trees were discovered versus their likelihood indicates that trees with high likelihoods have much larger basins of attraction than those with lower likelihoods. While this result indicates that single searches are more likely to find high- than low-likelihood tree islands, it also indicates that searching only for the single best tree may lose important information.

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

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Attention trees and semantic paths

NASA Astrophysics Data System (ADS)

Giusti, Christian; Pieroni, Goffredo G.; Pieroni, Laura

2007-02-01

In the last few decades several techniques for image content extraction, often based on segmentation, have been proposed. It has been suggested that under the assumption of very general image content, segmentation becomes unstable and classification becomes unreliable. According to recent psychological theories, certain image regions attract the attention of human observers more than others and, generally, the image main meaning appears concentrated in those regions. Initially, regions attracting our attention are perceived as a whole and hypotheses on their content are formulated; successively the components of those regions are carefully analyzed and a more precise interpretation is reached. It is interesting to observe that an image decomposition process performed according to these psychological visual attention theories might present advantages with respect to a traditional segmentation approach. In this paper we propose an automatic procedure generating image decomposition based on the detection of visual attention regions. A new clustering algorithm taking advantage of the Delaunay- Voronoi diagrams for achieving the decomposition target is proposed. By applying that algorithm recursively, starting from the whole image, a transformation of the image into a tree of related meaningful regions is obtained (Attention Tree). Successively, a semantic interpretation of the leaf nodes is carried out by using a structure of Neural Networks (Neural Tree) assisted by a knowledge base (Ontology Net). Starting from leaf nodes, paths toward the root node across the Attention Tree are attempted. The task of the path consists in relating the semantics of each child-parent node pair and, consequently, in merging the corresponding image regions. The relationship detected in this way between two tree nodes generates, as a result, the extension of the interpreted image area through each step of the path. The construction of several Attention Trees has been performed and partial results will be shown.

From learning taxonomies to phylogenetic learning: integration of 16S rRNA gene data into FAME-based bacterial classification.

PubMed

Slabbinck, Bram; Waegeman, Willem; Dawyndt, Peter; De Vos, Paul; De Baets, Bernard

2010-01-30

Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context.

From learning taxonomies to phylogenetic learning: Integration of 16S rRNA gene data into FAME-based bacterial classification

PubMed Central

2010-01-01

Background Machine learning techniques have shown to improve bacterial species classification based on fatty acid methyl ester (FAME) data. Nonetheless, FAME analysis has a limited resolution for discrimination of bacteria at the species level. In this paper, we approach the species classification problem from a taxonomic point of view. Such a taxonomy or tree is typically obtained by applying clustering algorithms on FAME data or on 16S rRNA gene data. The knowledge gained from the tree can then be used to evaluate FAME-based classifiers, resulting in a novel framework for bacterial species classification. Results In view of learning in a taxonomic framework, we consider two types of trees. First, a FAME tree is constructed with a supervised divisive clustering algorithm. Subsequently, based on 16S rRNA gene sequence analysis, phylogenetic trees are inferred by the NJ and UPGMA methods. In this second approach, the species classification problem is based on the combination of two different types of data. Herein, 16S rRNA gene sequence data is used for phylogenetic tree inference and the corresponding binary tree splits are learned based on FAME data. We call this learning approach 'phylogenetic learning'. Supervised Random Forest models are developed to train the classification tasks in a stratified cross-validation setting. In this way, better classification results are obtained for species that are typically hard to distinguish by a single or flat multi-class classification model. Conclusions FAME-based bacterial species classification is successfully evaluated in a taxonomic framework. Although the proposed approach does not improve the overall accuracy compared to flat multi-class classification, it has some distinct advantages. First, it has better capabilities for distinguishing species on which flat multi-class classification fails. Secondly, the hierarchical classification structure allows to easily evaluate and visualize the resolution of FAME data for the discrimination of bacterial species. Summarized, by phylogenetic learning we are able to situate and evaluate FAME-based bacterial species classification in a more informative context. PMID:20113515

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Explicit formulae for Yang-Mills-Einstein amplitudes from the double copy

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

Chiodaroli, Marco; Günaydin, Murat; Johansson, Henrik

Using the double-copy construction of Yang-Mills-Einstein theories formulated in our earlier work, we obtain compact presentations for single-trace Yang-Mills-Einstein tree amplitudes with up to five external gravitons and an arbitrary number of gluons. These are written as linear combinations of color-ordered Yang-Mills trees, where the coefficients are given by color/kinematics-satisfying numerators in a Yang-Mills + φ 3 theory. The construction outlined in this paper holds in general dimension and extends straightforwardly to supergravity theories. For one, two, and three external gravitons, our expressions give identical or simpler presentations of amplitudes already constructed through string-theory considerations or the scattering equations formalism.more » Our results are based on color/kinematics duality and gauge invariance, and strongly hint at a recursive structure underlying the single-trace amplitudes with an arbitrary number of gravitons. We also present explicit expressions for all-loop single-graviton Einstein-Yang-Mills amplitudes in terms of Yang-Mills amplitudes and, through gauge invariance, derive new all-loop amplitude relations for Yang-Mills theory.« less

Explicit formulae for Yang-Mills-Einstein amplitudes from the double copy

DOE PAGES

Chiodaroli, Marco; Günaydin, Murat; Johansson, Henrik; ...

2017-07-03

Using the double-copy construction of Yang-Mills-Einstein theories formulated in our earlier work, we obtain compact presentations for single-trace Yang-Mills-Einstein tree amplitudes with up to five external gravitons and an arbitrary number of gluons. These are written as linear combinations of color-ordered Yang-Mills trees, where the coefficients are given by color/kinematics-satisfying numerators in a Yang-Mills + φ 3 theory. The construction outlined in this paper holds in general dimension and extends straightforwardly to supergravity theories. For one, two, and three external gravitons, our expressions give identical or simpler presentations of amplitudes already constructed through string-theory considerations or the scattering equations formalism.more » Our results are based on color/kinematics duality and gauge invariance, and strongly hint at a recursive structure underlying the single-trace amplitudes with an arbitrary number of gravitons. We also present explicit expressions for all-loop single-graviton Einstein-Yang-Mills amplitudes in terms of Yang-Mills amplitudes and, through gauge invariance, derive new all-loop amplitude relations for Yang-Mills theory.« less

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

A Comparison of Two Tree Construction Methods for Obtaining Proximity Measures among Words. Number 47.

ERIC Educational Resources Information Center

Rapoport, Amnon

The prediction that two different methods of constructing linear, tree graphs will yield the same formal structure of semantic space and measurement of word proximity was tested by comparing the distribution of node degree, the distribution of the number of pairs of nodes connected y times, and the distribution of adjective degree in trees…

78 FR 5797 - Missisquoi Associates; Notice of Application for Amendment of License and Soliciting Comments...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-28

... to allow its affiliate, EGP Solar 1, LLC, to construct and maintain a 2.2 megawatt solar photovoltaic... solar array would be constructed on both sides of Heather Lane (the project's access road), but public... be used for the solar array is currently devoid of trees, although some grading and tree cutting is...

The ratio of NPP to GPP: evidence of change over the course of stand development.

PubMed

Mäkelä, A; Valentine, H T

2001-09-01

Using Scots pine (Pinus sylvestris L.) in Fenno-Scandia as a case study, we investigate whether net primary production (NPP) and maintenance respiration are constant fractions of gross primary production (GPP) as even-aged mono-specific stands progress from initiation to old age. A model of the ratio of NPP to GPP is developed based on (1) the classical model of respiration, which divides total respiration into construction and maintenance components, and (2) a process-based model, which derives respiration from processes including construction, nitrate uptake and reduction, ion uptake, phloem loading and maintenance. Published estimates of specific respiration and production rates, and some recent measurements of components of dry matter in stands of different ages, are used to quantify the two approaches over the course of stand development in an average environment. Both approaches give similar results, showing a decrease in the NPP/GPP ratio with increasing tree height. In addition, we show that stand-growth models fitted under three different sets of assumptions-(i) annual specific rates of maintenance respiration of sapwood (mW) and photosynthesis (sC) are constant; (ii) m(W) is constant, but sC decreases with increasing tree height; and (iii) total maintenance respiration is a constant fraction of GPP and s(C) decreases with increasing tree height-can lead to nearly identical model projections that agree with empirical observations of NPP and stand-growth variables. Remeasurements of GPP and respiration over time in chronosequences of stands may be needed to discern which set of assumptions is correct. Total (construction + maintenance) sapwood respiration per unit mass of sapwood (kg C (kg C year)-1) decreased with increasing stand age, sapwood stock, and average tree height under all three assumptions. However, total sapwood respiration (kg C (ha year)-1) increased over the course of stand development under (i) and (ii), contributing to a downward trend in the time course of the NPP/GPP ratio after closure. A moderate decrease in mW with increasing tree height or sapwood cross-sectional area had little effect on the downward trend. On the basis of this evidence, we argue that a significant decline in the NPP/GPP ratio with tree size or age seems highly probable, although the decline may appear insignificant over some segments of stand development. We also argue that, because stand-growth models can give correct answers for the wrong reasons, statistical calibration of such models should be avoided whenever possible; instead, values of physiological parameters should come from measurements of the physiological processes themselves.

Welcome to pandoraviruses at the ‘Fourth TRUC’ club

PubMed Central

Sharma, Vikas; Colson, Philippe; Chabrol, Olivier; Scheid, Patrick; Pontarotti, Pierre; Raoult, Didier

2015-01-01

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9–2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the ‘Fourth TRUC’ club, encompassing distinct life forms compared with cellular organisms. PMID:26042093

Welcome to pandoraviruses at the 'Fourth TRUC' club.

PubMed

Sharma, Vikas; Colson, Philippe; Chabrol, Olivier; Scheid, Patrick; Pontarotti, Pierre; Raoult, Didier

2015-01-01

Nucleocytoplasmic large DNA viruses, or representatives of the proposed order Megavirales, belong to families of giant viruses that infect a broad range of eukaryotic hosts. Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (things resisting uncompleted classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. In the present study, we updated the classification of pandoraviruses and other reported giant viruses. Phylogenetic trees were constructed based on six informational genes. Hierarchical clustering was performed based on a set of informational genes from Megavirales members and cellular organisms. Homologous sequences were selected from cellular organisms using TimeTree software, comprising comprehensive, and representative sets of members from Bacteria, Archaea, and Eukarya. Phylogenetic analyses based on three conserved core genes clustered pandoraviruses with phycodnaviruses, exhibiting their close relatedness. Additionally, hierarchical clustering analyses based on informational genes grouped pandoraviruses with Megavirales members as a super group distinct from cellular organisms. Thus, the analyses based on core conserved genes revealed that pandoraviruses are new genuine members of the 'Fourth TRUC' club, encompassing distinct life forms compared with cellular organisms.

a Gross Error Elimination Method for Point Cloud Data Based on Kd-Tree

NASA Astrophysics Data System (ADS)

Kang, Q.; Huang, G.; Yang, S.

2018-04-01

Point cloud data has been one type of widely used data sources in the field of remote sensing. Key steps of point cloud data's pro-processing focus on gross error elimination and quality control. Owing to the volume feature of point could data, existed gross error elimination methods need spend massive memory both in space and time. This paper employed a new method which based on Kd-tree algorithm to construct, k-nearest neighbor algorithm to search, settled appropriate threshold to determine with result turns out a judgement that whether target point is or not an outlier. Experimental results show that, our proposed algorithm will help to delete gross error in point cloud data and facilitate to decrease memory consumption, improve efficiency.

Tree tensor network approach to simulating Shor's algorithm

NASA Astrophysics Data System (ADS)

Dumitrescu, Eugene

2017-12-01

Constructively simulating quantum systems furthers our understanding of qualitative and quantitative features which may be analytically intractable. In this paper, we directly simulate and explore the entanglement structure present in the paradigmatic example for exponential quantum speedups: Shor's algorithm. To perform our simulation, we construct a dynamic tree tensor network which manifestly captures two salient circuit features for modular exponentiation. These are the natural two-register bipartition and the invariance of entanglement with respect to permutations of the top-register qubits. Our construction help identify the entanglement entropy properties, which we summarize by a scaling relation. Further, the tree network is efficiently projected onto a matrix product state from which we efficiently execute the quantum Fourier transform. Future simulation of quantum information states with tensor networks exploiting circuit symmetries is discussed.

Wnt signal transduction pathways: modules, development and evolution.

PubMed

Nayak, Losiana; Bhattacharyya, Nitai P; De, Rajat K

2016-08-01

Wnt signal transduction pathway (Wnt STP) is a crucial intracellular pathway mainly due to its participation in important biological processes, functions, and diseases, i.e., embryonic development, stem-cell management, and human cancers among others. This is why Wnt STP is one of the highest researched signal transduction pathways. Study and analysis of its origin, expansion and gradual development to the present state as found in humans is one aspect of Wnt research. The pattern of development and evolution of the Wnt STP among various species is not clear till date. A phylogenetic tree created from Wnt STPs of multiple species may address this issue. In this respect, we construct a phylogenetic tree from modules of Wnt STPs of diverse species. We term it as the 'Module Tree'. A module is nothing but a self-sufficient minimally-dependent subset of the original Wnt STP. Authenticity of the module tree is tested by comparing it with the two reference trees. The module tree performs better than an alternative phylogenetic tree constructed from pathway topology of Wnt STPs. Moreover, an evolutionary emergence pattern of the Wnt gene family is created and the module tree is tallied with it to showcase the significant resemblances.

Fuzzy fault tree assessment based on improved AHP for fire and explosion accidents for steel oil storage tanks.

PubMed

Shi, Lei; Shuai, Jian; Xu, Kui

2014-08-15

Fire and explosion accidents of steel oil storage tanks (FEASOST) occur occasionally during the petroleum and chemical industry production and storage processes and often have devastating impact on lives, the environment and property. To contribute towards the development of a quantitative approach for assessing the occurrence probability of FEASOST, a fault tree of FEASOST is constructed that identifies various potential causes. Traditional fault tree analysis (FTA) can achieve quantitative evaluation if the failure data of all of the basic events (BEs) are available, which is almost impossible due to the lack of detailed data, as well as other uncertainties. This paper makes an attempt to perform FTA of FEASOST by a hybrid application between an expert elicitation based improved analysis hierarchy process (AHP) and fuzzy set theory, and the occurrence possibility of FEASOST is estimated for an oil depot in China. A comparison between statistical data and calculated data using fuzzy fault tree analysis (FFTA) based on traditional and improved AHP is also made. Sensitivity and importance analysis has been performed to identify the most crucial BEs leading to FEASOST that will provide insights into how managers should focus effective mitigation. Copyright © 2014 Elsevier B.V. All rights reserved.

Genetic diversity analysis of tree peony germplasm using iPBS markers.

PubMed

Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

2015-07-06

We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties.

Using Tree-Rings and Remote Sensing to Investigate Forest Productivity Response to Landscape Fragmentation in Northeastern Algeria

NASA Astrophysics Data System (ADS)

Rouini, N.; Lepley, K. S.; Messaoudene, M.

2017-12-01

Remote sensing and dendrochronology are valuable tools in the face of climate change and land use change, yet the connection between these resources remains largely unexploited. Research on forest fragmentation is mainly focused on animal groups, while our work focuses on tree communities. We link tree-rings and remotely-sensed Normalized Difference Vegetation Index (NDVI) using seasonal correlation analysis to investigate forest primary productivity response to fragmentation. Tree core samples from Quercus afares have been taken from two sites within the Guerrouche Forest in northeastern Algeria. The first site is located within a very fragmented area while the second site is intact. Fragmentation is estimated to have occurred with the construction of a road in 1930. We find raw tree-ring width chronologies from each site reveal growth release in the disturbed site after 1930. The means of each chronology for the 1930 to 2016 period are statistically different (p < 0.01). Based on these preliminary results we hypothesize that reconstructed primary productivity (NDVI) will be higher in the fragmented site after fragmentation took place.

Patterns of thinking about phylogenetic trees: A study of student learning and the potential of tree thinking to improve comprehension of biological concepts

NASA Astrophysics Data System (ADS)

Naegle, Erin

Evolution education is a critical yet challenging component of teaching and learning biology. There is frequently an emphasis on natural selection when teaching about evolution and conducting educational research. A full understanding of evolution, however, integrates evolutionary processes, such as natural selection, with the resulting evolutionary patterns, such as species divergence. Phylogenetic trees are models of evolutionary patterns. The perspective gained from understanding biology through phylogenetic analyses is referred to as tree thinking. Due to the increasing prevalence of tree thinking in biology, understanding how to read phylogenetic trees is an important skill for students to learn. Interpreting graphics is not an intuitive process, as graphical representations are semiotic objects. This is certainly true concerning phylogenetic tree interpretation. Previous research and anecdotal evidence report that students struggle to correctly interpret trees. The objective of this research was to describe and investigate the rationale underpinning the prior knowledge of introductory biology students' tree thinking Understanding prior knowledge is valuable as prior knowledge influences future learning. In Chapter 1, qualitative methods such as semi-structured interviews were used to explore patterns of student rationale in regard to tree thinking. Seven common tree thinking misconceptions are described: (1) Equating the degree of trait similarity with the extent of relatedness, (2) Environmental change is a necessary prerequisite to evolution, (3) Essentialism of species, (4) Evolution is inherently progressive, (5) Evolution is a linear process, (6) Not all species are related, and (7) Trees portray evolution through the hybridization of species. These misconceptions are based in students' incomplete or incorrect understanding of evolution. These misconceptions are often reinforced by the misapplication of cultural conventions to make sense of trees. Chapter 2 explores the construction, validity, and reliability of a tree thinking concept inventory. Concept inventories are research based instruments that diagnose faulty reasoning among students. Such inventories are tools for improving teaching and learning of concepts. Test scores indicate that tree thinking misconceptions are held by novice and intermediate biology students. Finally, Chapter 3 presents a tree thinking rubric. The rubric aids teachers in selecting and improving introductory tree thinking learning exercises that address students' tree thinking misconceptions.

Alterations of chemical composition, construction cost and payback time in needles of Masson pine (Pinus massoniana L.) trees grown under pollution.

PubMed

Liu, Nan; Guan, Lan-Lan; Sun, Fang-Fang; Wen, Da-Zhi

2014-07-01

Previous studies show that Masson pine (Pinus massoniana L.) stands grown at the industrially-polluted site have experienced unprecedented growth decline, but the causal mechanisms are poorly understood. In this study, to understand the mechanisms of growth decline of Mason pine strands under pollution stresses, we determined the reactive oxygen species levels and chemical composition of the current-year (C) and one-year-old (C + 1) needles, and calculated the needle construction costs (CCmass) of Masson pine trees grown at an industrially-polluted site and an unpolluted remote site. Pine trees grown at the polluted site had significantly higher levels of hydroxyl radical and superoxide anion in their needles than those grown at the unpolluted site, and the former trees eventually exhibited needle early senescence. The contents of lipids, soluble phenolics and lignins in C and C + 1 needles were significantly higher at the polluted site than at the unpolluted site, but the total amounts of non-construction carbohydrates were lower in non-polluted needles than in polluted needles. Elevated levels of the reactive oxygen species and early senescence in polluted needles together led to significant increases in CCmass and a longer payback time. We infer that the lengthened payback time and needle early senescence under pollution stress may reduce the Masson pine tree growth and consequently accelerate tree decline.

OpenGL in Multi-User Web-Based Applications

NASA Astrophysics Data System (ADS)

Szostek, K.; Piórkowski, A.

In this article construction and potential of OpenGL multi-user web-based application are presented. The most common technologies like: .NET ASP, Java and Mono were used with specific OpenGL libraries to visualize tree-dimensional medical data. The most important conclusion of this work is that server side applications can easily take advantage of fast GPU and produce efficient results of advanced computation just like the visualization.

A web-based tree crown condition training and evaluation tool for urban and community forestry

Treesearch

Matthew F. Winn; Neil A. Clark; Philip A. Araman; Sang-Mook Lee

2007-01-01

Training personnel for natural resource related field work can be a costly and time-consuming process. For that reason, web-based training is considered by many to be a more attractive alternative to on-site training. The U.S. Forest Service Southern Research Station unit with Virginia Tech cooperators in Blacksburg, Va., are in the process of constructing a web site...

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

PubMed Central

Ma, Yue; Tuskan, Gerald A.

2018-01-01

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln(L) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level. PMID:29686995

Tools for valuing tree and park services

Treesearch

E.G. McPherson

2010-01-01

Arborists and urban foresters plan, design, construct, and manage trees and parks in cities throughout the world. These civic improvements create walkable, cool environments, save energy, reduce stormwater runoff, sequester carbon dioxide, and absorb air pollutants. The presence of trees and green spaces in cities is associated with increases in property values,...

Tree growth and recruitment in a leveed floodplain forest in the Mississippi River Alluvial Valley, USA

USGS Publications Warehouse

Gee, Hugo K.W.; King, Sammy L.; Keim, Richard F.

2014-01-01

Flooding is a defining disturbance in floodplain forests affecting seed germination, seedling establishment, and tree growth. Globally, flood control, including artificial levees, dams, and channelization has altered flood regimes in floodplains. However, a paucity of data are available in regards to the long-term effects of levees on stand establishment and tree growth in floodplain forests. In this study, we used dendrochronological techniques to reconstruct tree recruitment and tree growth over a 90-year period at three stands within a ring levee in the Mississippi River Alluvial Valley (MAV) and to evaluate whether recruitment patterns and tree growth changed following levee construction. We hypothesized that: (1) sugarberry is increasing in dominance and overcup oak (Quercus lyrata) is becoming less dominant since the levee, and that changes in hydrology are playing a greater role than canopy disturbance in these changes in species dominance; and (2) that overcup oak growth has declined following construction of the levee and cessation of overbank flooding whereas that of sugarberry has increased. Recruitment patterns shifted from flood-tolerant overcup oak to flood-intolerant sugarberry (Celtis laevigata) after levee construction. None of the 122 sugarberry trees cored in this study established prior to the levee, but it was the most common species established after the levee. The mechanisms behind the compositional change are unknown, however, the cosmopolitan distribution of overcup oak during the pre-levee period and sugarberry during the post-levee period, the lack of sugarberry establishment in the pre-levee period, and the confinement of overcup oak regeneration to the lowest areas in each stand after harvest in the post-levee period indicate that species-specific responses to flooding and light availability are forcing recruitment patterns. Overcup oak growth was also affected by levee construction, but in contrast to our hypothesis, growth actually increased for several decades before declining during a drought in the late 1990s. We interpret this result as removal of flood stress following levee construction. This finding emphasizes the fact that flooding can be stressful to trees regardless of their flood tolerance and that growth in floodplain trees can be sustained provided adequate soil moisture is present, regardless of the source of soil moisture. However, future research efforts should focus on the long-term effect of hydrologic modification on stand development and on how hydrologic modifications, such as elimination of surface flooding and groundwater declines, affect the vulnerability of floodplain forests to drought.

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

NASA Astrophysics Data System (ADS)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Phylogenetic Reconstruction and DNA Barcoding for Closely Related Pine Moth Species (Dendrolimus) in China with Multiple Gene Markers

PubMed Central

Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

2012-01-01

Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), “best close match” (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10–97.40%, while ITS1 and ITS2 obtained a success rate of 64.70–81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our results indicate that the most closely related species D. punctatus, D. tabulaeformis, and D. spectabilis, may be still in the process of incomplete lineage sorting, with occasional hybridizations occurring among them. PMID:22509245

Automatic determination of trunk diameter, crown base and height of scots pine (Pinus Sylvestris L.) Based on analysis of 3D point clouds gathered from multi-station terrestrial laser scanning. (Polish Title: Automatyczne okreslanie srednicy pnia, podstawy korony oraz wysokosci sosny zwyczajnej (Pinus Silvestris L.) Na podstawie analiz chmur punktow 3D pochodzacych z wielostanowiskowego naziemnego skanowania laserowego)

NASA Astrophysics Data System (ADS)

Ratajczak, M.; Wężyk, P.

2015-12-01

Rapid development of terrestrial laser scanning (TLS) in recent years resulted in its recognition and implementation in many industries, including forestry and nature conservation. The use of the 3D TLS point clouds in the process of inventory of trees and stands, as well as in the determination of their biometric features (trunk diameter, tree height, crown base, number of trunk shapes), trees and lumber size (volume of trees) is slowly becoming a practice. In addition to the measurement precision, the primary added value of TLS is the ability to automate the processing of the clouds of points 3D in the direction of the extraction of selected features of trees and stands. The paper presents the original software (GNOM) for the automatic measurement of selected features of trees, based on the cloud of points obtained by the ground laser scanner FARO. With the developed algorithms (GNOM), the location of tree trunks on the circular research surface was specified and the measurement was performed; the measurement covered the DBH (l: 1.3m), further diameters of tree trunks at different heights of the tree trunk, base of the tree crown and volume of the tree trunk (the selection measurement method), as well as the tree crown. Research works were performed in the territory of the Niepolomice Forest in an unmixed pine stand (Pinussylvestris L.) on the circular surface with a radius of 18 m, within which there were 16 pine trees (14 of them were cut down). It was characterized by a two-storey and even-aged construction (147 years old) and was devoid of undergrowth. Ground scanning was performed just before harvesting. The DBH of 16 pine trees was specified in a fully automatic way, using the algorithm GNOM with an accuracy of +2.1%, as compared to the reference measurement by the DBH measurement device. The medium, absolute measurement error in the cloud of points - using semi-automatic methods "PIXEL" (between points) and PIPE (fitting the cylinder) in the FARO Scene 5.x., showed the error, 3.5% and 5.0%,.respectively The reference height was assumed as the measurement performed by the tape on the cut tree. The average error of automatic determination of the tree height by the algorithm GNOM based on the TLS point clouds amounted to 6.3% and was slightly higher than when using the manual method of measurements on profiles in the TerraScan (Terrasolid; the error of 5.6%). The relatively high value of the error may be mainly related to the small number of points TLS in the upper parts of crowns. The crown height measurement showed the error of +9.5%. The reference in this case was the tape measurement performed already on the trunks of cut pine trees. Processing the clouds of points by the algorithms GNOM for 16 analyzed trees took no longer than 10 min. (37 sec. /tree). The paper mainly showed the TLS measurement innovation and its high precision in acquiring biometric data in forestry, and at the same time also the further need to increase the degree of automation of processing the clouds of points 3D from terrestrial laser scanning.

hERG blocking potential of acids and zwitterions characterized by three thresholds for acidity, size and reactivity.

PubMed

Nikolov, Nikolai G; Dybdahl, Marianne; Jónsdóttir, Svava Ó; Wedebye, Eva B

2014-11-01

Ionization is a key factor in hERG K(+) channel blocking, and acids and zwitterions are known to be less probable hERG blockers than bases and neutral compounds. However, a considerable number of acidic compounds block hERG, and the physico-chemical attributes which discriminate acidic blockers from acidic non-blockers have not been fully elucidated. We propose a rule for prediction of hERG blocking by acids and zwitterionic ampholytes based on thresholds for only three descriptors related to acidity, size and reactivity. The training set of 153 acids and zwitterionic ampholytes was predicted with a concordance of 91% by a decision tree based on the rule. Two external validations were performed with sets of 35 and 48 observations, respectively, both showing concordances of 91%. In addition, a global QSAR model of hERG blocking was constructed based on a large diverse training set of 1374 chemicals covering all ionization classes, externally validated showing high predictivity and compared to the decision tree. The decision tree was found to be superior for the acids and zwitterionic ampholytes classes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Erie Canal Technology: Stump Pullers

ERIC Educational Resources Information Center

Greenslade, Thomas B., Jr.

2013-01-01

Many years ago I saw a picture of a huge set of wheels that was used to remove tree stumps during the construction of the Erie Canal (1817-1825) and was intrigued by its use of leverage, mechanical advantage, and torque. Figure 1 is a scale model of the device based on my memory of the (lost) picture and published accounts.

Fault diagnosis of power transformer based on fault-tree analysis (FTA)

NASA Astrophysics Data System (ADS)

Wang, Yongliang; Li, Xiaoqiang; Ma, Jianwei; Li, SuoYu

2017-05-01

Power transformers is an important equipment in power plants and substations, power distribution transmission link is made an important hub of power systems. Its performance directly affects the quality and health of the power system reliability and stability. This paper summarizes the five parts according to the fault type power transformers, then from the time dimension divided into three stages of power transformer fault, use DGA routine analysis and infrared diagnostics criterion set power transformer running state, finally, according to the needs of power transformer fault diagnosis, by the general to the section by stepwise refinement of dendritic tree constructed power transformer fault

A short note on the paper of Liu et al. (2012). A relative Lempel-Ziv complexity: Application to comparing biological sequences. Chemical Physics Letters, volume 530, 19 March 2012, pages 107-112

NASA Astrophysics Data System (ADS)

Arit, Turkan; Keskin, Burak; Firuzan, Esin; Cavas, Cagin Kandemir; Liu, Liwei; Cavas, Levent

2018-04-01

The report entitled "L. Liu, D. Li, F. Bai, A relative Lempel-Ziv complexity: Application to comparing biological sequences, Chem. Phys. Lett. 530 (2012) 107-112" mentions on the powerful construction of phylogenetic trees based on Lempel-Ziv algorithm. On the other hand, the method explained in the paper does not give promising result on the data set on invasive Caulerpa taxifolia in the Mediterranean Sea. The phylogenetic trees are obtained by the proposed method of the aforementioned paper in this short note.

Failure analysis of energy storage spring in automobile composite brake chamber

NASA Astrophysics Data System (ADS)

Luo, Zai; Wei, Qing; Hu, Xiaofeng

2015-02-01

This paper set energy storage spring of parking brake cavity, part of automobile composite brake chamber, as the research object. And constructed the fault tree model of energy storage spring which caused parking brake failure based on the fault tree analysis method. Next, the parking brake failure model of energy storage spring was established by analyzing the working principle of composite brake chamber. Finally, the data of working load and the push rod stroke measured by comprehensive test-bed valve was used to validate the failure model above. The experimental result shows that the failure model can distinguish whether the energy storage spring is faulted.

Your Tree's Trouble May Be You

Treesearch

USDA Forest Service

1974-01-01

People spend much time, effort and money to plant and maintain trees around their homes, businesses, public buildings and parks. People are attracted by the scenic and recreational qualities of forest environments. Yet people who love trees the most may unknowingly cause them injury, directly or indirectly, as a result of: Building and road construction, Flooding ,Soil...

A Single Camera Motion Capture System for Human-Computer Interaction

NASA Astrophysics Data System (ADS)

Okada, Ryuzo; Stenger, Björn

This paper presents a method for markerless human motion capture using a single camera. It uses tree-based filtering to efficiently propagate a probability distribution over poses of a 3D body model. The pose vectors and associated shapes are arranged in a tree, which is constructed by hierarchical pairwise clustering, in order to efficiently evaluate the likelihood in each frame. Anew likelihood function based on silhouette matching is proposed that improves the pose estimation of thinner body parts, i. e. the limbs. The dynamic model takes self-occlusion into account by increasing the variance of occluded body-parts, thus allowing for recovery when the body part reappears. We present two applications of our method that work in real-time on a Cell Broadband Engine™: a computer game and a virtual clothing application.

Polynomial Supertree Methods Revisited

PubMed Central

Brinkmeyer, Malte; Griebel, Thasso; Böcker, Sebastian

2011-01-01

Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come. PMID:22229028

The effect of using genealogy-based haplotypes for genomic prediction

PubMed Central

2013-01-01

Background Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. Methods A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method. Results About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers. Conclusions Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy. PMID:23496971

The effect of using genealogy-based haplotypes for genomic prediction.

PubMed

Edriss, Vahid; Fernando, Rohan L; Su, Guosheng; Lund, Mogens S; Guldbrandtsen, Bernt

2013-03-06

Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method. About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers. Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.

Scaling of xylem and phloem transport capacity and resource usage with tree size

PubMed Central

Hölttä, Teemu; Kurppa, Miika; Nikinmaa, Eero

2013-01-01

Xylem and phloem need to maintain steady transport rates of water and carbohydrates to match the exchange rates of these compounds at the leaves. A major proportion of the carbon and nitrogen assimilated by a tree is allocated to the construction and maintenance of the xylem and phloem long distance transport tissues. This proportion can be expected to increase with increasing tree size due to the growing transport distances between the assimilating tissues, i.e., leaves and fine roots, at the expense of their growth. We formulated whole tree level scaling relations to estimate how xylem and phloem volume, nitrogen content and hydraulic conductance scale with tree size, and how these properties are distributed along a tree height. Xylem and phloem thicknesses and nitrogen contents were measured within varying positions in four tree species from Southern Finland. Phloem volume, nitrogen amount and hydraulic conductance were found to be concentrated toward the branch and stem apices, in contrast to the xylem where these properties were more concentrated toward the tree base. All of the species under study demonstrated very similar trends. Total nitrogen amount allocated to xylem and phloem was predicted to be comparable to the nitrogen amount allocated to the leaves in small and medium size trees, and to increase significantly above the nitrogen content of the leaves in larger trees. Total volume, hydraulic conductance and nitrogen content of the xylem were predicted to increase faster than that of the phloem with increasing tree height in small trees (<~10 m in height). In larger trees, xylem sapwood turnover to heartwood, if present, would maintain phloem conductance at the same level with xylem conductance with further increases in tree height. Further simulations with a previously published xylem-phloem transport model demonstrated that the Münch pressure flow hypothesis could explain phloem transport with increasing tree height even for the tallest trees. PMID:24367373

Phylogenetic tree construction using trinucleotide usage profile (TUP).

PubMed

Chen, Si; Deng, Lih-Yuan; Bowman, Dale; Shiau, Jyh-Jen Horng; Wong, Tit-Yee; Madahian, Behrouz; Lu, Henry Horng-Shing

2016-10-06

It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length). The total number of possible words needed for FFP-k can range from 4 6 =4096 to 4 15 . We propose a simple improvement over the popular FFP method using only a typical word length of 3. A new method, called Trinucleotide Usage Profile (TUP), is proposed based only on the (relative) frequency distribution using non-overlapping windows of length 3. The total number of possible words needed for TUP is 4 3 =64, which is much less than the total count for the recommended optimal "resolution" for FFP. To build a phylogenetic tree, we propose first representing each of the species by a TUP vector and then using an appropriate distance measure between pairs of the TUP vectors for the tree construction. In particular, we propose summarizing a DNA sequence by a matrix of three rows corresponding to three reading frames, recording the frequency distribution of the non-overlapping words of length 3 in each of the reading frame. We also provide a numerical measure for comparing trees constructed with various methods. Compared to the FFP method, our empirical study showed that the proposed TUP method is more capable of building phylogenetic trees with a stronger biological support. We further provide some justifications on this from the information theory viewpoint. Unlike the FFP method, the TUP method takes the advantage that the starting of the first reading frame is (usually) known. Without this information, the FFP method could only rely on the frequency distribution of overlapping words, which is the average (or mixture) of the frequency distributions of three possible reading frames. Consequently, we show (from the entropy viewpoint) that the FFP procedure could dilute important gene information and therefore provides less accurate classification.

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

Treesearch

Eric H. Wharton; Tiberius Cunia

1987-01-01

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

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

PubMed

Cheng, Feon W; Gao, Xiang; Bao, Le; Mitchell, Diane C; Wood, Craig; Sliwinski, Martin J; Smiciklas-Wright, Helen; Still, Christopher D; Rolston, David D K; Jensen, Gordon L

2017-07-01

To examine the risk factors of developing functional decline and make probabilistic predictions by using a tree-based method that allows higher order polynomials and interactions of the risk factors. The conditional inference tree analysis, a data mining approach, was used to construct a risk stratification algorithm for developing functional limitation based on BMI and other potential risk factors for disability in 1,951 older adults without functional limitations at baseline (baseline age 73.1 ± 4.2 y). We also analyzed the data with multivariate stepwise logistic regression and compared the two approaches (e.g., cross-validation). Over a mean of 9.2 ± 1.7 years of follow-up, 221 individuals developed functional limitation. Higher BMI, age, and comorbidity were consistently identified as significant risk factors for functional decline using both methods. Based on these factors, individuals were stratified into four risk groups via the conditional inference tree analysis. Compared to the low-risk group, all other groups had a significantly higher risk of developing functional limitation. The odds ratio comparing two extreme categories was 9.09 (95% confidence interval: 4.68, 17.6). Higher BMI, age, and comorbid disease were consistently identified as significant risk factors for functional decline among older individuals across all approaches and analyses. © 2017 The Obesity Society.

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population.

PubMed

Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

2017-08-15

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.

Shortcomings with Tree-Structured Edge Encodings for Neural Networks

NASA Technical Reports Server (NTRS)

Hornby, Gregory S.

2004-01-01

In evolutionary algorithms a common method for encoding neural networks is to use a tree structured assembly procedure for constructing them. Since node operators have difficulties in specifying edge weights and these operators are execution-order dependent, an alternative is to use edge operators. Here we identify three problems with edge operators: in the initialization phase most randomly created genotypes produce an incorrect number of inputs and outputs; variation operators can easily change the number of input/output (I/O) units; and units have a connectivity bias based on their order of creation. Instead of creating I/O nodes as part of the construction process we propose using parameterized operators to connect to preexisting I/O units. Results from experiments show that these parameterized operators greatly improve the probability of creating and maintaining networks with the correct number of I/O units, remove the connectivity bias with I/O units and produce better controllers for a goal-scoring task.

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…

Tree Owner's Manual for the Northeastern Midwestern United States

Treesearch

Jill Johnson; Gary Johnson; Maureen McDonough; Lisa Burban; Janette Monear

2008-01-01

One common issue facing our urban forests is the fact that trees are dying prematurely. Many are planted improperly, setting them up for failure. Many do not receive regular maintenance. And few are adequately protected during construction projects. To help remedy this issue, the Forest Service has created this Tree Owner's Manual. Just like the owner...

Sanio's laws revisited. Size-dependent changes in the xylem architecture of trees.

PubMed

Mencuccini, Maurizio; Hölttä, Teemu; Petit, Giai; Magnani, Federico

2007-11-01

Early observations led Sanio [Wissen. Bot., 8, (1872) 401] to state that xylem conduit diameters and lengths in a coniferous tree increase from the apex down to a height below which they begin to decrease towards the tree base. Sanio's law of vertical tapering has been repeatedly tested with contradictory results and the debate over the scaling of conduit diameters with distance from the apex has not been settled. The debate has recently acquired new vigour, as an accurate knowledge of the vertical changes in wood anatomy has been shown to be crucial to scaling metabolic properties to plant and ecosystem levels. Contrary to Sanio's hypothesis, a well known model (MST, metabolic scaling theory) assumes that xylem conduits monotonically increase in diameter with distance from the apex following a power law. This has been proposed to explain the three-fourth power scaling between size and metabolism seen across plants. Here, we (i) summarized available data on conduit tapering in trees and (ii) propose a new numerical model that could explain the observed patterns. Data from 101 datasets grouped into 48 independent profiles supported the notions that phylogenetic group (angiosperms versus gymnosperms) and tree size strongly affected the vertical tapering of conduit diameter. For both angiosperms and gymnosperms, within-tree tapering also varied with distance from the apex. The model (based on the concept that optimal conduit tapering occurs when the difference between photosynthetic gains and wall construction costs is maximal) successfully predicted all three major empirical patterns. Our results are consistent with Sanio's law only for large trees and reject the MST assumptions that vertical tapering in conduit diameter is universal and independent of rank number.

How Fast Do Trees Grow? Using Tables and Graphs to Explore Slope

ERIC Educational Resources Information Center

Joram, Elana; Oleson, Vicki

2007-01-01

This article describes a lesson unit in which students constructed tables and graphs to represent the growth of different trees. Students then compared the graphs to develop an understanding of slope.

New star on the stage: amount of ray parenchyma in tree rings shows a link to climate.

PubMed

Olano, José Miguel; Arzac, Alberto; García-Cervigón, Ana I; von Arx, Georg; Rozas, Vicente

2013-04-01

Tree-ring anatomy reflects the year-by-year impact of environmental factors on tree growth. Up to now, research in this field has mainly focused on the hydraulic architecture, with ray parenchyma neglected despite the growing recognition of its relevance for xylem function. Our aim was to address this gap by exploring the potential of the annual patterns of xylem parenchyma as a climate proxy. We constructed ring-width and ray-parenchyma chronologies from 1965 to 2004 for 20 Juniperus thurifera trees growing in a Mediterranean continental climate. Chronologies were related to climate records by means of correlation, multiple regression and partial correlation analyses. Ray parenchyma responded to climatic conditions at critical stages during the xylogenetic process; namely, at the end of the previous year's xylogenesis (October) and at the onset of earlywood (May) and latewood formation (August). Ray parenchyma-based chronologies have potential to complement ring-width chronologies as a tool for climate reconstructions. Furthermore, medium- and low-frequency signals in the variation of ray parenchyma may improve our understanding of how trees respond to environmental fluctuations and to global change. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Alzheimer Classification Using a Minimum Spanning Tree of High-Order Functional Network on fMRI Dataset

PubMed Central

Guo, Hao; Liu, Lei; Chen, Junjie; Xu, Yong; Jie, Xiang

2017-01-01

Functional magnetic resonance imaging (fMRI) is one of the most useful methods to generate functional connectivity networks of the brain. However, conventional network generation methods ignore dynamic changes of functional connectivity between brain regions. Previous studies proposed constructing high-order functional connectivity networks that consider the time-varying characteristics of functional connectivity, and a clustering method was performed to decrease computational cost. However, random selection of the initial clustering centers and the number of clusters negatively affected classification accuracy, and the network lost neurological interpretability. Here we propose a novel method that introduces the minimum spanning tree method to high-order functional connectivity networks. As an unbiased method, the minimum spanning tree simplifies high-order network structure while preserving its core framework. The dynamic characteristics of time series are not lost with this approach, and the neurological interpretation of the network is guaranteed. Simultaneously, we propose a multi-parameter optimization framework that involves extracting discriminative features from the minimum spanning tree high-order functional connectivity networks. Compared with the conventional methods, our resting-state fMRI classification method based on minimum spanning tree high-order functional connectivity networks greatly improved the diagnostic accuracy for Alzheimer's disease. PMID:29249926

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

PubMed Central

2009-01-01

Background The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for essential genes discovery are labor-intensive and time-consuming. Considering these experimental constraints, a computational approach capable of accurately predicting essential genes would be of great value. We therefore present here a machine learning-based computational approach relying on network topological features, cellular localization and biological process information for prediction of essential genes. Results We constructed a decision tree-based meta-classifier and trained it on datasets with individual and grouped attributes-network topological features, cellular compartments and biological processes-to generate various predictors of essential genes. We showed that the predictors with better performances are those generated by datasets with integrated attributes. Using the predictor with all attributes, i.e., network topological features, cellular compartments and biological processes, we obtained the best predictor of essential genes that was then used to classify yeast genes with unknown essentiality status. Finally, we generated decision trees by training the J48 algorithm on datasets with all network topological features, cellular localization and biological process information to discover cellular rules for essentiality. We found that the number of protein physical interactions, the nuclear localization of proteins and the number of regulating transcription factors are the most important factors determining gene essentiality. Conclusion We were able to demonstrate that network topological features, cellular localization and biological process information are reliable predictors of essential genes. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing essentiality. PMID:19758426

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

DOE PAGES

Guo, Hao-Bo; Ma, Yue; Tuskan, Gerald A.; ...

2018-01-01

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here)more » from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.« less

Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins

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

Guo, Hao-Bo; Ma, Yue; Tuskan, Gerald A.

The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here)more » from the protein distribution densities in the LD space defined by ln( L ) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.« less

Association Analysis with One Scan of Databases

DTIC Science & Technology

2006-01-01

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

Construction of the influenza A virus transmission tree in a college-based population: co-transmission and interactions between influenza A viruses.

PubMed

Zhang, Xu-Sheng; De Angelis, Daniela

2016-01-29

Co-infection of different influenza A viruses is known to occur but how viruses interact within co-infection remains unknown. An outbreak in a college campus during the 2009 pandemic involved two subtypes of influenza A: persons infected with pandemic A/H1N1; persons infected with seasonal A/H3N2 viruses; and persons infected with both at the same time (co-infection). This provides data to analyse the possible interaction between influenza A viruses within co-infection. We extend a statistical inference method designed for outbreaks caused by one virus to that caused by two viruses. The method uses knowledge of which subtype each case is infected with (and whether they were co-infected), contact information and symptom onset date of each case in the influenza outbreak. We then apply it to construct the most likely transmission tree during the outbreak in the college campus. Analysis of the constructed transmission tree shows that the simultaneous presence of the two influenza viruses increases the infectivity and the transmissibility of A/H1N1 virus but whether it changes the infectivity of A/H3N2 is unclear. The estimation also shows that co-transmission of both subtypes from co-infection is low and therefore co-infection cannot be sustained on its own. This study suggests that influenza A viruses within co-infected patients can interact in some ways rather than transmit independently, and this can enhance the spread of influenza A virus infection.

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories.

PubMed

Vitalis, Andreas; Caflisch, Amedeo

2012-03-13

The coarse-graining of data from molecular simulations yields conformational space networks that may be used for predicting the system's long time scale behavior, to discover structural pathways connecting free energy basins in the system, or simply to represent accessible phase space regions of interest and their connectivities in a two-dimensional plot. In this contribution, we present a tree-based algorithm to partition conformations of biomolecules into sets of similar microstates, i.e., to coarse-grain trajectory data into mesostates. On account of utilizing an architecture similar to that of established tree-based algorithms, the proposed scheme operates in near-linear time with data set size. We derive expressions needed for the fast evaluation of mesostate properties and distances when employing typical choices for measures of similarity between microstates. Using both a pedagogically useful and a real-word application, the algorithm is shown to be robust with respect to tree height, which in addition to mesostate threshold size is the main adjustable parameter. It is demonstrated that the derived mesostate networks can preserve information regarding the free energy basins and barriers by which the system is characterized.

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

PubMed

Bogdanowicz, Damian; Giaro, Krzysztof

2017-05-01

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

The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation.

PubMed

van Riemsdijk, Isolde; Arntzen, Jan W; Bogaerts, Sergé; Franzen, Michael; Litvinchuk, Spartak N; Olgun, Kurtuluş; Wielstra, Ben

2017-09-01

The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8-13Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity. Copyright © 2017 Elsevier Inc. All rights reserved.

Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

PubMed

Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

2018-01-01

Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

Sectional Pole for Measuring Tree Heights

Treesearch

R. H. Brendemuehl; James B. Baker

1965-01-01

A sectional aluminum pole designed by the Silviculture Laboratory at Marianna, Florida, has proved useful for measuring tree heights. It is more convenient than a sectional bamboo pole 1 or a telescoping fiberglass pole. A tree 5 to 30 feet in height can be measured to the nearest tenth of a foot in 30 seconds. The pole is constructed of low-cost, readily available...

Stress Wave Propagation in Larch Plantation Trees-Numerical Simulation

Treesearch

Fenglu Liu; Fang Jiang; Xiping Wang; Houjiang Zhang; Wenhua Yu

2015-01-01

In this paper, we attempted to simulate stress wave propagation in virtual tree trunks and construct two dimensional (2D) wave-front maps in the longitudinal-radial section of the trunk. A tree trunk was modeled as an orthotropic cylinder in which wood properties along the fiber and in each of the two perpendicular directions were different. We used the COMSOL...

A new tool for post-AGB SED classification

NASA Astrophysics Data System (ADS)

Bendjoya, P.; Suarez, O.; Galluccio, L.; Michel, O.

We present the results of an unsupervised classification method applied on a set of 344 spectral energy distributions (SED) of post-AGB stars extracted from the Torun catalogue of Galactic post-AGB stars. This method aims to find a new unbiased method for post-AGB star classification based on the information contained in the IR region of the SED (fluxes, IR excess, colours). We used the data from IRAS and MSX satellites, and from the 2MASS survey. We applied a classification method based on the construction of the dataset of a minimal spanning tree (MST) with the Prim's algorithm. In order to build this tree, different metrics have been tested on both flux and color indices. Our method is able to classify the set of 344 post-AGB stars in 9 distinct groups according to their SEDs.

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

NASA Astrophysics Data System (ADS)

Iliev, Iliycho; Gocheva-Ilieva, Snezhana; Kulin, Chavdar

2018-01-01

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

Deer stand fatalities in Kentucky: two cases of reverse suspension and blunt force trauma.

PubMed

Shields, Lisa B E; Stewart, Donna

2011-03-01

Hunting many types of wild game is an avidly pursued outdoor activity that attracts all ages and both genders at various times of the year. Deer hunting is a popular sport in many regions of North America. A variety of weapons are used in the hunting, trapping, and killing of game. As a variety of different modalities are used, myriad types of injuries unique to the type of hunting can occur. Most deer hunting-related fatalities identified at the Office of the Chief Medical Examiner in Kentucky are accidental firearm injuries. Less commonly encountered are fatalities resulting from elevation of the hunter in a tree stand, often associated with poor design or construction of the perch. We present 2 tree stand-related deaths. One victim died of positional asphyxia due to reverse suspension from a hunting tree stand. The second victim died of multiple blunt force injuries sustained in a 20-foot fall from a tree stand. We summarize the features of morbidity and mortality related to deer hunting based on investigations by the Office of the Chief Medical Examiner.

Genetic speciation of environmental Legionella isolates in Thailand.

PubMed

Paveenkittiporn, Wantana; Dejsirilert, Surang; Kalambaheti, Thareerat

2012-10-01

Legionella-like organisms were isolated during 2003-2007 from various water resources by culturing on selective media of Wadowsky-Yee-Okuda agar. The 256 isolates were identified as belonging to the Legionella genus based on detection of 108 bp PCR product of the 5S rRNA gene, while the inclusion as Legionella pneumophila were confirmed by PCR detection of a specific mip gene region of 168 bp. The 50 isolates, identified as non-pneumophila, were then subjected to DNA tree analysis, based on mip gene of ~650 bp and rnpB genes product ranged from 304 to 354 bp. Phylogenetic tree was constructed to predict their species in relative to the available database. The isolates of which their speciation, based on those two genes were inconclusive, were then investigated for the almost full-length of 16S rRNA sequences. The isolates were assigned as 16 known Legionella species, and proposed seven novel species based on their unique 16S rRNA sequence. Copyright © 2012 Elsevier B.V. All rights reserved.

A voting-based statistical cylinder detection framework applied to fallen tree mapping in terrestrial laser scanning point clouds

NASA Astrophysics Data System (ADS)

Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

2017-07-01

This paper introduces a statistical framework for detecting cylindrical shapes in dense point clouds. We target the application of mapping fallen trees in datasets obtained through terrestrial laser scanning. This is a challenging task due to the presence of ground vegetation, standing trees, DTM artifacts, as well as the fragmentation of dead trees into non-collinear segments. Our method shares the concept of voting in parameter space with the generalized Hough transform, however two of its significant drawbacks are improved upon. First, the need to generate samples on the shape's surface is eliminated. Instead, pairs of nearby input points lying on the surface cast a vote for the cylinder's parameters based on the intrinsic geometric properties of cylindrical shapes. Second, no discretization of the parameter space is required: the voting is carried out in continuous space by means of constructing a kernel density estimator and obtaining its local maxima, using automatic, data-driven kernel bandwidth selection. Furthermore, we show how the detected cylindrical primitives can be efficiently merged to obtain object-level (entire tree) semantic information using graph-cut segmentation and a tailored dynamic algorithm for eliminating cylinder redundancy. Experiments were performed on 3 plots from the Bavarian Forest National Park, with ground truth obtained through visual inspection of the point clouds. It was found that relative to sample consensus (SAC) cylinder fitting, the proposed voting framework can improve the detection completeness by up to 10 percentage points while maintaining the correctness rate.

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

DTIC Science & Technology

2016-08-01

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

Personal Database Management System I TRIAS

NASA Astrophysics Data System (ADS)

Yamamoto, Yoneo; Kashihara, Akihiro; Kawagishi, Keisuke

The current paper provides TRIAS (TRIple Associative System) which is a database management system for a personal use. In order to implement TRIAS, we have developed an associative database, whose format is (e,a,v) : e for entity, a for attribute, v for value. ML-TREE is used to construct (e,a,v). ML-TREE is a reversion of B+-tree that is multiway valanced tree. The paper focuses mainly on the usage of associative database, demonstrating how to use basic commands, primary functions and applcations.

Bialgebra deformations and algebras of trees

NASA Technical Reports Server (NTRS)

Grossman, Robert; Radford, David

1991-01-01

Let A denote a bialgebra over a field k and let A sub t = A((t)) denote the ring of formal power series with coefficients in A. Assume that A is also isomorphic to a free, associative algebra over k. A simple construction is given which makes A sub t a bialgebra deformation of A. In typical applications, A sub t is neither commutative nor cocommutative. In the terminology of Drinfeld, (1987), A sub t is a quantum group. This construction yields quantum groups associated with families of trees.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

PubMed

Hagopian, Raffi; Davidson, John R; Datta, Ruchira S; Samad, Bushra; Jarvis, Glen R; Sjölander, Kimmen

2010-07-01

We present the jump-start simultaneous alignment and tree construction using hidden Markov models (SATCHMO-JS) web server for simultaneous estimation of protein multiple sequence alignments (MSAs) and phylogenetic trees. The server takes as input a set of sequences in FASTA format, and outputs a phylogenetic tree and MSA; these can be viewed online or downloaded from the website. SATCHMO-JS is an extension of the SATCHMO algorithm, and employs a divide-and-conquer strategy to jump-start SATCHMO at a higher point in the phylogenetic tree, reducing the computational complexity of the progressive all-versus-all HMM-HMM scoring and alignment. Results on a benchmark dataset of 983 structurally aligned pairs from the PREFAB benchmark dataset show that SATCHMO-JS provides a statistically significant improvement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT), ClustalW and the original SATCHMO algorithm. The SATCHMO-JS webserver is available at http://phylogenomics.berkeley.edu/satchmo-js. The datasets used in these experiments are available for download at http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.

Hardwood tree growth on amended mine soils in west virginia.

PubMed

Wilson-Kokes, Lindsay; Delong, Curtis; Thomas, Calene; Emerson, Paul; O'Dell, Keith; Skousen, Jeff

2013-09-01

Each year surface mining in Appalachia disrupts large areas of forested land. The Surface Mining Control and Reclamation Act requires coal mine operators to establish a permanent vegetative cover after mining, and current practice emphasizes soil compaction and planting of competitive forage grasses to stabilize the site and control erosion. These practices hinder recolonization of native hardwood trees on these reclaimed sites. Recently reclamation scientists and regulators have encouraged re-establishment of hardwood forests on surface mined land through careful selection and placement of rooting media and proper selection and planting of herbaceous and tree species. To evaluate the effect of rooting media and soil amendments, a 2.8-ha experimental plot was established, with half of the plot being constructed of weathered brown sandstone and half constructed of unweathered gray sandstone. Bark mulch was applied to an area covering both sandstone types, and the ends of the plot were hydroseeded with a tree-compatible herbaceous seed mix, resulting in eight soil treatments. Twelve hardwood tree species were planted, and soil chemical properties and tree growth were measured annually from 2007 to 2012. After six growing seasons, average tree volume index was higher for trees grown on brown sandstone (5333 cm) compared with gray sandstone (3031 cm). Trees planted in mulch outperformed trees on nonmulched treatments (volume index of 6187 cm vs. 4194 cm). Hydroseeding with a tree-compatible mix produced greater ground cover (35 vs. 15%) and resulted in greater tree volume index than nonhydroseed areas (5809 vs. 3403 cm). Soil chemical properties were improved by mulch and improved tree growth, especially on gray sandstone. The average pH of brown sandstone was 5.0 to 5.4, and gray sandstone averaged pH 6.9 to 7.7. The mulch treatment on gray sandstone resulted in tree growth similar to brown sandstone alone and with mulch. After 6 yr, tree growth on brown sandstone was about double the tree growth on gray sandstone, and mulch was a successful amendment to improve tree growth. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Board-level optical clock signal distribution using Si CMOS-compatible polyimide-based 1- to 48-fanout H-tree

NASA Astrophysics Data System (ADS)

Wu, Linghui; Bihari, Bipin; Gan, Jianhua; Chen, Ray T.; Tang, Suning

1998-08-01

Si-CMOS compatible polymer-based waveguides for optoelectronic interconnects and packaging have been fabricated and characterized. A 1-to-48 fanout optoelectronic interconnection layer (OIL) structure based on Ultradel 9120/9020 for the high-speed massive clock signal distribution for a Cray T-90 supercomputer board has been constructed. The OIL employs multimode polymeric channel waveguides in conjunction with surface-normal waveguide output coupler and 1-to-2 splitter. A total insertion loss of 7.98 dB at 850 nm was measured experimentally.

Constructing Phylogenies.

ERIC Educational Resources Information Center

Bilardello, Nicholas; Valdes, Linda

1998-01-01

Introduces a method for constructing phylogenies using molecular traits and elementary graph theory. Discusses analyzing molecular data and using weighted graphs, minimum-weight spanning trees, and rooted cube phylogenies to display the data. (DDR)

Merchantable height of trees in Oregon—a comparison of current logging practice and volume table specifications.

Treesearch

Don Minore; Donald R. Gedney

1960-01-01

A large proportion of present-day timber cruising is done by measuring or estimating three tree dimensions: diameter at breast height, form class, and merchantable height. Tree volumes are then determined from tables which equate volume to the varying combinations of height, d.b.h., and form class. Assumptions concerning merchantable height were made in constructing...

Probability of Damage to Sidewalks and Curbs by Street Trees in the Tropics

Treesearch

John K. Francis; Bernard R. Parresol; Juana Marin de Patino

1996-01-01

For 75 trees each of 12 species growing along streets in San Juan, Puerto Rico and Merida, Mexico, diameter at breast height and distance to sidewalk or curb was measured and damage (cracking or raising) was evaluated. Logistic analysis was used to construct a model to predict probability of damage to sidewalk or curb. Distance to the pavement, diameter of the tree,...

Wood quality for longleaf pines: a spacing, thinning and pruning study on the Kisatchie National Forest

Treesearch

Chi-Leung So; Thomas L. Eberhardt; Daniel J. Leduc; Leslie H. Groom; Jeffery C. G. Goelz

2010-01-01

Twenty 70-year-old longleaf pine (Pinus palustris Mill.) trees were harvested from a spacing, thinning, and pruning study on the Kisatchie National Forest, LA. Tree property mapping was used to show the property variation within and between three of the trees. The construction of such maps is both time consuming and cost prohibitive using traditional...

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

PubMed Central

Cui, Yun; Jansson, Jesper

2012-01-01

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

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

PubMed

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

2012-09-01

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

Decision Tree Algorithm-Generated Single-Nucleotide Polymorphism Barcodes of rbcL Genes for 38 Brassicaceae Species Tagging.

PubMed

Yang, Cheng-Hong; Wu, Kuo-Chuan; Chuang, Li-Yeh; Chang, Hsueh-Wei

2018-01-01

DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination. To address this issue, we tested a r ibulose diphosphate carboxylase ( rbcL ) S NP b arcoding (RSB) strategy using a decision tree algorithm. After alignment and trimming, 31 SNPs were discovered in the rbcL sequences from 38 Brassicaceae plant species. In the decision tree construction, these SNPs were computed to set up the decision rule to assign the sequences into 2 groups level by level. After algorithm processing, 37 nodes and 31 loci were required for discriminating 38 species. Finally, the sequence tags consisting of 31 rbcL SNP barcodes were identified for discriminating 38 Brassicaceae species based on the decision tree-selected SNP pattern using RSB method. Taken together, this study provides the rational that the SNP aspect of DNA barcode for rbcL gene is a useful and effective sequence for tagging 38 Brassicaceae species.

A comparative assessment of decision trees algorithms for flash flood susceptibility modeling at Haraz watershed, northern Iran.

PubMed

Khosravi, Khabat; Pham, Binh Thai; Chapi, Kamran; Shirzadi, Ataollah; Shahabi, Himan; Revhaug, Inge; Prakash, Indra; Tien Bui, Dieu

2018-06-15

Floods are one of the most damaging natural hazards causing huge loss of property, infrastructure and lives. Prediction of occurrence of flash flood locations is very difficult due to sudden change in climatic condition and manmade factors. However, prior identification of flood susceptible areas can be done with the help of machine learning techniques for proper timely management of flood hazards. In this study, we tested four decision trees based machine learning models namely Logistic Model Trees (LMT), Reduced Error Pruning Trees (REPT), Naïve Bayes Trees (NBT), and Alternating Decision Trees (ADT) for flash flood susceptibility mapping at the Haraz Watershed in the northern part of Iran. For this, a spatial database was constructed with 201 present and past flood locations and eleven flood-influencing factors namely ground slope, altitude, curvature, Stream Power Index (SPI), Topographic Wetness Index (TWI), land use, rainfall, river density, distance from river, lithology, and Normalized Difference Vegetation Index (NDVI). Statistical evaluation measures, the Receiver Operating Characteristic (ROC) curve, and Freidman and Wilcoxon signed-rank tests were used to validate and compare the prediction capability of the models. Results show that the ADT model has the highest prediction capability for flash flood susceptibility assessment, followed by the NBT, the LMT, and the REPT, respectively. These techniques have proven successful in quickly determining flood susceptible areas. Copyright © 2018 Elsevier B.V. All rights reserved.

Recapitulating phylogenies using k-mers: from trees to networks.

PubMed

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

PubMed

Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

2015-10-01

Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

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

PubMed

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

2018-01-01

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

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

PubMed Central

Liu, Yao-Shun; Chen, Jian-Gang; Mei, Ting; Guo, Yu-Xin; Meng, Hao-Tian; Li, Jian-Fei; Wei, Yuan-Yuan; Jin, Xiao-Ye; Zhu, Bo-Feng; Zhang, Li-Ping

2017-01-01

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations. PMID:28903432

Arterial tree tracking from anatomical landmarks in magnetic resonance angiography scans

NASA Astrophysics Data System (ADS)

O'Neil, Alison; Beveridge, Erin; Houston, Graeme; McCormick, Lynne; Poole, Ian

2014-03-01

This paper reports on arterial tree tracking in fourteen Contrast Enhanced MRA volumetric scans, given the positions of a predefined set of vascular landmarks, by using the A* algorithm to find the optimal path for each vessel based on voxel intensity and a learnt vascular probability atlas. The algorithm is intended for use in conjunction with an automatic landmark detection step, to enable fully automatic arterial tree tracking. The scan is filtered to give two further images using the top-hat transform with 4mm and 8mm cubic structuring elements. Vessels are then tracked independently on the scan in which the vessel of interest is best enhanced, as determined from knowledge of typical vessel diameter and surrounding structures. A vascular probability atlas modelling expected vessel location and orientation is constructed by non-rigidly registering the training scans to the test scan using a 3D thin plate spline to match landmark correspondences, and employing kernel density estimation with the ground truth center line points to form a probability density distribution. Threshold estimation by histogram analysis is used to segment background from vessel intensities. The A* algorithm is run using a linear cost function constructed from the threshold and the vascular atlas prior. Tracking results are presented for all major arteries excluding those in the upper limbs. An improvement was observed when tracking was informed by contextual information, with particular benefit for peripheral vessels.

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

PubMed

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

2017-08-01

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

An object-oriented approach to risk and reliability analysis : methodology and aviation safety applications.

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

Dandini, Vincent John; Duran, Felicia Angelica; Wyss, Gregory Dane

2003-09-01

This article describes how features of event tree analysis and Monte Carlo-based discrete event simulation can be combined with concepts from object-oriented analysis to develop a new risk assessment methodology, with some of the best features of each. The resultant object-based event scenario tree (OBEST) methodology enables an analyst to rapidly construct realistic models for scenarios for which an a priori discovery of event ordering is either cumbersome or impossible. Each scenario produced by OBEST is automatically associated with a likelihood estimate because probabilistic branching is integral to the object model definition. The OBEST methodology is then applied to anmore » aviation safety problem that considers mechanisms by which an aircraft might become involved in a runway incursion incident. The resulting OBEST model demonstrates how a close link between human reliability analysis and probabilistic risk assessment methods can provide important insights into aviation safety phenomenology.« less

Rényi indices of financial minimum spanning trees

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao; Song, Fu-Tie; Li, Sai-Ping

2016-02-01

The Rényi index is used here to describe topological structures of minimum spanning trees (MSTs) of financial markets. We categorize the topological structures of MSTs as dragon, star and super-star types. The MST based on Geometric Brownian motion is of dragon type, the MST constructed by One-Factor Model is super-star type, and most MSTs based on real market data belong to the star type. The Rényi index of the MST corresponding to S&P500 is evaluated, and the result shows that the Rényi index varies significantly in different time periods. In particular, it rose during crises and dropped when the S&P500 index rose significantly. A comparison study between the CSI300 index of the Chinese market and the S&P500 index shows that the MST structure of the CSI300 index varies more dramatically than the MST structure of the S&P500.

An approach for automated fault diagnosis based on a fuzzy decision tree and boundary analysis of a reconstructed phase space.

PubMed

Aydin, Ilhan; Karakose, Mehmet; Akin, Erhan

2014-03-01

Although reconstructed phase space is one of the most powerful methods for analyzing a time series, it can fail in fault diagnosis of an induction motor when the appropriate pre-processing is not performed. Therefore, boundary analysis based a new feature extraction method in phase space is proposed for diagnosis of induction motor faults. The proposed approach requires the measurement of one phase current signal to construct the phase space representation. Each phase space is converted into an image, and the boundary of each image is extracted by a boundary detection algorithm. A fuzzy decision tree has been designed to detect broken rotor bars and broken connector faults. The results indicate that the proposed approach has a higher recognition rate than other methods on the same dataset. © 2013 ISA Published by ISA All rights reserved.

Man-made objects cuing in satellite imagery

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

Skurikhin, Alexei N

2009-01-01

We present a multi-scale framework for man-made structures cuing in satellite image regions. The approach is based on a hierarchical image segmentation followed by structural analysis. A hierarchical segmentation produces an image pyramid that contains a stack of irregular image partitions, represented as polygonized pixel patches, of successively reduced levels of detail (LOOs). We are jumping off from the over-segmented image represented by polygons attributed with spectral and texture information. The image is represented as a proximity graph with vertices corresponding to the polygons and edges reflecting polygon relations. This is followed by the iterative graph contraction based on Boruvka'smore » Minimum Spanning Tree (MST) construction algorithm. The graph contractions merge the patches based on their pairwise spectral and texture differences. Concurrently with the construction of the irregular image pyramid, structural analysis is done on the agglomerated patches. Man-made object cuing is based on the analysis of shape properties of the constructed patches and their spatial relations. The presented framework can be used as pre-scanning tool for wide area monitoring to quickly guide the further analysis to regions of interest.« less

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

PubMed

Francis, Andrew; Moulton, Vincent

2018-06-07

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Trap For Capturing Arthropods Crawling up Tree Boles

Treesearch

James L. Hanula; Kirsten C.P. New

1996-01-01

A simple trap is described that captures arthropods as they crawl up tree boles. Constructed from metal funnels, plastic sandwich containers, and specimen cups, the traps can be assembled by one person at a rate of 5 to 6 per hour and installed in 2 to 3 minutes. Specimen collection required 15 to 20 seconds per trap. In 1993, three traps were placed on each tree. In...

Detection of Single Tree Stems in Forested Areas from High Density ALS Point Clouds Using 3d Shape Descriptors

NASA Astrophysics Data System (ADS)

Amiri, N.; Polewski, P.; Yao, W.; Krzystek, P.; Skidmore, A. K.

2017-09-01

Airborne Laser Scanning (ALS) is a widespread method for forest mapping and management purposes. While common ALS techniques provide valuable information about the forest canopy and intermediate layers, the point density near the ground may be poor due to dense overstory conditions. The current study highlights a new method for detecting stems of single trees in 3D point clouds obtained from high density ALS with a density of 300 points/m2. Compared to standard ALS data, due to lower flight height (150-200 m) this elevated point density leads to more laser reflections from tree stems. In this work, we propose a three-tiered method which works on the point, segment and object levels. First, for each point we calculate the likelihood that it belongs to a tree stem, derived from the radiometric and geometric features of its neighboring points. In the next step, we construct short stem segments based on high-probability stem points, and classify the segments by considering the distribution of points around them as well as their spatial orientation, which encodes the prior knowledge that trees are mainly vertically aligned due to gravity. Finally, we apply hierarchical clustering on the positively classified segments to obtain point sets corresponding to single stems, and perform ℓ1-based orthogonal distance regression to robustly fit lines through each stem point set. The ℓ1-based method is less sensitive to outliers compared to the least square approaches. From the fitted lines, the planimetric tree positions can then be derived. Experiments were performed on two plots from the Hochficht forest in Oberösterreich region located in Austria.We marked a total of 196 reference stems in the point clouds of both plots by visual interpretation. The evaluation of the automatically detected stems showed a classification precision of 0.86 and 0.85, respectively for Plot 1 and 2, with recall values of 0.7 and 0.67.

Reconsidering Tree Fruit as Candidate Crops Through the Use of Rapid Cycle Crop Breeding Technologies

NASA Technical Reports Server (NTRS)

Graham, Gary Thomas

2014-01-01

Tree fruit, although desirable from a crew nutrition and menu diversity perspective, have long been dismissed as candidate crops based on their long juvenile phase, large architecture, low short-term harvest index, and dormancy requirements. Recent developments in Rapid Cycle Crop Breeding (RCCB) have overcome these historical limitations, opening the door to a new era in candidate crop research. Researchers at the United States Department of Agriculture (USDA) have developed FT-construct (Flowering Locus T) dwarf plum lines that have a very short juvenile phase, vine-like architecture, and no obligate dormancy period. In a collaborative research effort, NASA and the USDA are evaluating the performance of these FT-lines under controlled environment conditions relevant to spaceflight.

Identifying pollution sources and predicting urban air quality using ensemble learning methods

NASA Astrophysics Data System (ADS)

Singh, Kunwar P.; Gupta, Shikha; Rai, Premanjali

2013-12-01

In this study, principal components analysis (PCA) was performed to identify air pollution sources and tree based ensemble learning models were constructed to predict the urban air quality of Lucknow (India) using the air quality and meteorological databases pertaining to a period of five years. PCA identified vehicular emissions and fuel combustion as major air pollution sources. The air quality indices revealed the air quality unhealthy during the summer and winter. Ensemble models were constructed to discriminate between the seasonal air qualities, factors responsible for discrimination, and to predict the air quality indices. Accordingly, single decision tree (SDT), decision tree forest (DTF), and decision treeboost (DTB) were constructed and their generalization and predictive performance was evaluated in terms of several statistical parameters and compared with conventional machine learning benchmark, support vector machines (SVM). The DT and SVM models discriminated the seasonal air quality rendering misclassification rate (MR) of 8.32% (SDT); 4.12% (DTF); 5.62% (DTB), and 6.18% (SVM), respectively in complete data. The AQI and CAQI regression models yielded a correlation between measured and predicted values and root mean squared error of 0.901, 6.67 and 0.825, 9.45 (SDT); 0.951, 4.85 and 0.922, 6.56 (DTF); 0.959, 4.38 and 0.929, 6.30 (DTB); 0.890, 7.00 and 0.836, 9.16 (SVR) in complete data. The DTF and DTB models outperformed the SVM both in classification and regression which could be attributed to the incorporation of the bagging and boosting algorithms in these models. The proposed ensemble models successfully predicted the urban ambient air quality and can be used as effective tools for its management.

Using spectrotemporal indices to improve the fruit-tree crop classification accuracy

NASA Astrophysics Data System (ADS)

Peña, M. A.; Liao, R.; Brenning, A.

2017-06-01

This study assesses the potential of spectrotemporal indices derived from satellite image time series (SITS) to improve the classification accuracy of fruit-tree crops. Six major fruit-tree crop types in the Aconcagua Valley, Chile, were classified by applying various linear discriminant analysis (LDA) techniques on a Landsat-8 time series of nine images corresponding to the 2014-15 growing season. As features we not only used the complete spectral resolution of the SITS, but also all possible normalized difference indices (NDIs) that can be constructed from any two bands of the time series, a novel approach to derive features from SITS. Due to the high dimensionality of this "enhanced" feature set we used the lasso and ridge penalized variants of LDA (PLDA). Although classification accuracies yielded by the standard LDA applied on the full-band SITS were good (misclassification error rate, MER = 0.13), they were further improved by 23% (MER = 0.10) with ridge PLDA using the enhanced feature set. The most important bands to discriminate the crops of interest were mainly concentrated on the first two image dates of the time series, corresponding to the crops' greenup stage. Despite the high predictor weights provided by the red and near infrared bands, typically used to construct greenness spectral indices, other spectral regions were also found important for the discrimination, such as the shortwave infrared band at 2.11-2.19 μm, sensitive to foliar water changes. These findings support the usefulness of spectrotemporal indices in the context of SITS-based crop type classifications, which until now have been mainly constructed by the arithmetic combination of two bands of the same image date in order to derive greenness temporal profiles like those from the normalized difference vegetation index.

Fault Tree Analysis: An Emerging Methodology for Instructional Science.

ERIC Educational Resources Information Center

Wood, R. Kent; And Others

1979-01-01

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

The use of copulas to practical estimation of multivariate stochastic differential equation mixed effects models

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

Rupšys, P.

A system of stochastic differential equations (SDE) with mixed-effects parameters and multivariate normal copula density function were used to develop tree height model for Scots pine trees in Lithuania. A two-step maximum likelihood parameter estimation method is used and computational guidelines are given. After fitting the conditional probability density functions to outside bark diameter at breast height, and total tree height, a bivariate normal copula distribution model was constructed. Predictions from the mixed-effects parameters SDE tree height model calculated during this research were compared to the regression tree height equations. The results are implemented in the symbolic computational language MAPLE.

a Novel Approach of Indexing and Retrieving Spatial Polygons for Efficient Spatial Region Queries

NASA Astrophysics Data System (ADS)

Zhao, J. H.; Wang, X. Z.; Wang, F. Y.; Shen, Z. H.; Zhou, Y. C.; Wang, Y. L.

2017-10-01

Spatial region queries are more and more widely used in web-based applications. Mechanisms to provide efficient query processing over geospatial data are essential. However, due to the massive geospatial data volume, heavy geometric computation, and high access concurrency, it is difficult to get response in real time. Spatial indexes are usually used in this situation. In this paper, based on k-d tree, we introduce a distributed KD-Tree (DKD-Tree) suitbable for polygon data, and a two-step query algorithm. The spatial index construction is recursive and iterative, and the query is an in memory process. Both the index and query methods can be processed in parallel, and are implemented based on HDFS, Spark and Redis. Experiments on a large volume of Remote Sensing images metadata have been carried out, and the advantages of our method are investigated by comparing with spatial region queries executed on PostgreSQL and PostGIS. Results show that our approach not only greatly improves the efficiency of spatial region query, but also has good scalability, Moreover, the two-step spatial range query algorithm can also save cluster resources to support a large number of concurrent queries. Therefore, this method is very useful when building large geographic information systems.

Chapter 3: Selecting materials for mine soil construction when establishing forests on Appalachian mined lands

Treesearch

Jeff Skousen; Carl Zipper; Jim Burger; Christopher Barton; Patrick. Angel

2017-01-01

The Forestry Reclamation Approach (FRA), a method for reclaiming coal-mined land to forest (Chapter 2, this volume), is based on research, knowledge, and experience of forest soil scientists and reclamation practitioners. Step 1 of the FRA is to create a suitable rooting medium for good tree growth that is no less than 4 feet deep and consists of topsoil, weathered...

Constructing a Graphic Organizer in the Classroom: Introductory Students' Perception of Achievement Using a Decision Map to Solve Aqueous Acid-Base Equilibria Problems

ERIC Educational Resources Information Center

DeMeo, Stephen

2007-01-01

Common examples of graphic organizers include flow diagrams, concept maps, and decision trees. The author has created a novel type of graphic organizer called a decision map. A decision map is a directional heuristic that helps learners solve problems within a generic framework. It incorporates questions that the user must answer and contains…

A Fast Framework for Abrupt Change Detection Based on Binary Search Trees and Kolmogorov Statistic

PubMed Central

Qi, Jin-Peng; Qi, Jie; Zhang, Qing

2016-01-01

Change-Point (CP) detection has attracted considerable attention in the fields of data mining and statistics; it is very meaningful to discuss how to quickly and efficiently detect abrupt change from large-scale bioelectric signals. Currently, most of the existing methods, like Kolmogorov-Smirnov (KS) statistic and so forth, are time-consuming, especially for large-scale datasets. In this paper, we propose a fast framework for abrupt change detection based on binary search trees (BSTs) and a modified KS statistic, named BSTKS (binary search trees and Kolmogorov statistic). In this method, first, two binary search trees, termed as BSTcA and BSTcD, are constructed by multilevel Haar Wavelet Transform (HWT); second, three search criteria are introduced in terms of the statistic and variance fluctuations in the diagnosed time series; last, an optimal search path is detected from the root to leaf nodes of two BSTs. The studies on both the synthetic time series samples and the real electroencephalograph (EEG) recordings indicate that the proposed BSTKS can detect abrupt change more quickly and efficiently than KS, t-statistic (t), and Singular-Spectrum Analyses (SSA) methods, with the shortest computation time, the highest hit rate, the smallest error, and the highest accuracy out of four methods. This study suggests that the proposed BSTKS is very helpful for useful information inspection on all kinds of bioelectric time series signals. PMID:27413364

A Fast Framework for Abrupt Change Detection Based on Binary Search Trees and Kolmogorov Statistic.

PubMed

Qi, Jin-Peng; Qi, Jie; Zhang, Qing

2016-01-01

Change-Point (CP) detection has attracted considerable attention in the fields of data mining and statistics; it is very meaningful to discuss how to quickly and efficiently detect abrupt change from large-scale bioelectric signals. Currently, most of the existing methods, like Kolmogorov-Smirnov (KS) statistic and so forth, are time-consuming, especially for large-scale datasets. In this paper, we propose a fast framework for abrupt change detection based on binary search trees (BSTs) and a modified KS statistic, named BSTKS (binary search trees and Kolmogorov statistic). In this method, first, two binary search trees, termed as BSTcA and BSTcD, are constructed by multilevel Haar Wavelet Transform (HWT); second, three search criteria are introduced in terms of the statistic and variance fluctuations in the diagnosed time series; last, an optimal search path is detected from the root to leaf nodes of two BSTs. The studies on both the synthetic time series samples and the real electroencephalograph (EEG) recordings indicate that the proposed BSTKS can detect abrupt change more quickly and efficiently than KS, t-statistic (t), and Singular-Spectrum Analyses (SSA) methods, with the shortest computation time, the highest hit rate, the smallest error, and the highest accuracy out of four methods. This study suggests that the proposed BSTKS is very helpful for useful information inspection on all kinds of bioelectric time series signals.

A Method of Data Aggregation for Wearable Sensor Systems

PubMed Central

Shen, Bo; Fu, Jun-Song

2016-01-01

Data aggregation has been considered as an effective way to decrease the data to be transferred in sensor networks. Particularly for wearable sensor systems, smaller battery has less energy, which makes energy conservation in data transmission more important. Nevertheless, wearable sensor systems usually have features like frequently dynamic changes of topologies and data over a large range, of which current aggregating methods can’t adapt to the demand. In this paper, we study the system composed of many wearable devices with sensors, such as the network of a tactical unit, and introduce an energy consumption-balanced method of data aggregation, named LDA-RT. In the proposed method, we develop a query algorithm based on the idea of ‘happened-before’ to construct a dynamic and energy-balancing routing tree. We also present a distributed data aggregating and sorting algorithm to execute top-k query and decrease the data that must be transferred among wearable devices. Combining these algorithms, LDA-RT tries to balance the energy consumptions for prolonging the lifetime of wearable sensor systems. Results of evaluation indicate that LDA-RT performs well in constructing routing trees and energy balances. It also outperforms the filter-based top-k monitoring approach in energy consumption, load balance, and the network’s lifetime, especially for highly dynamic data sources. PMID:27347953

Complexity of possibly gapped histogram and analysis of histogram.

PubMed

Fushing, Hsieh; Roy, Tania

2018-02-01

We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information Theory from the perspective of data compression via uniformity. By defining a Hamiltonian (or energy) as a sum of total coding lengths of boundaries and total decoding errors within bins, this issue of computing the minimum energy macroscopic states is surprisingly resolved by applying the hierarchical clustering algorithm. Thus, a possibly gapped histogram corresponds to a macro-state. And then the first phase of ANOHT is developed for simultaneous comparison of multiple treatments, while the second phase of ANOHT is developed based on classical empirical process theory for a tree-geometry that can check the authenticity of branches of the treatment tree. The well-known Iris data are used to illustrate our technical developments. Also, a large baseball pitching dataset and a heavily right-censored divorce data are analysed to showcase the existential gaps and utilities of ANOHT.

Complexity of possibly gapped histogram and analysis of histogram

PubMed Central

Roy, Tania

2018-01-01

We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information Theory from the perspective of data compression via uniformity. By defining a Hamiltonian (or energy) as a sum of total coding lengths of boundaries and total decoding errors within bins, this issue of computing the minimum energy macroscopic states is surprisingly resolved by applying the hierarchical clustering algorithm. Thus, a possibly gapped histogram corresponds to a macro-state. And then the first phase of ANOHT is developed for simultaneous comparison of multiple treatments, while the second phase of ANOHT is developed based on classical empirical process theory for a tree-geometry that can check the authenticity of branches of the treatment tree. The well-known Iris data are used to illustrate our technical developments. Also, a large baseball pitching dataset and a heavily right-censored divorce data are analysed to showcase the existential gaps and utilities of ANOHT. PMID:29515829

Complexity of possibly gapped histogram and analysis of histogram

NASA Astrophysics Data System (ADS)

Fushing, Hsieh; Roy, Tania

2018-02-01

We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information Theory from the perspective of data compression via uniformity. By defining a Hamiltonian (or energy) as a sum of total coding lengths of boundaries and total decoding errors within bins, this issue of computing the minimum energy macroscopic states is surprisingly resolved by applying the hierarchical clustering algorithm. Thus, a possibly gapped histogram corresponds to a macro-state. And then the first phase of ANOHT is developed for simultaneous comparison of multiple treatments, while the second phase of ANOHT is developed based on classical empirical process theory for a tree-geometry that can check the authenticity of branches of the treatment tree. The well-known Iris data are used to illustrate our technical developments. Also, a large baseball pitching dataset and a heavily right-censored divorce data are analysed to showcase the existential gaps and utilities of ANOHT.

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

NASA Astrophysics Data System (ADS)

Krechowicz, Maria

2017-10-01

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

Sequential decision tree using the analytic hierarchy process for decision support in rectal cancer.

PubMed

Suner, Aslı; Çelikoğlu, Can Cengiz; Dicle, Oğuz; Sökmen, Selman

2012-09-01

The aim of the study is to determine the most appropriate method for construction of a sequential decision tree in the management of rectal cancer, using various patient-specific criteria and treatments such as surgery, chemotherapy, and radiotherapy. An analytic hierarchy process (AHP) was used to determine the priorities of variables. Relevant criteria used in two decision steps and their relative priorities were established by a panel of five general surgeons. Data were collected via a web-based application and analyzed using the "Expert Choice" software specifically developed for the AHP. Consistency ratios in the AHP method were calculated for each set of judgments, and the priorities of sub-criteria were determined. A sequential decision tree was constructed for the best treatment decision process, using priorities determined by the AHP method. Consistency ratios in the AHP method were calculated for each decision step, and the judgments were considered consistent. The tumor-related criterion "presence of perforation" (0.331) and the patient-surgeon-related criterion "surgeon's experience" (0.630) had the highest priority in the first decision step. In the second decision step, the tumor-related criterion "the stage of the disease" (0.230) and the patient-surgeon-related criterion "surgeon's experience" (0.281) were the paramount criteria. The results showed some variation in the ranking of criteria between the decision steps. In the second decision step, for instance, the tumor-related criterion "presence of perforation" was just the fifth. The consistency of decision support systems largely depends on the quality of the underlying decision tree. When several choices and variables have to be considered in a decision, it is very important to determine priorities. The AHP method seems to be effective for this purpose. The decision algorithm developed by this method is more realistic and will improve the quality of the decision tree. Copyright © 2012 Elsevier B.V. All rights reserved.

Soft context clustering for F0 modeling in HMM-based speech synthesis

NASA Astrophysics Data System (ADS)

Khorram, Soheil; Sameti, Hossein; King, Simon

2015-12-01

This paper proposes the use of a new binary decision tree, which we call a soft decision tree, to improve generalization performance compared to the conventional `hard' decision tree method that is used to cluster context-dependent model parameters in statistical parametric speech synthesis. We apply the method to improve the modeling of fundamental frequency, which is an important factor in synthesizing natural-sounding high-quality speech. Conventionally, hard decision tree-clustered hidden Markov models (HMMs) are used, in which each model parameter is assigned to a single leaf node. However, this `divide-and-conquer' approach leads to data sparsity, with the consequence that it suffers from poor generalization, meaning that it is unable to accurately predict parameters for models of unseen contexts: the hard decision tree is a weak function approximator. To alleviate this, we propose the soft decision tree, which is a binary decision tree with soft decisions at the internal nodes. In this soft clustering method, internal nodes select both their children with certain membership degrees; therefore, each node can be viewed as a fuzzy set with a context-dependent membership function. The soft decision tree improves model generalization and provides a superior function approximator because it is able to assign each context to several overlapped leaves. In order to use such a soft decision tree to predict the parameters of the HMM output probability distribution, we derive the smoothest (maximum entropy) distribution which captures all partial first-order moments and a global second-order moment of the training samples. Employing such a soft decision tree architecture with maximum entropy distributions, a novel speech synthesis system is trained using maximum likelihood (ML) parameter re-estimation and synthesis is achieved via maximum output probability parameter generation. In addition, a soft decision tree construction algorithm optimizing a log-likelihood measure is developed. Both subjective and objective evaluations were conducted and indicate a considerable improvement over the conventional method.

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

PubMed

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

2012-05-01

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

The Influence of Vegetation Function towards the Langsep Street Thermal Comfort

NASA Astrophysics Data System (ADS)

Alfian, R.; Setyabudi, I.; Uran, R. S.

2017-10-01

Streetscape is an important element for character building of the environment, spatial, and visual in order to provide an urban identity, especially in Malang City protocol streets. Langsep Street is one of the protocol streets in Malang City. Langsep Street famous with central education and offices area. This study aims (1) to identify vegetation of streetscape; (2) to analyze the thermal comfort of the streetscape, and (3) to evaluate the comfort level of Langsep Street. The method used was the THI approach. THI value that obtained was analyzed using the standard of Laurie (1990). Based on observations, the THI value of Langsep Street was 27.60. This was influenced by the trees canopy density and spacing of the trees on the streetscape. It can be concluded that streetscape required (1) shaded plants that have root systems that do not damage the construction of roads, (2) the branching plants are not easily broken and easy to maintain, and (3) the combination of trees, shrubs and ground cover.

[Molecular identification of astragali radix and its adulterants by ITS sequences].

PubMed

Cui, Zhan-Hu; Li, Yue; Yuan, Qing-Jun; Zhou, Li-She; Li, Min-Hui

2012-12-01

To explore a new method for identification Astragali Radix from its adulterants by using ITS sequence. Thirteen samples of the different Astragali Radix materials and 6 samples of the adulterants of the roots of Hedysarum polybotrys, Medicago sativa and Althaea rosea were collected. ITS sequence was amplified by PCR and sequenced unidirectionally. The interspecific K-2-P distances of Astragali Radix and its adulterants were calculated, and NJ tree and UPGMA tree were constructed by MEGA 4. ITS sequences were obtained from 19 samples respectively, there were Astragali Radix 646-650 bp, H. polybotrys 664 bp, Medicago sativa 659 bp, Althaea rosea 728 bp, which were registered in the GenBank. Phylogeny trees reconstruction using NJ and UPGMA analysis based on ITS nucleotide sequences can effectively distinguish Astragali Radix from adulterants. ITS sequence can be used to identify Astragali Radix from its adulterants successfully and is an efficient molecular marker for authentication of Astragali Radix and its adulterants.

Predicting diabetes mellitus using SMOTE and ensemble machine learning approach: The Henry Ford ExercIse Testing (FIT) project.

PubMed

Alghamdi, Manal; Al-Mallah, Mouaz; Keteyian, Steven; Brawner, Clinton; Ehrman, Jonathan; Sakr, Sherif

2017-01-01

Machine learning is becoming a popular and important approach in the field of medical research. In this study, we investigate the relative performance of various machine learning methods such as Decision Tree, Naïve Bayes, Logistic Regression, Logistic Model Tree and Random Forests for predicting incident diabetes using medical records of cardiorespiratory fitness. In addition, we apply different techniques to uncover potential predictors of diabetes. This FIT project study used data of 32,555 patients who are free of any known coronary artery disease or heart failure who underwent clinician-referred exercise treadmill stress testing at Henry Ford Health Systems between 1991 and 2009 and had a complete 5-year follow-up. At the completion of the fifth year, 5,099 of those patients have developed diabetes. The dataset contained 62 attributes classified into four categories: demographic characteristics, disease history, medication use history, and stress test vital signs. We developed an Ensembling-based predictive model using 13 attributes that were selected based on their clinical importance, Multiple Linear Regression, and Information Gain Ranking methods. The negative effect of the imbalance class of the constructed model was handled by Synthetic Minority Oversampling Technique (SMOTE). The overall performance of the predictive model classifier was improved by the Ensemble machine learning approach using the Vote method with three Decision Trees (Naïve Bayes Tree, Random Forest, and Logistic Model Tree) and achieved high accuracy of prediction (AUC = 0.92). The study shows the potential of ensembling and SMOTE approaches for predicting incident diabetes using cardiorespiratory fitness data.

Automatic Generation of English-Japanese Translation Pattern Utilizing Genetic Programming Technique

NASA Astrophysics Data System (ADS)

Matsumura, Koki; Tamekuni, Yuji; Kimura, Shuhei

There are a lot of constructional differences in an English-Japanese phrase template, and that often makes the act of translation difficult. Moreover, there exist various and tremendous phrase templates and sentence to be refered to. It is not easy to prepare the corpus that covers the all. Therefore, it is very significant to generate the translation pattern of the sentence pattern automatically from a viewpoint of the translation success rate and the capacity of the pattern dictionary. Then, for the purpose of realizing the automatic generation of the translation pattern, this paper proposed the new method for the generation of the translation pattern by using the genetic programming technique (GP). The technique tries to generate the translation pattern of various sentences which are not registered in the phrase template dictionary automatically by giving the genetic operation to the parsing tree of a basic pattern. The tree consists of the pair of the English-Japanese sentence generated as the first stage population. The analysis tree data base with 50,100,150,200 pairs was prepared as the first stage population. And this system was applied and executed for an English input of 1,555 sentences. As a result, the analysis tree increases from 200 to 517, and the accuracy rate of the translation pattern has improved from 42.57% to 70.10%. And, 86.71% of the generated translations was successfully done, whose meanings are enough acceptable and understandable. It seemed that this proposal technique became a clue to raise the translation success rate, and to find the possibility of the reduction of the analysis tree data base.

Sampling-based real-time motion planning under state uncertainty for autonomous micro-aerial vehicles in GPS-denied environments.

PubMed

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-11-18

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints.

Sampling-Based Real-Time Motion Planning under State Uncertainty for Autonomous Micro-Aerial Vehicles in GPS-Denied Environments

PubMed Central

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-01-01

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints. PMID:25412217

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Fault Network Reconstruction using Agglomerative Clustering: Applications to South Californian Seismicity

NASA Astrophysics Data System (ADS)

Kamer, Yavor; Ouillon, Guy; Sornette, Didier; Wössner, Jochen

2014-05-01

We present applications of a new clustering method for fault network reconstruction based on the spatial distribution of seismicity. Unlike common approaches that start from the simplest large scale and gradually increase the complexity trying to explain the small scales, our method uses a bottom-up approach, by an initial sampling of the small scales and then reducing the complexity. The new approach also exploits the location uncertainty associated with each event in order to obtain a more accurate representation of the spatial probability distribution of the seismicity. For a given dataset, we first construct an agglomerative hierarchical cluster (AHC) tree based on Ward's minimum variance linkage. Such a tree starts out with one cluster and progressively branches out into an increasing number of clusters. To atomize the structure into its constitutive protoclusters, we initialize a Gaussian Mixture Modeling (GMM) at a given level of the hierarchical clustering tree. We then let the GMM converge using an Expectation Maximization (EM) algorithm. The kernels that become ill defined (less than 4 points) at the end of the EM are discarded. By incrementing the number of initialization clusters (by atomizing at increasingly populated levels of the AHC tree) and repeating the procedure above, we are able to determine the maximum number of Gaussian kernels the structure can hold. The kernels in this configuration constitute our protoclusters. In this setting, merging of any pair will lessen the likelihood (calculated over the pdf of the kernels) but in turn will reduce the model's complexity. The information loss/gain of any possible merging can thus be quantified based on the Minimum Description Length (MDL) principle. Similar to an inter-distance matrix, where the matrix element di,j gives the distance between points i and j, we can construct a MDL gain/loss matrix where mi,j gives the information gain/loss resulting from the merging of kernels i and j. Based on this matrix, merging events resulting in MDL gain are performed in descending order until no gainful merging is possible anymore. We envision that the results of this study could lead to a better understanding of the complex interactions within the Californian fault system and hopefully use the acquired insights for earthquake forecasting.

Environmental Impact Research Program. Restoration of Problem Soil Materials at Corps of Engineers Construction Sites.

DTIC Science & Technology

1985-05-01

the total weight of a given population of organisms. Browse: Twigs or shoots, with or without attached leaves, of shrubs , trees, or woody vines ...volunteer woody plants, or the fsuccessful establishment, later on, of planted shrubs , trees, and ground covers. 184. Some problem soils absolutely...properly prepared seedbed. Woody plants, such as shrubs and trees, are established by seedling transplants. However, some woody species can be seeded

Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches.

PubMed

Makita, Yuko; Kawashima, Mika; Lau, Nyok Sean; Othman, Ahmad Sofiman; Matsui, Minami

2018-01-19

Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .

Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea).

PubMed

Tarcz, Sebastian; Potekhin, Alexey; Rautian, Maria; Przyboś, Ewa

2012-05-01

This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of several sibling species within taxonomic species. Our analysis revealed the existence of 10 haplotypes for the rDNA fragment and 15 haplotypes for the COI fragment in the studied material. The mean distance for all of the studied P. multimicronucleatum sequence pairs was p=0.025/0.082 (rDNA/COI). Despite the greater variation of the COI fragment, the COI-derived tree topology is similar to the tree topology constructed on the basis of the rDNA fragment. P. multimicronucleatum strains are divided into three main clades. The tree based on COI fragment analysis presents a greater resolution of the studied P. multimicronucleatum strains. Our results indicate that the strains of P. multimicronucleatum that appear in different clades on the trees could belong to different syngens. Copyright © 2012 Elsevier Inc. All rights reserved.

Snakes and Eels and Dogs! Oh, My! Evaluating High School Students' Tree-Thinking Skills: An Entry Point to Understanding Evolution

NASA Astrophysics Data System (ADS)

Catley, Kefyn M.; Phillips, Brenda C.; Novick, Laura R.

2013-12-01

The biological community is currently undertaking one its greatest scientific endeavours, that of constructing the Tree of Life, a phylogeny intended to be an evidenced-based, predictive road map of evolutionary relationships among Earth's biota. Unfortunately, we know very little about how such diagrams are understood, interpreted, or used as inferential tools by students—collectively referred to as tree thinking. The present study provides the first in-depth look at US high school students' competence at tree thinking and reports how they engage cognitively with tree representations as a precursor to developing curricula that will provide an entry point into macroevolution. Sixty tenth graders completed a 12-question instrument that assessed five basic tree-thinking skills. We present data that show patterns of misunderstandings are largely congruent between tenth graders and undergraduates and identify competences that are pivotal to address during instruction. Two general principles that emerge from this study are: (a) Students need to be taught that cladograms are an authoritative source of evidence that should be weighted more than other superficial or ecological similarities; (b) students need to understand the vital importance and critical difference between most recent common ancestry and common ancestry. Further, we show how the objectives of this study are closely aligned with US and International Standards and argue that scientifically-literate citizens need at least a basic understanding of the science behind the Tree of Life to understand and engage in twenty-first century societal issues such as human health, agriculture, and biotechnology.

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

PubMed

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

2012-02-03

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

A systematic risk management approach employed on the CloudSat project

NASA Technical Reports Server (NTRS)

Basilio, R. R.; Plourde, K. S.; Lam, T.

2000-01-01

The CloudSat Project has developed a simplified approach for fault tree analysis and probabilistic risk assessment. A system-level fault tree has been constructed to identify credible fault scenarios and failure modes leading up to a potential failure to meet the nominal mission success criteria.

Soy protein adhesives

Treesearch

Charles R. Frihart

2010-01-01

In the quest to manufacture and use building materials that are more environmentally friendly, soy adhesives can be an important component. Trees fix and store carbon dioxide in the atmosphere. After the trees are harvested, machinery converts the wood into strands, which are then bonded together with adhesives to form strandboard, used in constructing long-lasting...

Growing trees in child brains: graph theoretical analysis of electroencephalography-derived minimum spanning tree in 5- and 7-year-old children reflects brain maturation.

PubMed

Boersma, Maria; Smit, Dirk J A; Boomsma, Dorret I; De Geus, Eco J C; Delemarre-van de Waal, Henriette A; Stam, Cornelis J

2013-01-01

The child brain is a small-world network, which is hypothesized to change toward more ordered configurations with development. In graph theoretical studies, comparing network topologies under different conditions remains a critical point. Constructing a minimum spanning tree (MST) might present a solution, since it does not require setting a threshold and uses a fixed number of nodes and edges. In this study, the MST method is introduced to examine developmental changes in functional brain network topology in young children. Resting-state electroencephalography was recorded from 227 children twice at 5 and 7 years of age. Synchronization likelihood (SL) weighted matrices were calculated in three different frequency bands from which MSTs were constructed, which represent constructs of the most important routes for information flow in a network. From these trees, several parameters were calculated to characterize developmental change in network organization. The MST diameter and eccentricity significantly increased, while the leaf number and hierarchy significantly decreased in the alpha band with development. Boys showed significant higher leaf number, betweenness, degree and hierarchy and significant lower SL, diameter, and eccentricity than girls in the theta band. The developmental changes indicate a shift toward more decentralized line-like trees, which supports the previously hypothesized increase toward regularity of brain networks with development. Additionally, girls showed more line-like decentralized configurations, which is consistent with the view that girls are ahead of boys in brain development. MST provides an elegant method sensitive to capture subtle developmental changes in network organization without the bias of network comparison.

On the genre-fication of music: a percolation approach

NASA Astrophysics Data System (ADS)

Lambiotte, R.; Ausloos, M.

2006-03-01

We analyze web-downloaded data on people sharing their music library. By attributing to each music group usual music genres (Rock, Pop ...), and analysing correlations between music groups of different genres with percolation-idea based methods, we probe the reality of these subdivisions and construct a music genre cartography, with a tree representation. We also discuss an alternative objective way to classify music, that is based on the complex structure of the groups audience. Finally, a link is drawn with the theory of hidden variables in complex networks.

A Unified Methodology for Aerospace Systems Integration Based on Entropy and the Second Law of Thermodynamics: Aerodynamics Assessment

DTIC Science & Technology

2004-08-01

Based on Exergy Methods”, Journal of Aircraft Vol.40, No.1, January-February 2003. [2] Bejan, A., “Constructal Theory: Tree-Shaped Flows and Energy... Journal of Aircraft Vol. 36, No. 2, March- April 1999. [15] Bourdin, P., Numerical Prediction of Wing-Tip Effects On Lift-Induced Drag. International Council of the Aeronautical Sciences, 2002. ...methods were used to calculate the induced drag. The objective of this project is to relate work-potential losses ( exergy destruction) to the

Vegetation succession and impacts of biointrusion on covers used to limit acid mine drainage.

PubMed

Smirnova, Evgeniya; Bussière, Bruno; Tremblay, Francine; Bergeron, Yves

2011-01-01

A cover with capillary barrier effects (CCBE) was constructed in 1998 on the abandoned Lorraine mine tailings impoundment to limit the generation of acid mine drainage. The Ministry of Natural Resources and Fauna of Quebec (MRNF) is responsible for the site and for all restoration works on it, including CCBE construction. The CCBE is made up of three layers: a 0.3-m layer of sand used as a support and capillary break layer; a moisture-retaining layer with a thickness of 0.5 m (this layer is constructed of a nonplastic silt); and a 0.3-m sand and gravel layer on top. The main objective of the CCBE is to maintain one (or more) of the layers at a high degree of water saturation to impede oxygen migration and acid generation. Vegetation succession on the Lorraine CCBE results in an improvement in soil conditions, leading to the installation of deep-rooted species, which could represent a risk to CCBE long-term performance. Hence, the characterization of vegetation succession is an important aspect of the monitoring strategy for the Lorraine CCBE. Species occurrence was documented, and depth of tree roots was measured by excavation on a regular basis. Eight functional groups of plants were identified; herbaceous plants were the most abundant ecological plant groups. Tree ring counts confirmed that tree colonization started the year of CCBE construction (1999). Of the 11 tree species identified, the most abundant were poplar (Populus spp.), paper birch (Betula payrifera Marsh.), black spruce (Picea mariana Mill.), and willow (Salix spp.). Significant differences in occurrence related to environmental conditions were observed for most functional groups. Root excavation showed that tree roots exceeded the depth of the protective layer and started to reach the moisture-retaining layer; in 2008, root average depth was 0.4 m and the maximal root depth was 1.7 m.

Finding Minimum-Power Broadcast Trees for Wireless Networks

NASA Technical Reports Server (NTRS)

Arabshahi, Payman; Gray, Andrew; Das, Arindam; El-Sharkawi, Mohamed; Marks, Robert, II

2004-01-01

Some algorithms have been devised for use in a method of constructing tree graphs that represent connections among the nodes of a wireless communication network. These algorithms provide for determining the viability of any given candidate connection tree and for generating an initial set of viable trees that can be used in any of a variety of search algorithms (e.g., a genetic algorithm) to find a tree that enables the network to broadcast from a source node to all other nodes while consuming the minimum amount of total power. The method yields solutions better than those of a prior algorithm known as the broadcast incremental power algorithm, albeit at a slightly greater computational cost.

Effects of male fecundity, interindividual distance and anisotropic pollen dispersal on mating success in a Scots pine (Pinus sylvestris) seed orchard

PubMed Central

Torimaru, T; Wennström, U; Lindgren, D; Wang, X-R

2012-01-01

Quantifying the effect of pollen dispersal and flowering traits on mating success is essential for understanding evolutionary responses to changing environments and establishing strategies for forest tree breeding. This study examined, quantitatively, the effects of male fecundity, interindividual distance and anisotropic pollen dispersal on the mating success of Scots pine (Pinus sylvestris), utilizing a well-mapped Scots pine seed orchard. Paternity analysis of 1021 seeds sampled from 87 trees representing 28 clones showed that 53% of the seeds had at least one potential pollen parent within the orchard. Pronounced variation in paternal contribution was observed among clones. Variations in pollen production explained up to 78% of the variation in mating success, which was 11.2 times greater for clones producing the largest amount of pollen than for clones producing the least pollen. Mating success also varied with intertree distance and direction, which explained up to 28% of the variance. Fertilization between neighboring trees 2.3 m apart was 2.4 times more frequent than between trees 4.6 m apart, and up to 12.4 times higher for trees downwind of the presumed prevailing wind direction than for upwind trees. The effective number of pollen donors recorded in the seed orchard (12.2) was smaller than the theoretical expectation (19.7). Based on the empirical observations, a mating model that best describes the gene dispersal pattern in clonal seed orchards was constructed. PMID:21897440

Representations of the language recognition problem for a theorem prover

NASA Technical Reports Server (NTRS)

Minker, J.; Vanderbrug, G. J.

1972-01-01

Two representations of the language recognition problem for a theorem prover in first order logic are presented and contrasted. One of the representations is based on the familiar method of generating sentential forms of the language, and the other is based on the Cocke parsing algorithm. An augmented theorem prover is described which permits recognition of recursive languages. The state-transformation method developed by Cordell Green to construct problem solutions in resolution-based systems can be used to obtain the parse tree. In particular, the end-order traversal of the parse tree is derived in one of the representations. An inference system, termed the cycle inference system, is defined which makes it possible for the theorem prover to model the method on which the representation is based. The general applicability of the cycle inference system to state space problems is discussed. Given an unsatisfiable set S, where each clause has at most one positive literal, it is shown that there exists an input proof. The clauses for the two representations satisfy these conditions, as do many state space problems.

Formal modeling of a system of chemical reactions under uncertainty.

PubMed

Ghosh, Krishnendu; Schlipf, John

2014-10-01

We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

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

DTIC Science & Technology

2017-08-01

SUPPLEMENTARY NOTES 14. ABSTRACT The goal of this project is to sequence the exomes of single tumor cells from tumors in order to construct evolutionary trees...dissociation, tumor cell isolation, whole genome amplification, and exome sequencing. We have begun to sequence the exomes of single cells and to...of populations, the evolution of tumor cells within a tumor can be diagrammed on a phylogenetic tree. The more diverse a tumor’s phylogenetic tree

Multiplying Forest Garden Systems with biochar based organic fertilization for high carbon accumulation, improved water storage, nutrient cycling, and increased food diversity and farm productivity

NASA Astrophysics Data System (ADS)

Schmidt, Hans-Peter; Pandit, Bishnu Hari; Lucht, Wolfgang; Gerten, Dieter; Kammann, Claudia

2017-04-01

On abandoned, erosion prone terraces in the middle hills of Nepal, 86 participating farmer families planted >25,000 mixed trees in 2015/16. Since it was convincingly demonstrated by more than 20 field trials in this region that this was the most plant-growth promoting method, all trees were planted with farmer-made organic biochar-based fertilizer. Planting pits were mulched with rice straw and were pipe irrigated from newly established water retention ponds during the 7 months of the dry season. A peer control system of farmer triads ensured an efficient maintenance of the plantations. Tree survival rate was above 80% after one year compared to below 50% on average for countrywide forestation projects over the last 30 years. In between the young Cinnamon, Moringa, Mulberry, Lemon, Michelia, Paulownia, nut and other trees, other secondary crops were cultivated such as ginger, turmeric, black beans, onions, lentils, all with organic biochar-based fertilizer and mulching. The objective of this forest garden project was to establish robust social-agronomic systems that can be multiplied from village to village for increasing soil fertility, protecting abandoned terraces from erosion, replenishing natural water resources, generating a stable income with climate-smart agriculture, as well as capturing and sequestering atmospheric carbon. The initial financing of the set-up of the forest garden systems (tree nursery, plantation, preparation of organic biochar based fertilizer, mulching materials, building of irrigation pits and pipe irrigation system, and general maintenance) was covered by carbon credits paid in advance by the international community in the form of a monthly carbon compensation subscription. All planted trees are GIS inventoried and the yearly biomass carbon uptake will be calculated as an average value of the first ten years of tree growth. The 25,000 mixed trees accumulated the equivalent of 350 t CO2 per year (10 years total C-accumulation divided by 10 years). Besides covering the set-up costs, farmers received and continue to receive carbon payments for each survived tree during the first three years. Based on a voluntary carbon credit price of 35 USD per t CO2, the annual income of the farmers increase by 6 to 13% depending on their poverty level. After this initial period of three years, the income from tree crops (fruits, nuts, medicine, essential oil, silk, perfume, honey, timber, animal fodder) exceeds by far the (catalyzer) carbon credits (average crop income for the 25,000 trees including secondary mixed cropping > 150,000 USD). The trees will accumulate carbon for 15 to 75 years depending on the tree species. While trunk wood will be used for construction timber and thus continue to sequester carbon for probably 50 years. While part of the wood will be used for cooking, at least 50% of the tree biomass will be pyrolyzed to biochar to produce organic biochar-based fertilizers and for using the pyrolysis heat for the production of essential oil, pasteurization and fruit or tea leaves drying. Compared to the barren terraces, sparsely covered with grasses and prone to erosion, the forest garden system with organic biochar-based fertilizer, continuous soil cover, mulching, leaf litter fall, root growth and root exudates, rotating cover crops and animal pasture, soil organic carbon (SOC) is expected to increase annually. Therefore, for each participating farmer at least one land spot is GIS marked for soil organic carbon analysis to be executed every five years and to calculate and certify soil organic carbon increases for additional or bonus carbon credits. In our presentation we will show and document the establishment of the forest garden systems, and discuss the link between local carbon sequestration and global carbon markets, the carbon calculation and certification procedures, and the challenge for multiplying such systems inter-regional and internationally.

Distributed-observer-based cooperative control for synchronization of linear discrete-time multi-agent systems.

PubMed

Liang, Hongjing; Zhang, Huaguang; Wang, Zhanshan

2015-11-01

This paper considers output synchronization of discrete-time multi-agent systems with directed communication topologies. The directed communication graph contains a spanning tree and the exosystem as its root. Distributed observer-based consensus protocols are proposed, based on the relative outputs of neighboring agents. A multi-step algorithm is presented to construct the observer-based protocols. In light of the discrete-time algebraic Riccati equation and internal model principle, synchronization problem is completed. At last, numerical simulation is provided to verify the effectiveness of the theoretical results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Coalescent histories for caterpillar-like families.

PubMed

Rosenberg, Noah A

2013-01-01

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

Situation-Assessment And Decision-Aid Production-Rule Analysis System For Nuclear Plant Monitoring And Emergency Preparedness

NASA Astrophysics Data System (ADS)

Gvillo, D.; Ragheb, M.; Parker, M.; Swartz, S.

1987-05-01

A Production-Rule Analysis System is developed for Nuclear Plant Monitoring. The signals generated by the Zion-1 Plant are considered. A Situation-Assessment and Decision-Aid capability is provided for monitoring the integrity of the Plant Radiation, the Reactor Coolant, the Fuel Clad, and the Containment Systems. A total of 41 signals are currently fed as facts to an Inference Engine functioning in the backward-chaining mode and built along the same structure as the E-Mycin system. The Goal-Tree constituting the Knowledge Base was generated using a representation in the form of Fault Trees deduced from plant procedures information. The system is constructed in support of the Data Analysis and Emergency Preparedness tasks at the Illinois Radiological Emergency Assessment Center (REAC).

Automated anatomical labeling of bronchial branches using multiple classifiers and its application to bronchoscopy guidance based on fusion of virtual and real bronchoscopy

NASA Astrophysics Data System (ADS)

Ota, Shunsuke; Deguchi, Daisuke; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Hasegawa, Yoshinori; Imaizumi, Kazuyoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi

2008-03-01

This paper presents a method for automated anatomical labeling of bronchial branches (ALBB) extracted from 3D CT datasets. The proposed method constructs classifiers that output anatomical names of bronchial branches by employing the machine-learning approach. We also present its application to a bronchoscopy guidance system. Since the bronchus has a complex tree structure, bronchoscopists easily tend to get disoriented and lose the way to a target location. A bronchoscopy guidance system is strongly expected to be developed to assist bronchoscopists. In such guidance system, automated presentation of anatomical names is quite useful information for bronchoscopy. Although several methods for automated ALBB were reported, most of them constructed models taking only variations of branching patterns into account and did not consider those of running directions. Since the running directions of bronchial branches differ greatly in individuals, they could not perform ALBB accurately when running directions of bronchial branches were different from those of models. Our method tries to solve such problems by utilizing the machine-learning approach. Actual procedure consists of three steps: (a) extraction of bronchial tree structures from 3D CT datasets, (b) construction of classifiers using the multi-class AdaBoost technique, and (c) automated classification of bronchial branches by using the constructed classifiers. We applied the proposed method to 51 cases of 3D CT datasets. The constructed classifiers were evaluated by leave-one-out scheme. The experimental results showed that the proposed method could assign correct anatomical names to bronchial branches of 89.1% up to segmental lobe branches. Also, we confirmed that it was quite useful to assist the bronchoscopy by presenting anatomical names of bronchial branches on real bronchoscopic views.

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

NASA Astrophysics Data System (ADS)

Wright, Heather; Pallister, John; Newhall, Chris

2015-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

Constructing the tree-level Yang-Mills S-matrix using complex factorization

NASA Astrophysics Data System (ADS)

Schuster, Philip C.; Toro, Natalia

2009-06-01

A remarkable connection between BCFW recursion relations and constraints on the S-matrix was made by Benincasa and Cachazo in 0705.4305, who noted that mutual consistency of different BCFW constructions of four-particle amplitudes generates non-trivial (but familiar) constraints on three-particle coupling constants — these include gauge invariance, the equivalence principle, and the lack of non-trivial couplings for spins > 2. These constraints can also be derived with weaker assumptions, by demanding the existence of four-point amplitudes that factorize properly in all unitarity limits with complex momenta. From this starting point, we show that the BCFW prescription can be interpreted as an algorithm for fully constructing a tree-level S-matrix, and that complex factorization of general BCFW amplitudes follows from the factorization of four-particle amplitudes. The allowed set of BCFW deformations is identified, formulated entirely as a statement on the three-particle sector, and using only complex factorization as a guide. Consequently, our analysis based on the physical consistency of the S-matrix is entirely independent of field theory. We analyze the case of pure Yang-Mills, and outline a proof for gravity. For Yang-Mills, we also show that the well-known scaling behavior of BCFW-deformed amplitudes at large z is a simple consequence of factorization. For gravity, factorization in certain channels requires asymptotic behavior ~ 1/z2.

Nuttall Oak Volume and Weight Tables

Treesearch

Bryce E. Schlaegel; Regan B. Willson

1983-01-01

Volume and weight tables were constructed from a 62-tree sample of Nuttall oak (Quercus nuttallii Palmer) taken in the Mississippi Delta. The tables present volume, green weight, and dry weight of bole wood, bole wood plus bark, and total tree above a one-foot stump as predicted from the nonlinear model Y = 0Db

An Apparatus for Pressure Injection of Solutions into Trees

Treesearch

Thomas W. Jones; Garold F. Gregory; Garold F. Gregory

1971-01-01

The construction and use of an apparatus for injecting solutions under pressure into trees is described. A unique and important feature of the apparatus is that it permits injection of solutions into the outermost sapwood. It has been used to inject dye solutions and solubilized benomyl into elm, oak, and maple.

Parks, Trees, and Environmental Justice: Field Notes from Washington, DC

ERIC Educational Resources Information Center

Buckley, Geoffrey L.; Whitmer, Ali; Grove, J. Morgan

2013-01-01

Students enrolled in a graduate seminar benefited in multiple ways from an intensive 3-day field trip to Washington, DC. Constructed around the theme of environmental justice, the trip gave students a chance to learn about street tree distribution, park quality, and racial segregation "up close." Working with personnel from the United…

Radiocarbon content in the annual tree rings during last 150 years and time variation of cosmic rays

NASA Technical Reports Server (NTRS)

Kocharov, G. E.; Metskvarishvili, R. Y.; Tsereteli, S. L.

1985-01-01

The results of the high accuracy measurements of radiocarbon abundance in precisely dated tree rings in the interval 1800 to 1950 yrs are discussed. Radiocarbon content caused by solar activity is established. The temporal dependence of cosmic rays is constructed, by use of radio abundance data.

If BZ medium did spanning trees these would be the same trees as Physarum built

NASA Astrophysics Data System (ADS)

Adamatzky, Andrew

2009-03-01

A sub-excitable Belousov-Zhabotinsky (BZ) medium exhibits self-localized wave-fragments which may travel for relatively long time preserving their shape. Using Oregonator model of the BZ medium we imitate foraging behavior of a true slime mold, Physarum polycephalum, on a nutrient-poor substrate. We show that given erosion post-processing operations the BZ medium can approximate a spanning tree of a planar set and thus is computationally equivalent to Physarum in the domain of proximity graph construction.

Structural system reliability calculation using a probabilistic fault tree analysis method

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Infinite tension limit of the pure spinor superstring

NASA Astrophysics Data System (ADS)

Berkovits, Nathan

2014-03-01

Mason and Skinner recently constructed a chiral infinite tension limit of the Ramond-Neveu-Schwarz superstring which was shown to compute the Cachazo-He-Yuan formulae for tree-level d = 10 Yang-Mills amplitudes and the NS-NS sector of tree-level d = 10 supergravity amplitudes. In this letter, their chiral infinite tension limit is generalized to the pure spinor superstring which computes a d = 10 superspace version of the Cachazo-He-Yuan formulae for tree-level d = 10 super-Yang-Mills and supergravity amplitudes.

The complete mitochondrial genome of Acanthosaura lepidogaster (Squamata: Agamidae).

PubMed

Yu, Xiu-Li; Du, Yu; Yao, Yun-Tao; Lin, Chi-Xian; Lin, Long-Hui

2017-03-01

In this paper, we report the complete mitochondrial genome of Acanthosaura lepidogaster (Squamata, Agamidae), which is a circular molecule of 16 899 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The overall base composition is as follows: T (22.8%), C (30.5%), A (32.3%), and G (14.4%). We constructed a phylogeny that included for 10 species of Leiolepidinae lizards and one outgroup Leiocephalus personatus constructed in BEAST, based on 15 mitochondrial genes (12S, 16S, ND1, ND2, COI, COII, ATP8, ATP6, COIII, ND3, ND4L, ND4, ND5, ND6, and cytochrome b). The topology of the phylogenetic tree is broadly similar to that mentioned by Pyron et al.

Hydrochemical analysis of groundwater using a tree-based model

NASA Astrophysics Data System (ADS)

Litaor, M. Iggy; Brielmann, H.; Reichmann, O.; Shenker, M.

2010-06-01

SummaryHydrochemical indices are commonly used to ascertain aquifer characteristics, salinity problems, anthropogenic inputs and resource management, among others. This study was conducted to test the applicability of a binary decision tree model to aquifer evaluation using hydrochemical indices as input. The main advantage of the tree-based model compared to other commonly used statistical procedures such as cluster and factor analyses is the ability to classify groundwater samples with assigned probability and the reduction of a large data set into a few significant variables without creating new factors. We tested the model using data sets collected from headwater springs of the Jordan River, Israel. The model evaluation consisted of several levels of complexity, from simple separation between the calcium-magnesium-bicarbonate water type of karstic aquifers to the more challenging separation of calcium-sodium-bicarbonate water type flowing through perched and regional basaltic aquifers. In all cases, the model assigned measures for goodness of fit in the form of misclassification errors and singled out the most significant variable in the analysis. The model proceeded through a sequence of partitions providing insight into different possible pathways and changing lithology. The model results were extremely useful in constraining the interpretation of geological heterogeneity and constructing a conceptual flow model for a given aquifer. The tree model clearly identified the hydrochemical indices that were excluded from the analysis, thus providing information that can lead to a decrease in the number of routinely analyzed variables and a significant reduction in laboratory cost.

Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes

PubMed Central

Chase, Mark W.; Kim, Joo-Hwan

2013-01-01

Phylogenetic analysis aims to produce a bifurcating tree, which disregards conflicting signals and displays only those that are present in a large proportion of the data. However, any character (or tree) conflict in a dataset allows the exploration of support for various evolutionary hypotheses. Although data-display network approaches exist, biologists cannot easily and routinely use them to compute rooted phylogenetic networks on real datasets containing hundreds of taxa. Here, we constructed an original neighbour-net for a large dataset of Asparagales to highlight the aspects of the resulting network that will be important for interpreting phylogeny. The analyses were largely conducted with new data collected for the same loci as in previous studies, but from different species accessions and greater sampling in many cases than in published analyses. The network tree summarised the majority data pattern in the characters of plastid sequences before tree building, which largely confirmed the currently recognised phylogenetic relationships. Most conflicting signals are at the base of each group along the Asparagales backbone, which helps us to establish the expectancy and advance our understanding of some difficult taxa relationships and their phylogeny. The network method should play a greater role in phylogenetic analyses than it has in the past. To advance the understanding of evolutionary history of the largest order of monocots Asparagales, absolute diversification times were estimated for family-level clades using relaxed molecular clock analyses. PMID:23544071

Metrics for comparing neuronal tree shapes based on persistent homology.

PubMed

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A; Mitra, Partha; Wang, Yusu

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework.

Metrics for comparing neuronal tree shapes based on persistent homology

PubMed Central

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A.; Mitra, Partha

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities—Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework. PMID:28809960

Hybridization among distantly related species: Examples from the polyploid genus Curcuma (Zingiberaceae).

PubMed

Záveská, Eliška; Fér, Tomáš; Šída, Otakar; Marhold, Karol; Leong-Škorničková, Jana

2016-07-01

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma, based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA (DCS, GAPDH, GLOBOSA3, LEAFY, ITS) and four non-coding cpDNA regions (trnL-trnF, trnT-trnL, psbA-trnH and matK), analysed as a single locus, were employed to construct a species tree and hybrid species trees using (*)BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma, which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida, C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin. Copyright © 2016 Elsevier Inc. All rights reserved.

Constructing bald eagle nests with natural materials

Treesearch

T. G. Grubb

1995-01-01

A technique for using natural materials to build artificial nests for bald eagles (Haliaeetus leucocephalus) and other raptors is detailed. Properly constructed nests are as permanently secured to the nest tree or cliff substrate as any eagle-built nest or human-made platform. Construction normally requires about three hours and at least two people. This technique is...

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

[Study on extraction method of Panax notoginseng plots in Wenshan of Yunnan province based on decision tree model].

PubMed

Shi, Ting-Ting; Zhang, Xiao-Bo; Guo, Lan-Ping; Huang, Lu-Qi

2017-11-01

The herbs used as the material for traditional Chinese medicine are always planted in the mountainous area where the natural environment is suitable. As the mountain terrain is complex and the distribution of planting plots is scattered, the traditional survey method is difficult to obtain accurate planting area. It is of great significance to provide decision support for the conservation and utilization of traditional Chinese medicine resources by studying the method of extraction of Chinese herbal medicine planting area based on remote sensing and realizing the dynamic monitoring and reserve estimation of Chinese herbal medicines. In this paper, taking the Panax notoginseng plots in Wenshan prefecture of Yunnan province as an example, the China-made GF-1multispectral remote sensing images with a 16 m×16 m resolution were obtained. Then, the time series that can reflect the difference of spectrum of P. notoginseng shed and the background objects were selected to the maximum extent, and the decision tree model of extraction the of P. notoginseng plots was constructed according to the spectral characteristics of the surface features. The results showed that the remote sensing classification method based on the decision tree model could extract P. notoginseng plots in the study area effectively. The method can provide technical support for extraction of P. notoginseng plots at county level. Copyright© by the Chinese Pharmaceutical Association.

Pattern Matcher for Trees Constructed from Lists

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

A software library has been developed that takes a high-level description of a pattern to be satisfied and applies it to a target. If the two match, it returns success; otherwise, it indicates a failure. The target is semantically a tree that is constructed from elements of terminal and non-terminal nodes represented through lists and symbols. Additionally, functionality is provided for finding the element in a set that satisfies a given pattern and doing a tree search, finding all occurrences of leaf nodes that match a given pattern. This process is valuable because it is a new algorithmic approach that significantly improves the productivity of the programmers and has the potential of making their resulting code more efficient by the introduction of a novel semantic representation language. This software has been used in many applications delivered to NASA and private industry, and the cost savings that have resulted from it are significant.

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

PubMed Central

Giaro, Krzysztof

2017-01-01

Abstract Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson–Foulds distance. In this article, we define a new metric for rooted trees—the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events. PMID:28177699

Node degree distribution in spanning trees

NASA Astrophysics Data System (ADS)

Pozrikidis, C.

2016-03-01

A method is presented for computing the number of spanning trees involving one link or a specified group of links, and excluding another link or a specified group of links, in a network described by a simple graph in terms of derivatives of the spanning-tree generating function defined with respect to the eigenvalues of the Kirchhoff (weighted Laplacian) matrix. The method is applied to deduce the node degree distribution in a complete or randomized set of spanning trees of an arbitrary network. An important feature of the proposed method is that the explicit construction of spanning trees is not required. It is shown that the node degree distribution in the spanning trees of the complete network is described by the binomial distribution. Numerical results are presented for the node degree distribution in square, triangular, and honeycomb lattices.

GSHR-Tree: a spatial index tree based on dynamic spatial slot and hash table in grid environments

NASA Astrophysics Data System (ADS)

Chen, Zhanlong; Wu, Xin-cai; Wu, Liang

2008-12-01

Computation Grids enable the coordinated sharing of large-scale distributed heterogeneous computing resources that can be used to solve computationally intensive problems in science, engineering, and commerce. Grid spatial applications are made possible by high-speed networks and a new generation of Grid middleware that resides between networks and traditional GIS applications. The integration of the multi-sources and heterogeneous spatial information and the management of the distributed spatial resources and the sharing and cooperative of the spatial data and Grid services are the key problems to resolve in the development of the Grid GIS. The performance of the spatial index mechanism is the key technology of the Grid GIS and spatial database affects the holistic performance of the GIS in Grid Environments. In order to improve the efficiency of parallel processing of a spatial mass data under the distributed parallel computing grid environment, this paper presents a new grid slot hash parallel spatial index GSHR-Tree structure established in the parallel spatial indexing mechanism. Based on the hash table and dynamic spatial slot, this paper has improved the structure of the classical parallel R tree index. The GSHR-Tree index makes full use of the good qualities of R-Tree and hash data structure. This paper has constructed a new parallel spatial index that can meet the needs of parallel grid computing about the magnanimous spatial data in the distributed network. This arithmetic splits space in to multi-slots by multiplying and reverting and maps these slots to sites in distributed and parallel system. Each sites constructs the spatial objects in its spatial slot into an R tree. On the basis of this tree structure, the index data was distributed among multiple nodes in the grid networks by using large node R-tree method. The unbalance during process can be quickly adjusted by means of a dynamical adjusting algorithm. This tree structure has considered the distributed operation, reduplication operation transfer operation of spatial index in the grid environment. The design of GSHR-Tree has ensured the performance of the load balance in the parallel computation. This tree structure is fit for the parallel process of the spatial information in the distributed network environments. Instead of spatial object's recursive comparison where original R tree has been used, the algorithm builds the spatial index by applying binary code operation in which computer runs more efficiently, and extended dynamic hash code for bit comparison. In GSHR-Tree, a new server is assigned to the network whenever a split of a full node is required. We describe a more flexible allocation protocol which copes with a temporary shortage of storage resources. It uses a distributed balanced binary spatial tree that scales with insertions to potentially any number of storage servers through splits of the overloaded ones. The application manipulates the GSHR-Tree structure from a node in the grid environment. The node addresses the tree through its image that the splits can make outdated. This may generate addressing errors, solved by the forwarding among the servers. In this paper, a spatial index data distribution algorithm that limits the number of servers has been proposed. We improve the storage utilization at the cost of additional messages. The structure of GSHR-Tree is believed that the scheme of this grid spatial index should fit the needs of new applications using endlessly larger sets of spatial data. Our proposal constitutes a flexible storage allocation method for a distributed spatial index. The insertion policy can be tuned dynamically to cope with periods of storage shortage. In such cases storage balancing should be favored for better space utilization, at the price of extra message exchanges between servers. This structure makes a compromise in the updating of the duplicated index and the transformation of the spatial index data. Meeting the needs of the grid computing, GSHRTree has a flexible structure in order to satisfy new needs in the future. The GSHR-Tree provides the R-tree capabilities for large spatial datasets stored over interconnected servers. The analysis, including the experiments, confirmed the efficiency of our design choices. The scheme should fit the needs of new applications of spatial data, using endlessly larger datasets. Using the system response time of the parallel processing of spatial scope query algorithm as the performance evaluation factor, According to the result of the simulated the experiments, GSHR-Tree is performed to prove the reasonable design and the high performance of the indexing structure that the paper presented.

Construction of Open Burning Facility Moody Air Force Base, Georgia Environmental Assessment and Finding of No Significant Impact

DTIC Science & Technology

2009-01-01

are smaller and more leathery, and the leaf canopy is less dense. The trees commonly found in the southeastern United States are pines ( Pinus spp...during periods of extreme drought . These periodic fires maintained the pine subclimax forest by controlling hardwood competition, encouraged the growth...cinnamomea), chain fern (Woodwardia virginica), and greenbrier (Smilax spp). In the transition areas from wetlands to uplands, pond pine ( Pinus serotina

Improved FTA methodology and application to subsea pipeline reliability design.

PubMed

Lin, Jing; Yuan, Yongbo; Zhang, Mingyuan

2014-01-01

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

Improved FTA Methodology and Application to Subsea Pipeline Reliability Design

PubMed Central

Lin, Jing; Yuan, Yongbo; Zhang, Mingyuan

2014-01-01

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

Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

PubMed

Marcelletti, Simone; Scortichini, Marco

2016-10-01

A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

Technology Tips: Using the Iterate Command to Construct Recursive Geometric Sketches

ERIC Educational Resources Information Center

Harper, Suzanne R.; Driskell, Shannon

2006-01-01

How to iterate geometric shapes to construct Baravelle spirals and Pythagorean trees is demonstrated in this article. The "Surfing Note" sends readers to a site with applets that will generate fractals such as the Sierpinski gasket or the Koch snowflake.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change.

PubMed

Ashraf, M Irfan; Meng, Fan-Rui; Bourque, Charles P-A; MacLean, David A

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm(2) 5-year(-1) and volume: 0.0008 m(3) 5-year(-1)). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm(2) 5-year(-1) and 0.0393 m(3) 5-year(-1) in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling.

A Novel Modelling Approach for Predicting Forest Growth and Yield under Climate Change

PubMed Central

Ashraf, M. Irfan; Meng, Fan-Rui; Bourque, Charles P.-A.; MacLean, David A.

2015-01-01

Global climate is changing due to increasing anthropogenic emissions of greenhouse gases. Forest managers need growth and yield models that can be used to predict future forest dynamics during the transition period of present-day forests under a changing climatic regime. In this study, we developed a forest growth and yield model that can be used to predict individual-tree growth under current and projected future climatic conditions. The model was constructed by integrating historical tree growth records with predictions from an ecological process-based model using neural networks. The new model predicts basal area (BA) and volume growth for individual trees in pure or mixed species forests. For model development, tree-growth data under current climatic conditions were obtained using over 3000 permanent sample plots from the Province of Nova Scotia, Canada. Data to reflect tree growth under a changing climatic regime were projected with JABOWA-3 (an ecological process-based model). Model validation with designated data produced model efficiencies of 0.82 and 0.89 in predicting individual-tree BA and volume growth. Model efficiency is a relative index of model performance, where 1 indicates an ideal fit, while values lower than zero means the predictions are no better than the average of the observations. Overall mean prediction error (BIAS) of basal area and volume growth predictions was nominal (i.e., for BA: -0.0177 cm2 5-year-1 and volume: 0.0008 m3 5-year-1). Model variability described by root mean squared error (RMSE) in basal area prediction was 40.53 cm2 5-year-1 and 0.0393 m3 5-year-1 in volume prediction. The new modelling approach has potential to reduce uncertainties in growth and yield predictions under different climate change scenarios. This novel approach provides an avenue for forest managers to generate required information for the management of forests in transitional periods of climate change. Artificial intelligence technology has substantial potential in forest modelling. PMID:26173081

A combined M5P tree and hazard-based duration model for predicting urban freeway traffic accident durations.

PubMed

Lin, Lei; Wang, Qian; Sadek, Adel W

2016-06-01

The duration of freeway traffic accidents duration is an important factor, which affects traffic congestion, environmental pollution, and secondary accidents. Among previous studies, the M5P algorithm has been shown to be an effective tool for predicting incident duration. M5P builds a tree-based model, like the traditional classification and regression tree (CART) method, but with multiple linear regression models as its leaves. The problem with M5P for accident duration prediction, however, is that whereas linear regression assumes that the conditional distribution of accident durations is normally distributed, the distribution for a "time-to-an-event" is almost certainly nonsymmetrical. A hazard-based duration model (HBDM) is a better choice for this kind of a "time-to-event" modeling scenario, and given this, HBDMs have been previously applied to analyze and predict traffic accidents duration. Previous research, however, has not yet applied HBDMs for accident duration prediction, in association with clustering or classification of the dataset to minimize data heterogeneity. The current paper proposes a novel approach for accident duration prediction, which improves on the original M5P tree algorithm through the construction of a M5P-HBDM model, in which the leaves of the M5P tree model are HBDMs instead of linear regression models. Such a model offers the advantage of minimizing data heterogeneity through dataset classification, and avoids the need for the incorrect assumption of normality for traffic accident durations. The proposed model was then tested on two freeway accident datasets. For each dataset, the first 500 records were used to train the following three models: (1) an M5P tree; (2) a HBDM; and (3) the proposed M5P-HBDM, and the remainder of data were used for testing. The results show that the proposed M5P-HBDM managed to identify more significant and meaningful variables than either M5P or HBDMs. Moreover, the M5P-HBDM had the lowest overall mean absolute percentage error (MAPE). Copyright © 2016 Elsevier Ltd. All rights reserved.

Reforestation strategies amid social instability: lessons from Afghanistan.

PubMed

Groninger, John W

2012-04-01

Foreign and domestic government agencies and other international organizations pursue reforestation programs in rural upper watershed areas of Afghanistan over the past decade to alleviate poverty, combat the insurgency and rehabilitate a depleted forest resource base. Popular programs incorporate cash-for-work to conduct hillside terracing, check dam construction and tree-planting for nut production, fuel wood, timber, dune stabilization, and erosion abatement. Programmatic approaches have varied as a function of accessibility, security and local objectives. Uncertain land tenure and use rights, weak local environmental management capacity, and a focus on agricultural production to meet immediate needs limit interest, nationally and locally. Unreliable security, a lack of high quality tree planting stock, limited technical knowledge and coordination among government agencies, and poor security hamper program expansion. Reforestation success would be most likely where these issues are least acute. The Afghan government should focus on supporting community based natural resource management, developing and disseminating improved conservation tree nursery strategies, and promoting watershed management schemes that incorporate forestry, range management and agronomic production. Reforestation practitioners could benefit from the human and material resources now present as part of the international war effort. Successes and failures encountered in Afghanistan should be considered in order to address similar problems in insecure regions elsewhere when reforestation may help reverse environmental degradation and contribute to broader social stabilization efforts.

Selecting Species Traits for Biomonitoring Applications in light of Phylogenetic Relationships among Lotic Insects

NASA Astrophysics Data System (ADS)

Poff, N.; Vieira, N. K.; Simmons, M. P.; Olden, J. D.; Kondratieff, B. C.; Finn, D. S.

2005-05-01

The use of species traits as indicators of environmental disturbance is being considered for biomonitoring programs globally. As such, methods to select relevant and informative traits for inclusion in biometrics need to be developed. In this research, we identified 20 traits of aquatic insects within six trait groups: morphology, mobility, life-history strategy, thermal tolerance, feeding guild and ecology (e.g., habitat preference). We constructed phylogenetic trees for 1) all lotic insect species of North America and 2) all Ephemeroptera, Plecoptera and Trichoptera species based on morphology- and molecular-based analyses and classifications. We then measured variability (i.e., plasticity) of the 20 traits and six trait groups across the two phylogenetic trees. Traits with higher degrees of plasticity indicated traits that were less phylogenetically constrained, and were considered informative for biomonitoring purposes. Thermal tolerance, rheophily, body size at maturity and feeding guild showed the highest plasticity across both phylogenetic trees. Two mobility traits, occurrence in drift and adult dispersal distance, showed moderate plasticity. By contrast, adult exiting ability, degree of attachment, adult lifespan and body shape showed low variability and were thus less informative. Plastic species traits that are less phylogenetically constrained may be most useful in detecting community change along environmental gradients.

Climate Based Predictability of Oil Palm Tree Yield in Malaysia.

PubMed

Oettli, Pascal; Behera, Swadhin K; Yamagata, Toshio

2018-02-02

The influence of local conditions and remote climate modes on the interannual variability of oil palm fresh fruit bunches (FFB) total yields in Malaysia and two major regions (Peninsular Malaysia and Sabah/Sarawak) is explored. On a country scale, the state of sea-surface temperatures (SST) in the tropical Pacific Ocean during the previous boreal winter is found to influence the regional climate. When El Niño occurs in the Pacific Ocean, rainfall in Malaysia reduces but air temperature increases, generating a high level of water stress for palm trees. As a result, the yearly production of FFB becomes lower than that of a normal year since the water stress during the boreal spring has an important impact on the total annual yields of FFB. Conversely, La Niña sets favorable conditions for palm trees to produce more FFB by reducing chances of water stress risk. The region of the Leeuwin current also seems to play a secondary role through the Ningaloo Niño/ Niña in the interannual variability of FFB yields. Based on these findings, a linear model is constructed and its ability to reproduce the interannual signal is assessed. This model has shown some skills in predicting the total FFB yield.

Reforestation Strategies Amid Social Instability: Lessons from Afghanistan

NASA Astrophysics Data System (ADS)

Groninger, John W.

2012-04-01

Foreign and domestic government agencies and other international organizations pursue reforestation programs in rural upper watershed areas of Afghanistan over the past decade to alleviate poverty, combat the insurgency and rehabilitate a depleted forest resource base. Popular programs incorporate cash-for-work to conduct hillside terracing, check dam construction and tree-planting for nut production, fuel wood, timber, dune stabilization, and erosion abatement. Programmatic approaches have varied as a function of accessibility, security and local objectives. Uncertain land tenure and use rights, weak local environmental management capacity, and a focus on agricultural production to meet immediate needs limit interest, nationally and locally. Unreliable security, a lack of high quality tree planting stock, limited technical knowledge and coordination among government agencies, and poor security hamper program expansion. Reforestation success would be most likely where these issues are least acute. The Afghan government should focus on supporting community based natural resource management, developing and disseminating improved conservation tree nursery strategies, and promoting watershed management schemes that incorporate forestry, range management and agronomic production. Reforestation practitioners could benefit from the human and material resources now present as part of the international war effort. Successes and failures encountered in Afghanistan should be considered in order to address similar problems in insecure regions elsewhere when reforestation may help reverse environmental degradation and contribute to broader social stabilization efforts.

Lung tumor diagnosis and subtype discovery by gene expression profiling.

PubMed

Wang, Lu-yong; Tu, Zhuowen

2006-01-01

The optimal treatment of patients with complex diseases, such as cancers, depends on the accurate diagnosis by using a combination of clinical and histopathological data. In many scenarios, it becomes tremendously difficult because of the limitations in clinical presentation and histopathology. To accurate diagnose complex diseases, the molecular classification based on gene or protein expression profiles are indispensable for modern medicine. Moreover, many heterogeneous diseases consist of various potential subtypes in molecular basis and differ remarkably in their response to therapies. It is critical to accurate predict subgroup on disease gene expression profiles. More fundamental knowledge of the molecular basis and classification of disease could aid in the prediction of patient outcome, the informed selection of therapies, and identification of novel molecular targets for therapy. In this paper, we propose a new disease diagnostic method, probabilistic boosting tree (PB tree) method, on gene expression profiles of lung tumors. It enables accurate disease classification and subtype discovery in disease. It automatically constructs a tree in which each node combines a number of weak classifiers into a strong classifier. Also, subtype discovery is naturally embedded in the learning process. Our algorithm achieves excellent diagnostic performance, and meanwhile it is capable of detecting the disease subtype based on gene expression profile.

Positive selection on D-lactate dehydrogenases of Lactobacillus delbrueckii subspecies bulgaricus.

PubMed

Zhang, Jifeng; Gong, Guangyu; Wang, Xiao; Zhang, Hao; Tian, Weidong

2015-08-01

Lactobacillus delbrueckii has been widely used for yogurt fermentation. It has genes encoding both D- and L-type lactate dehydrogenases (LDHs) that catalyse the production of L(+) or D(-) stereoisomer of lactic acid. D-lactic acid is the primary lactate product by L. delbrueckii, yet it cannot be metabolised by human intestine. Since it has been domesticated for long time, an interesting question arises regarding to whether the selection pressure has affected the evolution of both L-LDH and D-LDH genes in the genome. To answer this question, in this study the authors first investigated the evolution of these two genes by constructing phylogenetic trees. They found that D-LDH-based phylogenetic tree could better represent the phylogenetic relationship in the acidophilus complex than L-LDH-based tree. They next investigated the evolutions of LDH genes of L. delbrueckii at amino acid level, and found that D-LDH gene in L. delbrueckii is positively selected, possibly a consequence of long-term domestication. They further identified four amino acids that are under positive selection. One of them, V261, is located at the centre of three catalytic active sites, indicating likely functional effects on the enzyme activity. The selection from the domestication process thus provides direction for future engineering of D-LDH.

The Pennsylvania defoliation application pilot test

NASA Technical Reports Server (NTRS)

Mcleod, R. G.; Zobrist, A. L.; Bryant, N. A.

1983-01-01

Satellite imagery for the State of Pennsylvania was digitally mosaicked to provide the seed data base for monitoring defoliation of hardwood trees by the gypsy moth. Two separate mosaics for the state were prepared, one before defoliation and one after defoliation, to determine the extent, direction, and impact of gypsy moth activity in the state. The digital mosaic technology used to construct the data base was transferred to Pennsylvania State University to permit periodic updates to the data base and to assist in planning and abatement activities. Participating agencies or institutions included Goddard Space Flight Center and the Pennsylvania State University Office for Remote Sensing of Earth Resources.

Propagation of dry tropical forest trees in Mexico

Treesearch

Martha A. Cervantes Sanchez

2002-01-01

There is a distinct lack of technical information on the propagation of native tree species from the dry tropical forest ecosystem in Mexico. This ecosystem has come under heavy human pressures to obtain several products such as specialty woods for fuel, posts for fences and construction, forage, edible fruits, stakes for horticulture crops, and medicinal products. The...

A Comparison of Height-Accumulation and Volume-Equation Methods for Estimating Tree and Stand Volumes

Treesearch

R.B. Ferguson; V. Clark Baldwin

1995-01-01

Estimating tree and stand volume in mature plantations is time consuming, involving much manpower and equipment; however, several sampling and volume-prediction techniques are available. This study showed that a well-constructed, volume-equation method yields estimates comparable to those of the often more time-consuming, height-accumulation method, even though the...

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

EPA Science Inventory

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

Choosing appropriate subpopulations for modeling tree canopy cover nationwide

Treesearch

Gretchen G. Moisen; John W. Coulston; Barry T. Wilson; Warren B. Cohen; Mark V. Finco

2012-01-01

In prior national mapping efforts, the country has been divided into numerous ecologically similar mapping zones, and individual models have been constructed for each zone. Additionally, a hierarchical approach has been taken within zones to first mask out areas of nonforest, then target models of tree attributes within forested areas only. This results in many models...

Technical Manual for the Conceptual Learning and Development Assessment Series IV: Tree. Technical Report No. 437. Reprinted December 1977.

ERIC Educational Resources Information Center

DiLuzio, Geneva J.; And Others

This document accompanies the Conceptual Learning and Development Assessment Series III: Tree, a test constructed to chart the conceptual development of individuals. As a technical manual, it contains information on the rationale, development, standardization, and reliability of the test, as well as essential information and statistical data for…

[Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism].

PubMed

Zelenina, D A; Khrustaleva, A M; Volkov, A A

2006-05-01

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.

Phylogenetic analysis of Fusobacterium prausnitzii based upon the 16S rRNA gene sequence and PCR confirmation.

PubMed

Wang, R F; Cao, W W; Cerniglia, C E

1996-01-01

In order to develop a PCR method to detect Fusobacterium prausnitzii in human feces and to clarify the phylogenetic position of this species, its 16S rRNA gene sequence was determined. The sequence described in this paper is different from the 16S rRNA gene sequence is specific for F. prausnitzii, and the results of this assay confirmed that F. prausnitzii is the most common species in human feces. However, a PCR assay based on the original GenBank sequence was negative when it was performed with two strains of F. prausnitzii obtained from the American Type Culture Collection. A phylogenetic tree based on the new 16S rRNA gene sequence was constructed. On this tree F. prausnitzii was not a member of the Fusobacterium group but was closer to some Eubacterium spp. and located between Clostridium "clusters III and IV" (M.D. Collins, P.A. Lawson, A. Willems, J.J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J.A.E. Farrow, Int. J. Syst. Bacteriol. 44:812-826, 1994).

Detection of climate signal in dendrochronological data analysis: a comparison of tree-ring standardization methods

NASA Astrophysics Data System (ADS)

Helama, S.; Lindholm, M.; Timonen, M.; Eronen, M.

2004-12-01

Tree-ring standardization methods were compared. Traditional methods along with the recently introduced approaches of regional curve standardization (RCS) and power-transformation (PT) were included. The difficulty in removing non-climatic variation (noise) while simultaneously preserving the low-frequency variability in the tree-ring series was emphasized. The potential risk of obtaining inflated index values was analysed by comparing methods to extract tree-ring indices from the standardization curve. The material for the tree-ring series, previously used in several palaeoclimate predictions, came from living and dead wood of high-latitude Scots pine in northernmost Europe. This material provided a useful example of a long composite tree-ring chronology with the typical strengths and weaknesses of such data, particularly in the context of standardization. PT stabilized the heteroscedastic variation in the original tree-ring series more efficiently than any other standardization practice expected to preserve the low-frequency variability. RCS showed great potential in preserving variability in tree-ring series at centennial time scales; however, this method requires a homogeneous sample for reliable signal estimation. It is not recommended to derive indices by subtraction without first stabilizing the variance in the case of series of forest-limit tree-ring data. Index calculation by division did not seem to produce inflated chronology values for the past one and a half centuries of the chronology (where mean sample cambial age is high). On the other hand, potential bias of high RCS chronology values was observed during the period of anomalously low mean sample cambial age. An alternative technique for chronology construction was proposed based on series age decomposition, where indices in the young vigorously behaving part of each series are extracted from the curve by division and in the mature part by subtraction. Because of their specific nature, the dendrochronological data here should not be generalized to all tree-ring records. The examples presented should be used as guidelines for detecting potential sources of bias and as illustrations of the usefulness of tree-ring records as palaeoclimate indicators.

Constructing high-quality bounding volume hierarchies for N-body computation using the acceptance volume heuristic

NASA Astrophysics Data System (ADS)

Olsson, O.

2018-01-01

We present a novel heuristic derived from a probabilistic cost model for approximate N-body simulations. We show that this new heuristic can be used to guide tree construction towards higher quality trees with improved performance over current N-body codes. This represents an important step beyond the current practice of using spatial partitioning for N-body simulations, and enables adoption of a range of state-of-the-art algorithms developed for computer graphics applications to yield further improvements in N-body simulation performance. We outline directions for further developments and review the most promising such algorithms.

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.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

Development of spatial scaling technique of forest health sample point information

NASA Astrophysics Data System (ADS)

Lee, J.; Ryu, J.; Choi, Y. Y.; Chung, H. I.; Kim, S. H.; Jeon, S. W.

2017-12-01

Most forest health assessments are limited to monitoring sampling sites. The monitoring of forest health in Britain in Britain was carried out mainly on five species (Norway spruce, Sitka spruce, Scots pine, Oak, Beech) Database construction using Oracle database program with density The Forest Health Assessment in GreatBay in the United States was conducted to identify the characteristics of the ecosystem populations of each area based on the evaluation of forest health by tree species, diameter at breast height, water pipe and density in summer and fall of 200. In the case of Korea, in the first evaluation report on forest health vitality, 1000 sample points were placed in the forests using a systematic method of arranging forests at 4Km × 4Km at regular intervals based on an sample point, and 29 items in four categories such as tree health, vegetation, soil, and atmosphere. As mentioned above, existing researches have been done through the monitoring of the survey sample points, and it is difficult to collect information to support customized policies for the regional survey sites. In the case of special forests such as urban forests and major forests, policy and management appropriate to the forest characteristics are needed. Therefore, it is necessary to expand the survey headquarters for diagnosis and evaluation of customized forest health. For this reason, we have constructed a method of spatial scale through the spatial interpolation according to the characteristics of each index of the main sample point table of 29 index in the four points of diagnosis and evaluation report of the first forest health vitality report, PCA statistical analysis and correlative analysis are conducted to construct the indicators with significance, and then weights are selected for each index, and evaluation of forest health is conducted through statistical grading.

Mummy Lake: An unroofed ceremonial structure within a large-scale ritual landscape

USGS Publications Warehouse

Benson, Larry V.; Griffin, Eleanor R.; Stein, J.R.; Friedman, R. A.; Andrae, S. W.

2014-01-01

The structure at Mesa Verde National Park known historically as Mummy Lake and more recently as Far View Reservoir is not part of a water collection, impoundment, or redistribution system. We offer an alternative explanation for the function of Mummy Lake. We suggest that it is an unroofed ceremonial structure, and that it serves as an essential component of a Chacoan ritual landscape. A wide constructed avenue articulates Mummy Lake with Far View House and Pipe Shrine House. The avenue continues southward for approximately 6 km where it apparently divides connecting with Spruce Tree House and Sun Temple/Cliff Palace. The avenue has previously been interpreted as an irrigation ditch fed by water impounded at Mummy Lake; however, it conforms in every respect to alignments described as Chacoan roads. Tree-ring dates indicate that the construction of Spruce Tree House and Cliff Palace began about A.D. 1225, roughly coincident with the abandonment of the Far View community. This pattern of periodically relocating the focus of an Anasazi community by retiring existing ritual structures and linking them to newly constructed facilities by means of broad avenues was first documented by Fowler and Stein (1992) in Manuelito Canyon, New Mexico. Periods of intense drought appear to have contributed to the relocation of prehistoric Native Americans from the Far View group to Cliff Palace/Spruce Tree House in the mid-13th century and eventually to the abandonment of all Anasazi communities in southwestern Colorado in the late-13th century.

Behaviour change in overweight and obese pregnancy: a decision tree to support the development of antenatal lifestyle interventions.

PubMed

Ainscough, Kate M; Lindsay, Karen L; O'Sullivan, Elizabeth J; Gibney, Eileen R; McAuliffe, Fionnuala M

2017-10-01

Antenatal healthy lifestyle interventions are frequently implemented in overweight and obese pregnancy, yet there is inconsistent reporting of the behaviour-change methods and behavioural outcomes. This limits our understanding of how and why such interventions were successful or not. The current paper discusses the application of behaviour-change theories and techniques within complex lifestyle interventions in overweight and obese pregnancy. The authors propose a decision tree to help guide researchers through intervention design, implementation and evaluation. The implications for adopting behaviour-change theories and techniques, and using appropriate guidance when constructing and evaluating interventions in research and clinical practice are also discussed. To enhance the evidence base for successful behaviour-change interventions during pregnancy, adoption of behaviour-change theories and techniques, and use of published guidelines when designing lifestyle interventions are necessary. The proposed decision tree may be a useful guide for researchers working to develop effective behaviour-change interventions in clinical settings. This guide directs researchers towards key literature sources that will be important in each stage of study development.

The tree to the left, the forest to the right: political attitude and perceptual bias.

PubMed

Caparos, Serge; Fortier-St-Pierre, Simon; Gosselin, Jérémie; Blanchette, Isabelle; Brisson, Benoit

2015-01-01

A prominent model suggests that individuals to the right of the political spectrum are more cognitively rigid and less tolerant of ambiguity than individuals to the left. On the basis of this model, we predicted that a psychological mechanism linked to the resolution of visual ambiguity--perceptual bias--would be linked to political attitude. Perceptual bias causes western individuals to favour a global interpretation when scrutinizing ambiguous hierarchical displays (e.g., alignment of trees) that can be perceived either in terms of their local elements (e.g., several trees) or in terms of their global structure (e.g., a forest). Using three tasks (based on Navon-like hierarchical figures or on the Ebbinghaus illusion), we demonstrate (1) that right-oriented Westerners present a stronger bias towards global perception than left-oriented Westerners and (2) that this stronger bias is linked to higher cognitive rigidity. This study establishes for the first time that political ideology, a high-level construct, is directly reflected in low-level perception. Right- and left-oriented individuals actually see the world differently. Copyright © 2014 Elsevier B.V. All rights reserved.

What contributes to perceived stress in later life? A recursive partitioning approach.

PubMed

Scott, Stacey B; Jackson, Brenda R; Bergeman, C S

2011-12-01

One possible explanation for the individual differences in outcomes of stress is the diversity of inputs that produce perceptions of being stressed. The current study examines how combinations of contextual features (e.g., social isolation, neighborhood quality, health problems, age discrimination, financial concerns, and recent life events) of later life contribute to overall feelings of stress. Recursive partitioning techniques (regression trees and random forests) were used to examine unique interrelations between predictors of perceived stress in a sample of 282 community-dwelling adults. Trees provided possible examples of equifinality (i.e., subsets of people with similar levels of perceived stress but different predictors) as well as identification both of contextual combinations that separated participants with very high and very low perceived stress. Random forest analyses aggregated across many trees based on permuted versions of the data and predictors; loneliness, financial strain, neighborhood strain, ageism, and to some extent life events emerged as important predictors. Interviews with a subsample of participants provided both thick description of the complex relationships identified in the trees, as well as additional risks not appearing in the survey results. Together, the analyses highlight what may be missed when stress is used as a simple unidimensional construct and can guide differential intervention efforts.

What contributes to perceived stress in later life? A recursive partitioning approach

PubMed Central

Scott, Stacey B.; Jackson, Brenda R.; Bergeman, C. S.

2011-01-01

One possible explanation for the individual differences in outcomes of stress is the diversity of inputs that produce perceptions of being stressed. The current study examines how combinations of contextual features (e.g., social isolation, neighborhood quality, health problems, age discrimination, financial concerns, and recent life events) of later life contribute to overall feelings of stress. Recursive partitioning techniques (regression trees and random forests) were used to examine unique interrelations between predictors of perceived stress in a sample of 282 community-dwelling adults. Trees provided possible examples of equifinality (i.e., subsets of people with similar levels of perceived stress but different predictors) as well as for the identification both of contextual combinations that separated participants with very high and very low perceived stress. Random forest analyses aggregated across many trees based on permuted versions of the data and predictors; loneliness, financial strain, neighborhood strain, ageism, and to some extent life events emerged as important predictors. Interviews with a subsample of participants provided both thick description of the complex relationships identified in the trees, as well as additional risks not appearing in the survey results. Together, the analyses highlight what may be missed when stress is used as a simple unidimensional construct and can guide differential intervention efforts. PMID:21604885

Two EST-derived marker systems for cultivar identification in tree peony.

PubMed

Zhang, J J; Shu, Q Y; Liu, Z A; Ren, H X; Wang, L S; De Keyser, E

2012-02-01

Tree peony (Paeonia suffruticosa Andrews), a woody deciduous shrub, belongs to the section Moutan DC. in the genus of Paeonia of the Paeoniaceae family. To increase the efficiency of breeding, two EST-derived marker systems were developed based on a tree peony expressed sequence tag (EST) database. Using target region amplification polymorphism (TRAP), 19 of 39 primer pairs showed good amplification for 56 accessions with amplicons ranging from 120 to 3,000 bp long, among which 99.3% were polymorphic. In contrast, 7 of 21 primer pairs demonstrated adequate amplification with clear bands for simple sequence repeats (SSRs) developed from ESTs, and a total of 33 alleles were found in 56 accessions. The similarity matrices generated by TRAP and EST-SSR markers were compared, and the Mantel test (r = 0.57778, P = 0.0020) showed a moderate correlation between the two types of molecular markers. TRAP markers were suitable for DNA fingerprinting and EST-SSR markers were more appropriate for discriminating synonyms (the same cultivars with different names due to limited information exchanged among different geographic areas). The two sets of EST-derived markers will be used further for genetic linkage map construction and quantitative trait locus detection in tree peony.

Information categorization approach to literary authorship disputes

NASA Astrophysics Data System (ADS)

Yang, Albert C.-C.; Peng, C.-K.; Yien, H.-W.; Goldberger, Ary L.

2003-11-01

Scientific analysis of the linguistic styles of different authors has generated considerable interest. We present a generic approach to measuring the similarity of two symbolic sequences that requires minimal background knowledge about a given human language. Our analysis is based on word rank order-frequency statistics and phylogenetic tree construction. We demonstrate the applicability of this method to historic authorship questions related to the classic Chinese novel “The Dream of the Red Chamber,” to the plays of William Shakespeare, and to the Federalist papers. This method may also provide a simple approach to other large databases based on their information content.

Formalized description and construction of semantic dictionary of graphic-text spatial relationship

NASA Astrophysics Data System (ADS)

Sun, Yizhong; Xue, Xiaolei; Zhao, Xiaoqin

2008-10-01

Graphic and text are two major elements in exhibiting of the results of urban planning and land administration. In combination, they convey the complex relationship resulting from spatial analysis and decision-making. Accurately interpreting and representing these relationships are important steps towards an intelligent GIS for urban planning. This paper employs concept-hierarchy-tree to formalize graphic-text relationships through a framework of spatial object lexicon, spatial relationship lexicon, restriction lexicon, applied pattern base, and word segmentation rule base. The methodology is further verified and shown effective on several urban planning archives.

Application of Boosting Regression Trees to Preliminary Cost Estimation in Building Construction Projects

PubMed Central

2015-01-01

Among the recent data mining techniques available, the boosting approach has attracted a great deal of attention because of its effective learning algorithm and strong boundaries in terms of its generalization performance. However, the boosting approach has yet to be used in regression problems within the construction domain, including cost estimations, but has been actively utilized in other domains. Therefore, a boosting regression tree (BRT) is applied to cost estimations at the early stage of a construction project to examine the applicability of the boosting approach to a regression problem within the construction domain. To evaluate the performance of the BRT model, its performance was compared with that of a neural network (NN) model, which has been proven to have a high performance in cost estimation domains. The BRT model has shown results similar to those of NN model using 234 actual cost datasets of a building construction project. In addition, the BRT model can provide additional information such as the importance plot and structure model, which can support estimators in comprehending the decision making process. Consequently, the boosting approach has potential applicability in preliminary cost estimations in a building construction project. PMID:26339227

Application of Boosting Regression Trees to Preliminary Cost Estimation in Building Construction Projects.

PubMed

Shin, Yoonseok

2015-01-01

Among the recent data mining techniques available, the boosting approach has attracted a great deal of attention because of its effective learning algorithm and strong boundaries in terms of its generalization performance. However, the boosting approach has yet to be used in regression problems within the construction domain, including cost estimations, but has been actively utilized in other domains. Therefore, a boosting regression tree (BRT) is applied to cost estimations at the early stage of a construction project to examine the applicability of the boosting approach to a regression problem within the construction domain. To evaluate the performance of the BRT model, its performance was compared with that of a neural network (NN) model, which has been proven to have a high performance in cost estimation domains. The BRT model has shown results similar to those of NN model using 234 actual cost datasets of a building construction project. In addition, the BRT model can provide additional information such as the importance plot and structure model, which can support estimators in comprehending the decision making process. Consequently, the boosting approach has potential applicability in preliminary cost estimations in a building construction project.

Potential speciation of morphotypes in the photosymbiotic ascidian Didemnum molle in the Ryukyu Archipelago, Japan

NASA Astrophysics Data System (ADS)

Hirose, M.; Yokobori, S.; Hirose, E.

2009-03-01

Four morphotypes are recognized in the photosymbiotic ascidian Didemnum molle in the Ryukyu Archipelago: three color morphs (white, dark gray, and brown) of small-type colonies and one large-type colony (white with gray patches). The genetic variation among these four morphotypes was investigated by constructing phylogenetic trees based on a 401-bp fragment of the cytochrome oxidase subunit I (COI) gene of 29 specimens collected from five islands (Okinawajima, Sesokojima, Ikeijima, Kumejima, and Ishigakijima). The results support the monophyly of the genus Didemnum and that of the four morphotypes of D. molle. Moreover, the phylogenetic trees discriminated four clades corresponding to each morphotype. The geographic differences of the sequences were much smaller than the differences among the morphotypes, suggesting that the four morphotypes in D. molle are discrete sibling species.

Deriving Safety Cases from Automatically Constructed Proofs

NASA Technical Reports Server (NTRS)

Basir, Nurlida; Denney, Ewen; Fischer, Bernd

2009-01-01

Formal proofs provide detailed justification for the validity of claims and are widely used in formal software development methods. However, they are often complex and difficult to understand, because the formalism in which they are constructed and encoded is usually machine-oriented, and they may also be based on assumptions that are not justified. This causes concerns about the trustworthiness of using formal proofs as arguments in safety-critical applications. Here, we present an approach to develop safety cases that correspond to formal proofs found by automated theorem provers and reveal the underlying argumentation structure and top-level assumptions. We concentrate on natural deduction style proofs, which are closer to human reasoning than resolution proofs, and show how to construct the safety cases by covering the natural deduction proof tree with corresponding safety case fragments. We also abstract away logical book-keeping steps, which reduces the size of the constructed safety cases. We show how the approach can be applied to the proofs found by the Muscadet prover.

Phenotip - a web-based instrument to help diagnosing fetal syndromes antenatally.

PubMed

Porat, Shay; de Rham, Maud; Giamboni, Davide; Van Mieghem, Tim; Baud, David

2014-12-10

Prenatal ultrasound can often reliably distinguish fetal anatomic anomalies, particularly in the hands of an experienced ultrasonographer. Given the large number of existing syndromes and the significant overlap in prenatal findings, antenatal differentiation for syndrome diagnosis is difficult. We constructed a hierarchic tree of 1140 sonographic markers and submarkers, organized per organ system. Subsequently, a database of prenatally diagnosable syndromes was built. An internet-based search engine was then designed to search the syndrome database based on a single or multiple sonographic markers. Future developments will include a database with magnetic resonance imaging findings as well as further refinements in the search engine to allow prioritization based on incidence of syndromes and markers.

Dynamics of investor spanning trees around dot-com bubble.

PubMed

Ranganathan, Sindhuja; Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles.

Dynamics of investor spanning trees around dot-com bubble

PubMed Central

Kivelä, Mikko; Kanniainen, Juho

2018-01-01

We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the minimum spanning tree measures pre-reacted the burst of the bubble. At the same time, we find less clear reactions in the minimal and maximal spanning trees of non-financial and financial institutions around the bubble, which suggests that household investors can have a greater herding tendency around bubbles. PMID:29897973

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

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Programmatic Environmental Assessment for the Construction, Maintenance and Demolition of Communications, Wind, Water, and Camera Towers at the 45th Space Wing, Florida

DTIC Science & Technology

2005-10-01

species (e.g., cogon grass ) have also been identified by 45 SW biologists. 3.1.4.2 Native Vegetation Communities and Wildlife Most (about 80%) of...towers/antenna equipment sites are located at PAFB. All towers are surrounded by either regularly maintained grasses or impervious surfaces...widespread of these is Australian pine. Australian pine trees grow singly or as small, dense groves scattered across the base. In addition, cogon

Environmental Assessment for Construction of the United States Air Force Technical Application Center (AFTAC) on Patrick Air Force Base, Florida (Amended)

DTIC Science & Technology

2010-07-01

ORGANIZATION NAME(S) AND ADDRESS(ES) SpecPro Inc,Environmental Services,12500 San Pedro Avenue Ste 670,San Antonio,TX,78216 8. PERFORMING ORGANIZATION ...FDEP’s state Clearinghouse which provided interagency review by several state organizations . The FDEP determined that the Proposed Action is consistent...locations, etc., that use more organic elements with landscaping, trees, grass, rock, and aesthetic views. The amount of impervious surface for roads and

Environmental Assessment. Construction and Maintenance of Wastewater Pipelines and Lift Stations and Installation of Fiber Optic Conduit at Eglin Air Force Base, Florida

DTIC Science & Technology

2012-06-01

habitats . However, on completion of the project, animals would likely return to the project site. There are known rare/protected species as well as...designated critical habitat occurring within the proposed project area. The threatened and endangered species field survey conducted on October 12- 13...critical habitat of the RCW. Numerous cavity trees used by the birds during breeding season were encounters along the Camp Rudder line route. Known as RCW

Text generation from Taiwanese Sign Language using a PST-based language model for augmentative communication.

PubMed

Wu, Chung-Hsien; Chiu, Yu-Hsien; Guo, Chi-Shiang

2004-12-01

This paper proposes a novel approach to the generation of Chinese sentences from ill-formed Taiwanese Sign Language (TSL) for people with hearing impairments. First, a sign icon-based virtual keyboard is constructed to provide a visualized interface to retrieve sign icons from a sign database. A proposed language model (LM), based on a predictive sentence template (PST) tree, integrates a statistical variable n-gram LM and linguistic constraints to deal with the translation problem from ill-formed sign sequences to grammatical written sentences. The PST tree trained by a corpus collected from the deaf schools was used to model the correspondence between signed and written Chinese. In addition, a set of phrase formation rules, based on trigger pair category, was derived for sentence pattern expansion. These approaches improved the efficiency of text generation and the accuracy of word prediction and, therefore, improved the input rate. For the assessment of practical communication aids, a reading-comprehension training program with ten profoundly deaf students was undertaken in a deaf school in Tainan, Taiwan. Evaluation results show that the literacy aptitude test and subjective satisfactory level are significantly improved.

Graph-based layout analysis for PDF documents

NASA Astrophysics Data System (ADS)

Xu, Canhui; Tang, Zhi; Tao, Xin; Li, Yun; Shi, Cao

2013-03-01

To increase the flexibility and enrich the reading experience of e-book on small portable screens, a graph based method is proposed to perform layout analysis on Portable Document Format (PDF) documents. Digital born document has its inherent advantages like representing texts and fractional images in explicit form, which can be straightforwardly exploited. To integrate traditional image-based document analysis and the inherent meta-data provided by PDF parser, the page primitives including text, image and path elements are processed to produce text and non text layer for respective analysis. Graph-based method is developed in superpixel representation level, and page text elements corresponding to vertices are used to construct an undirected graph. Euclidean distance between adjacent vertices is applied in a top-down manner to cut the graph tree formed by Kruskal's algorithm. And edge orientation is then used in a bottom-up manner to extract text lines from each sub tree. On the other hand, non-textual objects are segmented by connected component analysis. For each segmented text and non-text composite, a 13-dimensional feature vector is extracted for labelling purpose. The experimental results on selected pages from PDF books are presented.

Plasticity in dendroclimatic response across the distribution range of Aleppo Pine (Pinus halepensis)

Treesearch

Martin de Luis; Katarina Cufar; Alfredo Di Filippo; Klemen Novak; Andreas Papadopoulos; Gianluca Piovesan; Cyrille B. K. Rathgeber; José Raventós; Miguel Angel Saz; Kevin T. Smith

2013-01-01

We investigated the variability of the climate-growth relationship of Aleppo pine across its distribution range in the Mediterranean Basin. We constructed a network of tree-ring index chronologies from 63 sites across the region. Correlation function analysis identified the relationships of tree-ring index to climate factors for each site. We also estimated the...

On Tree-Based Phylogenetic Networks.

PubMed

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Expert risk perceptions and the social amplification of risk: A case study in invasive tree pests and diseases.

PubMed

Urquhart, Julie; Potter, Clive; Barnett, Julie; Fellenor, John; Mumford, John; Quine, Christopher P

2017-11-01

The Social Amplification of Risk Framework (SARF) is often used as a conceptual tool for studying diverse risk perceptions associated with environmental hazards. While widely applied, it has been criticised for implying that it is possible to define a benchmark 'real' risk that is determined by experts and around which public risk perceptions can subsequently become amplified. It has been argued that this objectification of risk is particularly problematic when there are high levels of scientific uncertainty and a lack of expert consensus about the nature of a risk and its impacts. In order to explore this further, this paper examines how 'experts' - defined in this case as scientists, policy makers, outbreak managers and key stakeholders - construct and assemble their understanding of the risks associated with two invasive tree pest and disease outbreaks in the UK, ash dieback and oak processionary moth. Through semi-structured interviews with experts in each of the case study outbreaks, the paper aims to better understand the nature of information sources drawn on to construct perceptions of tree health risks, especially when uncertainty is prevalent. A key conclusion is that risk assessment is a socially-mediated, relational and incremental process with experts drawing on a range of official, anecdotal and experiential sources of information, as well as reference to past events in order to assemble the risk case. Aligned with this, experts make attributions about public concern, especially when the evidence base is incomplete and there is a need to justify policy and management actions and safeguard reputation.

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

PubMed Central

2010-01-01

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

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

PubMed

Thomas, Paul D

2010-06-09

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

Where to nest? Ecological determinants of chimpanzee nest abundance and distribution at the habitat and tree species scale.

PubMed

Carvalho, Joana S; Meyer, Christoph F J; Vicente, Luis; Marques, Tiago A

2015-02-01

Conversion of forests to anthropogenic land-uses increasingly subjects chimpanzee populations to habitat changes and concomitant alterations in the plant resources available to them for nesting and feeding. Based on nest count surveys conducted during the dry season, we investigated nest tree species selection and the effect of vegetation attributes on nest abundance of the western chimpanzee, Pan troglodytes verus, at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau, a forest-savannah mosaic widely disturbed by humans. Further, we assessed patterns of nest height distribution to determine support for the anti-predator hypothesis. A zero-altered generalized linear mixed model showed that nest abundance was negatively related to floristic diversity (exponential form of the Shannon index) and positively with the availability of smaller-sized trees, reflecting characteristics of dense-canopy forest. A positive correlation between nest abundance and floristic richness (number of plant species) and composition indicated that species-rich open habitats are also important in nest site selection. Restricting this analysis to feeding trees, nest abundance was again positively associated with the availability of smaller-sized trees, further supporting the preference for nesting in food tree species from dense forest. Nest tree species selection was non-random, and oil palms were used at a much lower proportion (10%) than previously reported from other study sites in forest-savannah mosaics. While this study suggests that human disturbance may underlie the exclusive arboreal nesting at LCNP, better quantitative data are needed to determine to what extent the construction of elevated nests is in fact a response to predators able to climb trees. Given the importance of LCNP as refuge for Pan t. verus our findings can improve conservation decisions for the management of this important umbrella species as well as its remaining suitable habitats. © 2014 Wiley Periodicals, Inc.

The transmission process: A combinatorial stochastic process for the evolution of transmission trees over networks.

PubMed

Sainudiin, Raazesh; Welch, David

2016-12-07

We derive a combinatorial stochastic process for the evolution of the transmission tree over the infected vertices of a host contact network in a susceptible-infected (SI) model of an epidemic. Models of transmission trees are crucial to understanding the evolution of pathogen populations. We provide an explicit description of the transmission process on the product state space of (rooted planar ranked labelled) binary transmission trees and labelled host contact networks with SI-tags as a discrete-state continuous-time Markov chain. We give the exact probability of any transmission tree when the host contact network is a complete, star or path network - three illustrative examples. We then develop a biparametric Beta-splitting model that directly generates transmission trees with exact probabilities as a function of the model parameters, but without explicitly modelling the underlying contact network, and show that for specific values of the parameters we can recover the exact probabilities for our three example networks through the Markov chain construction that explicitly models the underlying contact network. We use the maximum likelihood estimator (MLE) to consistently infer the two parameters driving the transmission process based on observations of the transmission trees and use the exact MLE to characterize equivalence classes over the space of contact networks with a single initial infection. An exploratory simulation study of the MLEs from transmission trees sampled from three other deterministic and four random families of classical contact networks is conducted to shed light on the relation between the MLEs of these families with some implications for statistical inference along with pointers to further extensions of our models. The insights developed here are also applicable to the simplest models of "meme" evolution in online social media networks through transmission events that can be distilled from observable actions such as "likes", "mentions", "retweets" and "+1s" along with any concomitant comments. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Disturbance legacies and climate jointly drive tree growth and mortality in an intensively studied boreal forest.

PubMed

Bond-Lamberty, Ben; Rocha, Adrian V; Calvin, Katherine; Holmes, Bruce; Wang, Chuankuan; Goulden, Michael L

2014-01-01

Most North American forests are at some stage of post-disturbance regrowth, subject to a changing climate, and exhibit growth and mortality patterns that may not be closely coupled to annual environmental conditions. Distinguishing the possibly interacting effects of these processes is necessary to put short-term studies in a longer term context, and particularly important for the carbon-dense, fire-prone boreal forest. The goals of this study were to combine dendrochronological sampling, inventory records, and machine-learning algorithms to understand how tree growth and death have changed at one highly studied site (Northern Old Black Spruce, NOBS) in the central Canadian boreal forest. Over the 1999-2012 inventory period, mean tree diameter increased even as stand density and basal area declined significantly. Tree mortality averaged 1.4 ± 0.6% yr-(1), with most mortality occurring in medium-sized trees; new recruitment was minimal. There have been at least two, and probably three, significant influxes of new trees since stand initiation, but none in recent decades. A combined tree ring chronology constructed from sampling in 2001, 2004, and 2012 showed several periods of extreme growth depression, with increased mortality lagging depressed growth by ~5 years. Higher minimum and maximum air temperatures exerted a negative influence on tree growth, while precipitation and climate moisture index had a positive effect; both current- and previous-year data exerted significant effects. Models based on these variables explained 23-44% of the ring-width variability. We suggest that past climate extremes led to significant mortality still visible in the current forest structure, with decadal dynamics superimposed on slower patterns of fire and succession. These results have significant implications for our understanding of previous work at NOBS, the carbon sequestration capability of old-growth stands in a disturbance-prone landscape, and the sustainable management of regional forests in a changing climate.

Benefit-based tree valuation

Treesearch

E.G. McPherson

2007-01-01

Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...

GIS interpolations of witness tree records (1839-1866) for northern Wisconsin at multiple scales

USGS Publications Warehouse

He, H.S.; Mladenoff, D.J.; Sickley, T.A.; Guntenspergen, G.R.

2000-01-01

To construct forest landscape of pre-European settlement periods, we developed a GIS interpolation approach to convert witness tree records of the U.S. General Land Office (GLO) survey from point to polygon data, which better described continuously distributed vegetation. The witness tree records (1839-1866) were processed for a 3-million ha landscape in northern Wisconsin, U.S.A. at different scales. We provided implications of processing results at each scale. Compared with traditional GLO mapping that has fixed mapping scales and generalized classifications, our approach allows presettlement forest landscapes to be analysed at the individual species level and reconstructed under various classifications. We calculated vegetation indices including relative density, dominance, and importance value for each species, and quantitatively described the possible outcomes when GLO records are analysed at three different scales (resolution). The 1 x 1-section resolution preserved spatial information but derived the most conservative estimates of species distributions measured in percentage area, which increased at coarser resolutions. Such increases under the 2 x 2-section resolution were in the order of three to four times for the least common species, two to three times for the medium to most common species, and one to two times for the most common or highly contagious species. We marred the distributions of hemlock and sugar maple from the pre-European settlement period based on their witness tree locations and reconstructed presettlement forest landscapes based on species importance values derived for all species. The results provide a unique basis to further study land cover changes occurring after European settlement.

HBT+: an improved code for finding subhaloes and building merger trees in cosmological simulations

NASA Astrophysics Data System (ADS)

Han, Jiaxin; Cole, Shaun; Frenk, Carlos S.; Benitez-Llambay, Alejandro; Helly, John

2018-02-01

Dark matter subhalos are the remnants of (incomplete) halo mergers. Identifying them and establishing their evolutionary links in the form of merger trees is one of the most important applications of cosmological simulations. The HBT (Hierachical Bound-Tracing) code identifies haloes as they form and tracks their evolution as they merge, simultaneously detecting subhaloes and building their merger trees. Here we present a new implementation of this approach, HBT+ , that is much faster, more user friendly, and more physically complete than the original code. Applying HBT+ to cosmological simulations, we show that both the subhalo mass function and the peak-mass function are well fitted by similar double-Schechter functions. The ratio between the two is highest at the high-mass end, reflecting the resilience of massive subhaloes that experience substantial dynamical friction but limited tidal stripping. The radial distribution of the most-massive subhaloes is more concentrated than the universal radial distribution of lower mass subhaloes. Subhalo finders that work in configuration space tend to underestimate the masses of massive subhaloes, an effect that is stronger in the host centre. This may explain, at least in part, the excess of massive subhaloes in galaxy cluster centres inferred from recent lensing observations. We demonstrate that the peak-mass function is a powerful diagnostic of merger tree defects, and the merger trees constructed using HBT+ do not suffer from the missing or switched links that tend to afflict merger trees constructed from more conventional halo finders. We make the HBT+ code publicly available.

An investigation of hydraulic limitation and compensation in large, old Douglas-fir trees.

PubMed

McDowell, Nate G; Phillips, Nathan; Lunch, Claire; Bond, Barbara J; Ryan, Michael G

2002-08-01

The hydraulic limitation hypothesis (Ryan and Yoder 1997) proposes that leaf-specific hydraulic conductance (kl) and stomatal conductance (gs) decline as trees grow taller, resulting in decreased carbon assimilation. We tested the hydraulic limitation hypothesis by comparison of canopy-dominant Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) trees in stands that were approximately 15 m (20 years old), 32 m (40 years old) and 60 m (> 450 years old) tall in Wind River, Washington, USA. Carbon isotope discrimination (Delta) declined with tree height (18.6, 17.6 and 15.9 per thousand for stands 15, 32 and 60 m tall, respectively) indicating that gs may have declined proportionally with tree height in the spring months, when carbon used in the construction of new foliage is assimilated. Hydraulic conductance decreased by 44% as tree height increased from 15 to > 32 m, and showed a further decline of 6% with increasing height. The general nonlinear pattern of kl versus height was predicted by a model based on Darcy's Law. Stemwood growth efficiency also declined nonlinearly with height (60, 35 and 28 g C m-2 leaf area for the 15-, 32- and 60-m stands, respectively). Unlike kl and growth efficiency, gs and photosynthesis (A) during summer drought did not decrease with height. The lack of decline in cuvette-based A indicates that reduced A, at least during summer months, is not responsible for the decline in growth efficiency. The difference between the trend in gs and A and that in kl and D may indicate temporal changes (spring versus summer) in the response of gas exchange to height-related changes in kl or it may be a result of measurement inadequacies. The formal hydraulic limitation hypothesis was not supported by our mid-summer gs and A data. Future tests of the hydraulic limitation hypothesis in this forest should be conducted in the spring months, when carbon uptake is greatest. We used a model based on Darcy's Law to quantify the extent to which compensating mechanisms buffer hydraulic limitations to gas exchange. Sensitivity analyses indicated that without the observed increases in the soil-to-leaf water potential differential (DeltaPsi) and decreases in the leaf area/sapwood area ratio, kl would have been reduced by more than 70% in the 60-m trees compared with the 15-m trees, instead of the observed decrease of 44%. However, compensation may have a cost; for example, the greater DeltaPsi of the largest trees was associated with smaller tracheid diameters and increased sapwood cavitation, which may have a negative feedback on kl and gs.

Fractal spectral triples on Kellendonk's C∗-algebra of a substitution tiling

NASA Astrophysics Data System (ADS)

Mampusti, Michael; Whittaker, Michael F.

2017-02-01

We introduce a new class of noncommutative spectral triples on Kellendonk's C∗-algebra associated with a nonperiodic substitution tiling. These spectral triples are constructed from fractal trees on tilings, which define a geodesic distance between any two tiles in the tiling. Since fractals typically have infinite Euclidean length, the geodesic distance is defined using Perron-Frobenius theory, and is self-similar with scaling factor given by the Perron-Frobenius eigenvalue. We show that each spectral triple is θ-summable, and respects the hierarchy of the substitution system. To elucidate our results, we construct a fractal tree on the Penrose tiling, and explicitly show how it gives rise to a collection of spectral triples.

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

PubMed

Deshwar, Amit G; Vembu, Shankar; Morris, Quaid

2015-01-01

Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor…

Identification of Some Zeolite Group Minerals by Application of Artificial Neural Network and Decision Tree Algorithm Based on SEM-EDS Data

NASA Astrophysics Data System (ADS)

Akkaş, Efe; Evren Çubukçu, H.; Akin, Lutfiye; Erkut, Volkan; Yurdakul, Yasin; Karayigit, Ali Ihsan

2016-04-01

Identification of zeolite group minerals is complicated due to their similar chemical formulas and habits. Although the morphologies of various zeolite crystals can be recognized under Scanning Electron Microscope (SEM), it is relatively more challenging and problematic process to identify zeolites using their mineral chemical data. SEMs integrated with energy dispersive X-ray spectrometers (EDS) provide fast and reliable chemical data of minerals. However, considering elemental similarities of characteristic chemical formulae of zeolite species (e.g. Clinoptilolite ((Na,K,Ca)2 -3Al3(Al,Si)2Si13O3612H2O) and Erionite ((Na2,K2,Ca)2Al4Si14O36ṡ15H2O)) EDS data alone does not seem to be sufficient for correct identification. Furthermore, the physical properties of the specimen (e.g. roughness, electrical conductivity) and the applied analytical conditions (e.g. accelerating voltage, beam current, spot size) of the SEM-EDS should be uniform in order to obtain reliable elemental results of minerals having high alkali (Na, K) and H2O (approx. %14-18) contents. This study which was funded by The Scientific and Technological Research Council of Turkey (TUBITAK Project No: 113Y439), aims to construct a database as large as possible for various zeolite minerals and to develop a general prediction model for the identification of zeolite minerals using SEM-EDS data. For this purpose, an artificial neural network and rule based decision tree algorithm were employed. Throughout the analyses, a total of 1850 chemical data were collected from four distinct zeolite species, (Clinoptilolite-Heulandite, Erionite, Analcime and Mordenite) observed in various rocks (e.g. coals, pyroclastics). In order to obtain a representative training data set for each minerals, a selection procedure for reference mineral analyses was applied. During the selection procedure, SEM based crystal morphology data, XRD spectra and re-calculated cationic distribution, obtained by EDS have been used for the characterization of the training set. Consequently, for each zeolite species 250 EDS data (as elemental intensities) used for training and 200 ±50 analyses were tested. Finally, two prediction models were developed. The constructed models with various cross-correlation values (r) yielded an average accuracy of >91% for the best predictions using C5.0 Decision Tree algorithm and back propagation artificial neural network. Despite having similar accuracies, the developed models exhibit different prediction behaviors for some zeolite minerals. The results demonstrate that artificial neural network as a nonlinear tool and decision tree algorithm as a rule based prediction model would be employed to provide considerably efficient and reliable identification/classification of some zeolite minerals regardless of their similar elemental compositions. Keywords: mineral identification; zeolites; energy dispersive spectrometry; artificial neural networks; decision tree.

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL

PubMed Central

Hua, Guan-Jie; Hung, Che-Lun; Lin, Chun-Yuan; Wu, Fu-Che; Chan, Yu-Wei; Tang, Chuan Yi

2017-01-01

A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists. In this work, a novel parallel Unweighted Pair Group Method with Arithmetic Mean approach on multiple Graphics Processing Units is proposed to construct a phylogenetic tree from extremely large set of sequences. The experimental results present that the proposed approach on a DGX-1 server with 8 NVIDIA P100 graphic cards achieves approximately 3-fold to 7-fold speedup over the implementation of Unweighted Pair Group Method with Arithmetic Mean on a modern CPU and a single GPU, respectively. PMID:29051701

MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL.

PubMed

Hua, Guan-Jie; Hung, Che-Lun; Lin, Chun-Yuan; Wu, Fu-Che; Chan, Yu-Wei; Tang, Chuan Yi

2017-01-01

A phylogenetic tree is a visual diagram of the relationship between a set of biological species. The scientists usually use it to analyze many characteristics of the species. The distance-matrix methods, such as Unweighted Pair Group Method with Arithmetic Mean and Neighbor Joining, construct a phylogenetic tree by calculating pairwise genetic distances between taxa. These methods have the computational performance issue. Although several new methods with high-performance hardware and frameworks have been proposed, the issue still exists. In this work, a novel parallel Unweighted Pair Group Method with Arithmetic Mean approach on multiple Graphics Processing Units is proposed to construct a phylogenetic tree from extremely large set of sequences. The experimental results present that the proposed approach on a DGX-1 server with 8 NVIDIA P100 graphic cards achieves approximately 3-fold to 7-fold speedup over the implementation of Unweighted Pair Group Method with Arithmetic Mean on a modern CPU and a single GPU, respectively.

A laid-back trip through the Hennigian Forests

PubMed Central

2017-01-01

Background This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea’s efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as “source” of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation. Methods We focused our study on the binary data. We wrote the simple ruby-based script FORESTER version 1.0 that helps represent a binary matrix as an array of the rooted trees (as a “Hennigian forest”). The binary representations of the genomic (DNA) data have been made by script 1001. The Average Consensus method as well as the standard Maximum Parsimony (MP) approach has been used to analyze the data. Principle findings The binary matrix may be easily re-written as a set of rooted trees (maximal relationships). The latter might be analyzed by the Average Consensus method. Paradoxically, this method, if applied to the Hennigian forests, in principle can help to identify clades despite the absence of the direct evidence from the primary data. Our approach may handle the clock- or non clock-like matrices, as well as the hypothetical, molecular or morphological data. Discussion Our proposal clearly differs from the numerous phenetic alignment-free techniques of the construction of the phylogenetic trees. Dealing with the relations, not with the actual “data” also distinguishes our approach from all optimization-based methods, if the optimization is defined as a way to reconstruct the sequences of the character-state changes on a tree, either the standard alignment-based techniques or the “direct” alignment-free procedure. We are not viewing our recent framework as an alternative to the three-taxon statement analysis (3TA), but there are two major differences between our recent proposal and the 3TA, as originally designed and implemented: (1) the 3TA deals with the three-taxon statements or minimal relationships. According to the logic of 3TA, the set of the minimal trees must be established as a binary matrix and used as an input for the parsimony program. In this paper, we operate directly with maximal relationships written just as trees, not as binary matrices, while also using the Average Consensus method instead of the MP analysis. The solely ‘reversal’-based groups can always be found by our method without the separate scoring of the putative reversals before analyses. PMID:28740753

[Phylogenetic and diversity analysis of Acidithiobacillus spp. based on 16S rRNA and RubisCO genes homologues].

PubMed

Liu, Minrui; Lin, Pengwu; Qi, Xing'e; Ni, Yongqing

2016-04-14

The purpose of the study was to reveal geographic region-related Acidithiobacillus spp. distribution and allopatric speciation. Phylogenetic and diversity analysis was done to expand our knowledge on microbial phylogeography, diversity-maintaining mechanisms and molecular biogeography. We amplified 16S rRNA gene and RubisCO genes to construct corresponding phylogenetic trees based on the sequence homology and analyzed genetic diversity of Acidithiobacillus spp.. Thirty-five strains were isolated from three different regions in China (Yunnan, Hubei, Xinjiang). The whole isolates were classified into five groups. Four strains were identified as A. ferrivorans, six as A. ferridurans, YNTR4-15 Leptspirillum ferrooxidans and HBDY3-31 as Leptospirillum ferrodiazotrophum. The remaining strains were identified as A. ferrooxidans. Analysis of cbbL and cbbM genes sequences of representative 26 strains indicated that cbbL gene of 19 were two copies (cbbL1 and cbbL2) and 7 possessed only cbbL1. cbbM gene was single copy. In nucleotide-based trees, cbbL1 gene sequences of strains were separated into three sequence types, and the cbbL2 was similar to cbbL1 with three types. Codon bias of RubisCO genes was not obvious in Acidithiobacillus spp.. Strains isolated from three different regions in China indicated a great genetic diversity in Acidithiobacillus spp. and their 16S rRNA/RubisCO genes sequence was of significant difference. Phylogenetic tree based on 16S rRNA genes and RubisCO genes was different in Acidithiobacillus spp..

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

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

[Individual tree diameter increment model for natural Betula platyphylla forests based on meteorological factors].

PubMed

Zhang, Hai Ping; Li, Feng Ri; Dong, Li Hu; Liu, Qiang

2017-06-18

Based on the 212 re-measured permanent plots for natural Betula platyphylla fore-sts in Daxing'an Mountains and Xiaoxing'an Mountains and 30 meteorological stations data, an individual tree growth model based on meteorological factors was constructed. The differences of stand and meteorological factors between Daxing'an Mountains and Xiaoxing'an Mountains were analyzed and the diameter increment model including the regional effects was developed by dummy variable approach. The results showed that the minimum temperature (T g min ) and mean precipitation (P g m ) in growing season were the main meteorological factors which affected the diameter increment in the two study areas. T g min and P g m were positively correlated with the diameter increment, but the influence strength of T g min was obviously different between the two research areas. The adjusted coefficient of determination (R a 2 ) of the diameter increment model with meteorological factors was 0.56 and had an 11% increase compared to the one without meteorological factors. It was concluded that meteorological factors could well explain the diameter increment of B. platyphylla. R a 2 of the model with regional effects was 0.59, and increased by 18% compared to the one without regional effects, and effectively solved the incompatible problem of parameters between the two research areas. The validation results showed that the individual tree diameter growth model with regional effect had the best prediction accuracy in estimating the diameter increment of B. platyphylla. The mean error, mean absolute error, mean error percent and mean prediction error percent were 0.0086, 0.4476, 5.8% and 20.0%, respectively. Overall, dummy variable model of individual tree diameter increment based on meteorological factors could well describe the diameter increment process of natural B. platyphylla in Daxing'an Mountains and Xiaoxing'an Mountains.

The Floating Potential Probe (FPP) taken during the third EVA of STS-97

NASA Image and Video Library

2000-12-07

STS097-376-029 (7 December 2000) --- Space walking Endeavour astronauts topped off their scheduled space walk activities with an image of an evergreen tree placed atop the P6 solar array structure, the highest point in their construction project. They then took this photo of the "tree" before returning to the shirt-sleeve environment of the Space Shuttle Endeavour.

Constructing New York City's urban forest. The politics and governance of the MillionTreesNYC campaign

Treesearch

Lindsay K. Campbell

2014-01-01

In 2005-2006, bureaucrats at the New York City Department of Parks and Recreation (DPR) began to marshal quantitative evidence to argue for investment in tree planting as part of Mayor Bloomberg's long-term sustainability plan, PlaNYC 2030, launched in 2007. Concurrently, Bette Midler—the celebrity founder of the non-profit New York Restoration Project (...

Component biomass equations for black spruce in Maine

Treesearch

M. M. Czapowskyj; D. J. Robison; R. D. Briggs; E. H. White; E. H. White

1985-01-01

Component biomass prediction equations are presented for young black spruce (Picea mariana B.S.P. (Mill,:)) in northern Maine. A weighted least squares model was used to construct the eq~iationsfo r small trees from 1 to 15 cm d.b.h., and an ordinary least squares model for trees less than 2 m in height. A linearized allometric model was also tested but was not used....

Monitoring moisture content, temperature, and humidity in whole-tree pine chip piles

Treesearch

John Klepac; Dana Mitchell; Jason Thompson

2015-01-01

Two whole-tree chip piles were monitored for moisture content, temperature, and relative humidity from October 8th, 2010 to March 16th, 2011 at a location in south Alabama. Initial moisture content samples were collected immediately after chips were delivered to the study location on October 8th for Pile 1 and October 22nd for Pile 2. During pile construction, Lascar...

Natural enemies implicated in the regulation of an invasive pest: a life table analysis of the population dynamics of the emerald ash borer

Treesearch

Jian J. Duan; Kristopher J. Abell; Leah S. Bauer; Juli Gould; Roy. Van Driesche

2014-01-01

The emerald ash borer Agrilus planipennis Fairmaire is a serious invasive forest pest of ash (Fraxinus) trees in North America. Life tables were constructed for both experimentally established cohorts and wild populations of A. planipennis on healthy host trees from 2008 to 2011 in six forests in central Michigan...

Constructing Artifical Red-Cockaded Woodpecker Cavities

Treesearch

David H. Allen

1991-01-01

A complete guide is provided for excavating red-cockaded woodpecker (Picoides borealis) cavities. A hole 4 inches wide by 10 inches high by 6 inches deep is cut from a live pine(Pinusspp.) tree with a chainsaw, and a prefabricated cavity is inserted. Cavities can be excavated in pines of any age, but the diameter of the tree at the height of insertion must be greater...

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

Treesearch

Teresa J.F. Fonseca; Bernard R. Parresol

2001-01-01

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

Final Environmental Assessment, Construct Guard House at Cape Cod Air Force Station, Massachusetts

DTIC Science & Technology

2004-01-01

Pine - Scrub Oak Forest Northern Pine Barren with Oak Forest... barren vegetation communities were identified on Cape Cod AFS, pitch pine – scrub oak barren and northern pine barren with oak trees. The majority of...area on the east side of the access road just north of the installation is northern pine barren with oak trees. Pitch pine and scarlet oak

[Species composition and spatial structure of plants in urban parks of Beijing].

PubMed

Zhao, Juan-Juan; Ouyang, Zhi-Yun; Zheng, Hua; Xu, Wei-Hua; Wang, Xiao-Ke

2009-02-01

By the method of stratified random sampling, the species composition and spatial structure of the plants in 53 parks in Beijing urban area were investigated, aimed to provide basic information for the protection of plant diversity in the parks and the management of the parks. A total of 492 plant species belong to 96 families and 283 genera were recorded. Based on the data of 21 investigation items about the trees, shrubs, and grasses in the study area and related statistical analyses, the plant structural patterns commonly seen in the green space of the parks of Beijing urban area were introduced. Among the plants in the parks, native species occupied 53.86% of the total. The chorological composition of the genera embraced broad kinds of geographical elements in China, and the predominance of dominant plants was remarkable. In most green patches of the parks, herbaceous species were more abundant and had higher coverage, shrubs had relatively low coverage and were less beneath tree canopy, and trees and shrubs had lower species richness and density. The canopy breadth and the diameter of breast height of trees as well as the breadth of shrubs and the heights of trees and shrubs were basically at the second grade, but the canopy structure of the trees were better, with good conditions of sunlight and growth. The crown missing of the shrubs was relatively low. It was suggested from correlation analyses and document survey of Beijing parks construction history that park landscape design, alien species introduction; and cultivation management were the main factors affecting the species composition and spatial structure of the plants in Beijing urban parks.

Disturbance legacies and climate jointly drive tree growth and mortality in an intensively studied boreal forest

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

Bond-Lamberty, Benjamin; Rocha, Adrian; Calvin, Katherine V.

2014-01-01

How will regional growth and mortality change with even relatively small climate shifts, even independent of catastrophic disturbances? This question is particularly acute for the North American boreal forest, which is carbon-dense and subject The goals of this study were to combine dendrochronological sampling, inventory records, and machine-learning algorithms to understand how tree growth and death have changed at one highly studied site (Northern Old Black Spruce, NOBS) in the central Canadian boreal forest. Over the 1999-2012 inventory period, mean DBH increased even as stand density and basal area declined significantly from 41.3 to 37.5 m2 ha-1. Tree mortality averagedmore » 1.4±0.6% yr-1, with most mortality occurring in medium-sized trees. A combined tree ring chronology constructed from 2001, 2004, and 2012 sampling showed several periods of extreme growth depression, with increased mortality lagging depressed growth by ~5 years. Minimum and maximum air temperatures exerted a negative influence on tree growth, while precipitation and climate moisture index had a positive effect; both current- and previous-year data exerted significant effects. Models based on these variables explained 23-44% of the ring-width variability. There have been at least one, and probably two, significant recruitment episodes since stand initiation, and we infer that past climate extremes led to significant NOBS mortality still visible in the current forest structure. These results imply that a combination of successional and demographic processes, along with mortality driven by abiotic factors, continue to affect the stand, with significant implications for our understanding of previous work at NOBS and the sustainable management of regional forests.« less

Development of Riparian Tree Roots in Compacted Coarse Gravel Mixtures - Analysis of Alternative Measures to Decrease Asphalt Damages caused by Tree Roots

NASA Astrophysics Data System (ADS)

Gruber, Eva; Weissteiner, Clemens; Rauch, Hans Peter

2017-04-01

Tree roots are a major concern in the maintenance of roads in general, and infrequently used paths along rivers and cycling lanes specifically. High repairing costs paired with insufficient mitigation measures lead to the importance of developing a strategy to prevent tree roots from entering the infrastructural construction. Adding to this, damaged asphalt is a threat to cyclists and pedestrians, which makes the search for a solution altogether a pressing matter. In the process of an ongoing project with ViaDonau, during which different measures are tested on-site along the Danube, a field experiment has been set up to test the impact of coarse gravel as sublayer material on the development of tree roots. The aim is to present a recommendation of a certain gravel mixture to use as sublayer. It should reduce root penetration into the pavement construction and increases a drainage effect to prevent condensation and high moisture levels underneath the asphalt. The present work is focusing on the root development of the field experiment after two vegetation periods. The field experiment simulates a concrete-paved road with a vegetation strip next to it. The setup is identical for all fields with poplars and willow cuttings planted along the paved area and the possibility for the tree roots to enter the sublayers of the pavement. These sublayers are made up of six boxes filled with differently sized coarse gravel mixtures (0/32, 8/32, 8/32 hydraulic bound mixture, 16/32, 0/63 and 16/63) to test if the composition has an impact on the root penetration and permanent development. Root dry biomass data in the boxes was collected in 27 subplots. Root dry biomass data was put in relation to the biomass data of the vegetated soil strips in order to consider different biomass development. Additionally for one column of the subplots tree roots were scanned to gain information on the diameter distribution of the collected biomass. Biomass data was also compared to last year's to state the biomass development and a possible establishment of the tree roots. The prevailing hypothesis is that a mixture with coarse gravel is more likely to inhibit roots from entering the construction because of its draining features due to the lack of fine sediments. As for now, this assumption is mostly coherent with the results of the field experiment. Nevertheless, it seems that the best results were collected of the box with the 8/32 hydraulic bound mixture.

Eleventh-century shift in timber procurement areas for the great houses of Chaco Canyon

PubMed Central

Guiterman, Christopher H.; Dean, Jeffrey S.

2016-01-01

An enduring mystery from the great houses of Chaco Canyon is the origin of more than 240,000 construction timbers. We evaluate probable timber procurement areas for seven great houses by applying tree-ring width-based sourcing to a set of 170 timbers. To our knowledge, this is the first use of tree rings to assess timber origins in the southwestern United States. We found that the Chuska and Zuni Mountains (>75 km distant) were the most likely sources, accounting for 70% of timbers. Most notably, procurement areas changed through time. Before 1020 Common Era (CE) nearly all timbers originated from the Zunis (a previously unrecognized source), but by 1060 CE the Chuskas eclipsed the Zuni area in total wood imports. This shift occurred at the onset of Chaco florescence in the 11th century, a time with substantial expansion of existing great houses and the addition of seven new great houses in the Chaco Core area. It also coincides with the proliferation of Chuskan stone tools and pottery in the archaeological record of Chaco Canyon, further underscoring the link between land use and occupation in the Chuska area and the peak of great house construction. Our findings, based on the most temporally specific and replicated evidence of Chacoan resource procurement obtained to date, corroborate the long-standing but recently challenged interpretation that large numbers of timbers were harvested and transported from distant mountain ranges to build the great houses at Chaco Canyon. PMID:26644552

Eleventh-century shift in timber procurement areas for the great houses of Chaco Canyon.

PubMed

Guiterman, Christopher H; Swetnam, Thomas W; Dean, Jeffrey S

2016-02-02

An enduring mystery from the great houses of Chaco Canyon is the origin of more than 240,000 construction timbers. We evaluate probable timber procurement areas for seven great houses by applying tree-ring width-based sourcing to a set of 170 timbers. To our knowledge, this is the first use of tree rings to assess timber origins in the southwestern United States. We found that the Chuska and Zuni Mountains (>75 km distant) were the most likely sources, accounting for 70% of timbers. Most notably, procurement areas changed through time. Before 1020 Common Era (CE) nearly all timbers originated from the Zunis (a previously unrecognized source), but by 1060 CE the Chuskas eclipsed the Zuni area in total wood imports. This shift occurred at the onset of Chaco florescence in the 11th century, a time with substantial expansion of existing great houses and the addition of seven new great houses in the Chaco Core area. It also coincides with the proliferation of Chuskan stone tools and pottery in the archaeological record of Chaco Canyon, further underscoring the link between land use and occupation in the Chuska area and the peak of great house construction. Our findings, based on the most temporally specific and replicated evidence of Chacoan resource procurement obtained to date, corroborate the long-standing but recently challenged interpretation that large numbers of timbers were harvested and transported from distant mountain ranges to build the great houses at Chaco Canyon.

Quantifying construction and demolition waste: An analytical review

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

Wu, Zezhou; Yu, Ann T.W., E-mail: bsannyu@polyu.edu.hk; Shen, Liyin

2014-09-15

Highlights: • Prevailing C and D waste quantification methodologies are identified and compared. • One specific methodology cannot fulfill all waste quantification scenarios. • A relevance tree for appropriate quantification methodology selection is proposed. • More attentions should be paid to civil and infrastructural works. • Classified information is suggested for making an effective waste management plan. - Abstract: Quantifying construction and demolition (C and D) waste generation is regarded as a prerequisite for the implementation of successful waste management. In literature, various methods have been employed to quantify the C and D waste generation at both regional and projectmore » levels. However, an integrated review that systemically describes and analyses all the existing methods has yet to be conducted. To bridge this research gap, an analytical review is conducted. Fifty-seven papers are retrieved based on a set of rigorous procedures. The characteristics of the selected papers are classified according to the following criteria - waste generation activity, estimation level and quantification methodology. Six categories of existing C and D waste quantification methodologies are identified, including site visit method, waste generation rate method, lifetime analysis method, classification system accumulation method, variables modelling method and other particular methods. A critical comparison of the identified methods is given according to their characteristics and implementation constraints. Moreover, a decision tree is proposed for aiding the selection of the most appropriate quantification method in different scenarios. Based on the analytical review, limitations of previous studies and recommendations of potential future research directions are further suggested.« less

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

PubMed

Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Study on Ecological Risk Assessment of Guangxi Coastal Zone Based on 3s Technology

NASA Astrophysics Data System (ADS)

Zhong, Z.; Luo, H.; Ling, Z. Y.; Huang, Y.; Ning, W. Y.; Tang, Y. B.; Shao, G. Z.

2018-05-01

This paper takes Guangxi coastal zone as the study area, following the standards of land use type, divides the coastal zone of ecological landscape into seven kinds of natural wetland landscape types such as woodland, farmland, grassland, water, urban land and wetlands. Using TM data of 2000-2015 such 15 years, with the CART decision tree algorithm, for analysis the characteristic of types of landscape's remote sensing image and build decision tree rules of landscape classification to extract information classification. Analyzing of the evolution process of the landscape pattern in Guangxi coastal zone in nearly 15 years, we may understand the distribution characteristics and change rules. Combined with the natural disaster data, we use of landscape index and the related risk interference degree and construct ecological risk evaluation model in Guangxi coastal zone for ecological risk assessment results of Guangxi coastal zone.

Enterprise architecture availability analysis using fault trees and stakeholder interviews

NASA Astrophysics Data System (ADS)

Närman, Per; Franke, Ulrik; König, Johan; Buschle, Markus; Ekstedt, Mathias

2014-01-01

The availability of enterprise information systems is a key concern for many organisations. This article describes a method for availability analysis based on Fault Tree Analysis and constructs from the ArchiMate enterprise architecture (EA) language. To test the quality of the method, several case-studies within the banking and electrical utility industries were performed. Input data were collected through stakeholder interviews. The results from the case studies were compared with availability of log data to determine the accuracy of the method's predictions. In the five cases where accurate log data were available, the yearly downtime estimates were within eight hours from the actual downtimes. The cost of performing the analysis was low; no case study required more than 20 man-hours of work, making the method ideal for practitioners with an interest in obtaining rapid availability estimates of their enterprise information systems.

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

NASA Technical Reports Server (NTRS)

Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

1989-01-01

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Debt and growth: A non-parametric approach

NASA Astrophysics Data System (ADS)

Brida, Juan Gabriel; Gómez, David Matesanz; Seijas, Maria Nela

2017-11-01

In this study, we explore the dynamic relationship between public debt and economic growth by using a non-parametric approach based on data symbolization and clustering methods. The study uses annual data of general government consolidated gross debt-to-GDP ratio and gross domestic product for sixteen countries between 1977 and 2015. Using symbolic sequences, we introduce a notion of distance between the dynamical paths of different countries. Then, a Minimal Spanning Tree and a Hierarchical Tree are constructed from time series to help detecting the existence of groups of countries sharing similar economic performance. The main finding of the study appears for the period 2008-2016 when several countries surpassed the 90% debt-to-GDP threshold. During this period, three groups (clubs) of countries are obtained: high, mid and low indebted countries, suggesting that the employed debt-to-GDP threshold drives economic dynamics for the selected countries.

The assessment of environmentally sensitive forest road construction in Calabrian pine forest areas of Turkey.

PubMed

Tunay, Metin

2006-07-01

Forest road construction by bulldozers in Calabrian Pine (Pinus brutia Ten.) forests on mountainous terrain of Turkey causes considerable damage to the environment and the forest standing alongside the road. This situation obliges a study of environmentally sound road construction in Turkey. This study was carried out in 4 sample sites of Antalya Forest Directorate in steep (34-50% gradient) and very steep terrain (51-70% gradient) conditions with bulldozer and excavator machine and direct damages to forest during road construction was determined, including forest area losses and damages to downhill trees in mountainous areas. It was determined that in steep terrain when excavators were used, less forest area (22.16%) was destroyed compared to bulldozers and 26.54% less area in very steep terrain. The proportion of damage on trees where bulldozer worked was nearly twofold higher than excavator was used. The results of this research show that the environmentally sensitive techniques applied for the road construction projects are considerably superior to the traditional use of bulldozers on steep slopes. The environmentally sound forest road construction by use of excavator must be considered an appropriate and reliable solution for mountainous terrain where areas of sensitive forest ecosystems are to be opened up.

Gravitational tree-code on graphics processing units: implementation in CUDA

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Bédorf, Jeroen; Portegies Zwart, Simon

2010-05-01

We present a new very fast tree-code which runs on massively parallel Graphical Processing Units (GPU) with NVIDIA CUDA architecture. The tree-construction and calculation of multipole moments is carried out on the host CPU, while the force calculation which consists of tree walks and evaluation of interaction list is carried out on the GPU. In this way we achieve a sustained performance of about 100GFLOP/s and data transfer rates of about 50GB/s. It takes about a second to compute forces on a million particles with an opening angle of θ ≈ 0.5. The code has a convenient user interface and is freely available for use. http://castle.strw.leidenuniv.nl/software/octgrav.html

Development of an Accelerated Test Design for Predicting the Service Life of the Solar Array at Mead, Nebraska

NASA Technical Reports Server (NTRS)

Gaines, G. B.; Thomas, R. E.; Noel, G. T.; Shilliday, T. S.; Wood, V. E.; Carmichael, D. C.

1979-01-01

Potential long-term degradation modes for the two types of modules in the Mead array were determined and judgments were made as to those environmental stresses and combinations of stresses which accelerate the degradation of the power output. Hierarchical trees representing the severity of effects of stresses (test conditions) on eleven individual degradation modes were constructed and were pruned of tests judged to be nonessential. Composites of those trees were developed so that there is now one pruned tree covering eight degradation modes, another covering two degradation modes, and a third covering one degradation mode. These three composite trees form the basis for selection of test conditions in the final test plan which is now being prepared.

System and method for modeling and analyzing complex scenarios

DOEpatents

Shevitz, Daniel Wolf

2013-04-09

An embodiment of the present invention includes a method for analyzing and solving possibility tree. A possibility tree having a plurality of programmable nodes is constructed and solved with a solver module executed by a processor element. The solver module executes the programming of said nodes, and tracks the state of at least a variable through a branch. When a variable of said branch is out of tolerance with a parameter, the solver disables remaining nodes of the branch and marks the branch as an invalid solution. The valid solutions are then aggregated and displayed as valid tree solutions.

Pattern pluralism and the Tree of Life hypothesis

PubMed Central

Doolittle, W. Ford; Bapteste, Eric

2007-01-01

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL. PMID:17261804

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".

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

Psychometric and Edumetric Validity of Dimensions of Geomorphological Knowledge Which Are Tapped by Concept Mapping.

ERIC Educational Resources Information Center

Hoz, Ron; Bowman, Dan; Chacham, Tova

1997-01-01

Students (N=14) in a geomorphology course took an objective geomorphology test, the tree construction task, and the Standardized Concept Structuring Analysis Technique (SConSAT) version of concept mapping. Results suggest that the SConSAT knowledge structure dimensions have moderate to good construct validity. Contains 82 references. (DDR)

Classification Trees for Quality Control Processes in Automated Constructed Response Scoring.

ERIC Educational Resources Information Center

Williamson, David M.; Hone, Anne S.; Miller, Susan; Bejar, Isaac I.

As the automated scoring of constructed responses reaches operational status, the issue of monitoring the scoring process becomes a primary concern, particularly when the goal is to have automated scoring operate completely unassisted by humans. Using a vignette from the Architectural Registration Examination and data for 326 cases with both human…

Genetic characterization of Pompeii and Herculaneum Equidae buried by Vesuvius in 79 AD.

PubMed

Di Bernardo, G; Galderisi, U; Del Gaudio, S; D'Aniello, A; Lanave, C; De Robertis, M T; Cascino, Antonino; Cipollaro, M

2004-05-01

DNA extracted from the skeletons of five equids discovered in a Pompeii stable and of a horse found in Herculaneum was investigated. Amino acid racemization level was consistent with the presence of DNA. Post-mortem base modifications were excluded by sequencing a 146 bp fragment of the 16S rRNA mitochondrial gene. Sequencing of a 370 bp fragment of mitochondrial (mt)DNA control region allowed the construction of a phylogenetic tree that, along with sequencing of nuclear genes (epsilon globin, gamma interferon, and p53) fragments, gave us the possibility to address some questions puzzling archaeologists. What animals-donkeys, horses, or crossbreeds-were they? And, given they had been evidently assigned to one specific job, were they all akin or were they animals with different mitochondrial haplotypes? The conclusions provided by molecular analysis show that the Pompeii remains are those of horses and mules. Furthermore one of the equids (CAV5) seems to belong to a haplotype, which is either not yet documented in the GenBank or has since disappeared. As its characteristics closely recall those of donkeys, which is the out group chosen to construct the tree, that appears to have evolved within the Equidae family much earlier than horses, this assumption seems to be nearer the truth.

The Spatial Vision Tree: A Generic Pattern Recognition Engine- Scientific Foundations, Design Principles, and Preliminary Tree Design

NASA Technical Reports Server (NTRS)

Rahman, Zia-ur; Jobson, Daniel J.; Woodell, Glenn A.

2010-01-01

New foundational ideas are used to define a novel approach to generic visual pattern recognition. These ideas proceed from the starting point of the intrinsic equivalence of noise reduction and pattern recognition when noise reduction is taken to its theoretical limit of explicit matched filtering. This led us to think of the logical extension of sparse coding using basis function transforms for both de-noising and pattern recognition to the full pattern specificity of a lexicon of matched filter pattern templates. A key hypothesis is that such a lexicon can be constructed and is, in fact, a generic visual alphabet of spatial vision. Hence it provides a tractable solution for the design of a generic pattern recognition engine. Here we present the key scientific ideas, the basic design principles which emerge from these ideas, and a preliminary design of the Spatial Vision Tree (SVT). The latter is based upon a cryptographic approach whereby we measure a large aggregate estimate of the frequency of occurrence (FOO) for each pattern. These distributions are employed together with Hamming distance criteria to design a two-tier tree. Then using information theory, these same FOO distributions are used to define a precise method for pattern representation. Finally the experimental performance of the preliminary SVT on computer generated test images and complex natural images is assessed.

Identification of peanuts and tree nuts: are allergists smarter than their patients?

PubMed

Kao, Leon; Bhangoo, Parmbir S; Roy, Lonnie; Bird, J Andrew

2013-10-01

It has been reported that peanut- or tree nut-allergic individuals and their guardians are poorly capable of differentiating various tree nuts and peanuts. No information exists on the ability of allergists to differentiate peanuts and tree nuts. To measure the ability of allergists and other specialists within the allergy and immunology field to identify various types of tree nuts and peanuts. A nut box with a clear cover was constructed and contained various tree nuts and peanuts in shelled and unshelled forms. Attendees at the 2012 national meeting of the American Academy of Allergy, Asthma, and Immunology were offered participation by viewing the nut box and filling in their responses to a questionnaire. A similar procedure was conducted in the Food Allergy Center at Children's Medical Center (Dallas, TX) for guardians of children with and without peanut or tree nut allergies. Allergists were better able to identify and differentiate tree nuts and peanuts than guardians of peanut- or tree nut-allergic children, guardians of children without food allergies, and allergy and immunology fellows in training. It is important for allergists to educate peanut- and tree nut-allergic individuals and their guardians on the proper avoidance of peanuts and tree nuts. This includes education in the ability to identify peanuts and tree nuts. In addition, allergy and immunology fellows in training may benefit from education in proper peanut and tree nut identification. Copyright © 2013 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Hierarchical Learning of Tree Classifiers for Large-Scale Plant Species Identification.

PubMed

Fan, Jianping; Zhou, Ning; Peng, Jinye; Gao, Ling

2015-11-01

In this paper, a hierarchical multi-task structural learning algorithm is developed to support large-scale plant species identification, where a visual tree is constructed for organizing large numbers of plant species in a coarse-to-fine fashion and determining the inter-related learning tasks automatically. For a given parent node on the visual tree, it contains a set of sibling coarse-grained categories of plant species or sibling fine-grained plant species, and a multi-task structural learning algorithm is developed to train their inter-related classifiers jointly for enhancing their discrimination power. The inter-level relationship constraint, e.g., a plant image must first be assigned to a parent node (high-level non-leaf node) correctly if it can further be assigned to the most relevant child node (low-level non-leaf node or leaf node) on the visual tree, is formally defined and leveraged to learn more discriminative tree classifiers over the visual tree. Our experimental results have demonstrated the effectiveness of our hierarchical multi-task structural learning algorithm on training more discriminative tree classifiers for large-scale plant species identification.

Walking tree heuristics for biological string alignment, gene location, and phylogenies

NASA Astrophysics Data System (ADS)

Cull, P.; Holloway, J. L.; Cavener, J. D.

1999-03-01

Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. We propose a family of heuristics called walking trees to align biologically reasonable strings. Both edit-distance and walking tree methods can locate specific genes within a large string when the genes' sequences are given. When we attempt to match whole strings, the walking tree matches most genes, while the edit-distance method fails. We also give examples in which the walking tree matches substrings even if they have been moved or inverted. The edit-distance method was not designed to handle these problems. We include an example in which the walking tree "discovered" a gene. Calculating scores for whole genome matches gives a method for approximating evolutionary distance. We show two evolutionary trees for the picornaviruses which were computed by the walking tree heuristic. Both of these trees show great similarity to previously constructed trees. The point of this demonstration is that WHOLE genomes can be matched and distances calculated. The first tree was created on a Sequent parallel computer and demonstrates that the walking tree heuristic can be efficiently parallelized. The second tree was created using a network of work stations and demonstrates that there is suffient parallelism in the phylogenetic tree calculation that the sequential walking tree can be used effectively on a network.

Predicting cannabis abuse screening test (CAST) scores: a recursive partitioning analysis using survey data from Czech Republic, Italy, the Netherlands and Sweden.

PubMed

Blankers, Matthijs; Frijns, Tom; Belackova, Vendula; Rossi, Carla; Svensson, Bengt; Trautmann, Franz; van Laar, Margriet

2014-01-01

Cannabis is Europe's most commonly used illicit drug. Some users do not develop dependence or other problems, whereas others do. Many factors are associated with the occurrence of cannabis-related disorders. This makes it difficult to identify key risk factors and markers to profile at-risk cannabis users using traditional hypothesis-driven approaches. Therefore, the use of a data-mining technique called binary recursive partitioning is demonstrated in this study by creating a classification tree to profile at-risk users. 59 variables on cannabis use and drug market experiences were extracted from an internet-based survey dataset collected in four European countries (Czech Republic, Italy, Netherlands and Sweden), n = 2617. These 59 potential predictors of problematic cannabis use were used to partition individual respondents into subgroups with low and high risk of having a cannabis use disorder, based on their responses on the Cannabis Abuse Screening Test. Both a generic model for the four countries combined and four country-specific models were constructed. Of the 59 variables included in the first analysis step, only three variables were required to construct a generic partitioning model to classify high risk cannabis users with 65-73% accuracy. Based on the generic model for the four countries combined, the highest risk for cannabis use disorder is seen in participants reporting a cannabis use on more than 200 days in the last 12 months. In comparison to the generic model, the country-specific models led to modest, non-significant improvements in classification accuracy, with an exception for Italy (p = 0.01). Using recursive partitioning, it is feasible to construct classification trees based on only a few variables with acceptable performance to classify cannabis users into groups with low or high risk of meeting criteria for cannabis use disorder. The number of cannabis use days in the last 12 months is the most relevant variable. The identified variables may be considered for use in future screeners for cannabis use disorders.

Wavelet synthetic method for turbulent flow.

PubMed

Zhou, Long; Rauh, Cornelia; Delgado, Antonio

2015-07-01

Based on the idea of random cascades on wavelet dyadic trees and the energy cascade model known as the wavelet p model, a series of velocity increments in two-dimensional space are constructed in different levels of scale. The dynamics is imposed on the generated scales by solving the Euler equation in the Lagrangian framework. A dissipation model is used in order to cover the shortage of the p model, which only predicts in inertial range. Wavelet reconstruction as well as the multiresolution analysis are then performed on each scales. As a result, a type of isotropic velocity field is created. The statistical properties show that the constructed velocity fields share many important features with real turbulence. The pertinence of this approach in the prediction of flow intermittency is also discussed.

A parallel decision tree-based method for user authentication based on keystroke patterns.

PubMed

Sheng, Yong; Phoha, Vir V; Rovnyak, Steven M

2005-08-01

We propose a Monte Carlo approach to attain sufficient training data, a splitting method to improve effectiveness, and a system composed of parallel decision trees (DTs) to authenticate users based on keystroke patterns. For each user, approximately 19 times as much simulated data was generated to complement the 387 vectors of raw data. The training set, including raw and simulated data, is split into four subsets. For each subset, wavelet transforms are performed to obtain a total of eight training subsets for each user. Eight DTs are thus trained using the eight subsets. A parallel DT is constructed for each user, which contains all eight DTs with a criterion for its output that it authenticates the user if at least three DTs do so; otherwise it rejects the user. Training and testing data were collected from 43 users who typed the exact same string of length 37 nine consecutive times to provide data for training purposes. The users typed the same string at various times over a period from November through December 2002 to provide test data. The average false reject rate was 9.62% and the average false accept rate was 0.88%.

Computer-aided diagnosis of mammographic masses using geometric verification-based image retrieval

NASA Astrophysics Data System (ADS)

Li, Qingliang; Shi, Weili; Yang, Huamin; Zhang, Huimao; Li, Guoxin; Chen, Tao; Mori, Kensaku; Jiang, Zhengang

2017-03-01

Computer-Aided Diagnosis of masses in mammograms is an important indicator of breast cancer. The use of retrieval systems in breast examination is increasing gradually. In this respect, the method of exploiting the vocabulary tree framework and the inverted file in the mammographic masse retrieval have been proved high accuracy and excellent scalability. However it just considered the features in each image as a visual word and had ignored the spatial configurations of features. It greatly affect the retrieval performance. To overcome this drawback, we introduce the geometric verification method to retrieval in mammographic masses. First of all, we obtain corresponding match features based on the vocabulary tree framework and the inverted file. After that, we grasps the main point of local similarity characteristic of deformations in the local regions by constructing the circle regions of corresponding pairs. Meanwhile we segment the circle to express the geometric relationship of local matches in the area and generate the spatial encoding strictly. Finally we judge whether the matched features are correct or not, based on verifying the all spatial encoding are whether satisfied the geometric consistency. Experiments show the promising results of our approach.

Suitable utilization of woody plants for hibitation on Mars

NASA Astrophysics Data System (ADS)

Tomita-Yokotani, Kaori; Baba, Keiichi; Suzuki, Toshisada; Kimura, Shunta; Sato, Seigo; Katoh, Hiroshi; Abe, Yusuke; Katayama, Takeshi

2016-07-01

We have been investigating the usefulness of woody plants for habitation on Mars. During our research, we have found that woody plants have several properties which can be utilized for therapy and materials for enrage and construction even on Mars. Japanese people traditionally believe that "Bonsai" have therapeudic properties. Trees can become carbon fuel which can be used as energy on Mars. Tree materials could be used as a tool in closed bio-ecosystems such as for the purification and/or separation of solutions in an environment in space. Here, we will show some results of their abilities, the water leakage and vacuum seal test, separation of solutions using carbon materials made from trees. At the initiation of this research, we named the trees used as material for the experiment related to space environments "CosmoBon", small bonsai tree. To establish our research, as the first step, we will try to do the experiment using "CosmoBon".

Gibbs measures with memory of length 2 on an arbitrary-order Cayley tree

NASA Astrophysics Data System (ADS)

Akın, Hasan

In this paper, we consider the Ising-Vanniminus model on an arbitrary-order Cayley tree. We generalize the results conjectured by Akın [Chinese J. Phys. 54(4), 635-649 (2016) and Int. J. Mod. Phys. B 31(13), 1750093 (2017)] for an arbitrary-order Cayley tree. We establish the existence and a full classification of translation-invariant Gibbs measures (TIGMs) with a memory of length 2 associated with the model on arbitrary-order Cayley tree. We construct the recurrence equations corresponding to the generalized ANNNI model. We satisfy the Kolmogorov consistency condition. We propose a rigorous measure-theoretical approach to investigate the Gibbs measures with a memory of length 2 for the model. We explain if the number of branches of the tree does not change the number of Gibbs measures. Also, we try to determine when the phase transition does occur.

Constructing event trees for volcanic crises

USGS Publications Warehouse

Newhall, C.; Hoblitt, R.

2002-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Kingdoms in turmoil

NASA Technical Reports Server (NTRS)

Margulis, L.; Guerrero, R.

1991-01-01

How should the world's living organisms be classified? Into how many kingdoms should they be grouped? Scientists have been grappling with these questions since the time of Aristotle, drawing on a broad base of biological characteristics for clues. The fossil record, visible traits of living organisms and, more recently, results from cell biology have all shaped theories of biological classification. But last year a new and controversial concept emerged: a classification of life based solely on molecular traits. The focal point of the controversy is a tree of life, or "phylogeny", devised by Carl Woese of the University of Illinois, Otto Kandler of the University of Munich and Mark Wheelis of the University of California. The tree is unusual because, unlike all previous schemes, it is constructed solely from biochemical data such as DNA sequences rather than a range of different organism characteristics. But that is not all. The scheme also challenges the idea that life on Earth is best divided into five kingdoms, with the main split being between bacteria and all other organisms. Woese and his colleagues create three main groupings by dividing the bacteria in two and unifying all other organisms.

"Jesus Christ the Apple Tree": Preparing for Good Friday in a Literature and Environment Course

ERIC Educational Resources Information Center

Bowen, Deborah C.

2011-01-01

This paper reflects on a visit by Christian poet John Terpstra to the final class session (on a Maundy Thursday) of my Literature and Environment course, to read his poetry suite on making a cross for his church out of a fruit-tree in an orchard being ploughed under for construction. Terpstra plays on the Stations of the Cross by interweaving the…

Revegetation of Riparian Trees and Shrubs on Alluvial Soils Along the Upper Sacramento River, 1987-1988

Treesearch

Steven P. Chainey; F. Jordan Lang; Skip Mills

1989-01-01

Two sites on the Sacramento River near Red Bluff and Colusa, California were planted with seven native tree species plus valley elderberry (a shrub) in an effort to mitigate for the loss of woody riparian vegetation from bank protection construction projects in the area. The stateowned environmental easements on terraces on the river side of the levees had been planted...

Constructal Law of Vascular Trees for Facilitation of Flow

PubMed Central

Razavi, Mohammad S.; Shirani, Ebrahim; Salimpour, Mohammad Reza; Kassab, Ghassan S.

2014-01-01

Diverse tree structures such as blood vessels, branches of a tree and river basins exist in nature. The constructal law states that the evolution of flow structures in nature has a tendency to facilitate flow. This study suggests a theoretical basis for evaluation of flow facilitation within vascular structure from the perspective of evolution. A novel evolution parameter (Ev) is proposed to quantify the flow capacity of vascular structures. Ev is defined as the ratio of the flow conductance of an evolving structure (configuration with imperfection) to the flow conductance of structure with least imperfection. Attaining higher Ev enables the structure to expedite flow circulation with less energy dissipation. For both Newtonian and non-Newtonian fluids, the evolution parameter was developed as a function of geometrical shape factors in laminar and turbulent fully developed flows. It was found that the non-Newtonian or Newtonian behavior of fluid as well as flow behavior such as laminar or turbulent behavior affects the evolution parameter. Using measured vascular morphometric data of various organs and species, the evolution parameter was calculated. The evolution parameter of the tree structures in biological systems was found to be in the range of 0.95 to 1. The conclusion is that various organs in various species have high capacity to facilitate flow within their respective vascular structures. PMID:25551617

Factors associated with long-term species composition in dry tropical forests of Central India

NASA Astrophysics Data System (ADS)

Agarwala, M.; DeFries, R. S.; Qureshi, Q.; Jhala, Y. V.

2016-10-01

The long-term future of species composition in forests depends on regeneration. Many factors can affect regeneration, including human use, environmental conditions, and species’ traits. This study examines the influence of these factors in a tropical deciduous forest of Central India, which is heavily used by local, forest-dependent residents for livestock grazing, fuel-wood extraction, construction and other livelihood needs. We measure size-class proportions (the ratio of abundance of a species at a site in a higher size class to total abundance in both lower and higher size classes) for 39 tree species across 20 transects at different intensities of human use. The size-class proportions for medium to large trees and for small to medium-sized trees were negatively associated with species that are used for local construction, while size class proportions for saplings to small trees were positively associated with those species that are fire resistant and negatively associated with livestock density. Results indicate that grazing and fire prevent non-fire resistant species from reaching reproductive age, which can alter the long term composition and future availability of species that are important for local use and ecosystem services. Management efforts to reduce fire and forest grazing could reverse these impacts on long-term forest composition.

Learning accurate very fast decision trees from uncertain data streams

NASA Astrophysics Data System (ADS)

Liang, Chunquan; Zhang, Yang; Shi, Peng; Hu, Zhengguo

2015-12-01

Most existing works on data stream classification assume the streaming data is precise and definite. Such assumption, however, does not always hold in practice, since data uncertainty is ubiquitous in data stream applications due to imprecise measurement, missing values, privacy protection, etc. The goal of this paper is to learn accurate decision tree models from uncertain data streams for classification analysis. On the basis of very fast decision tree (VFDT) algorithms, we proposed an algorithm for constructing an uncertain VFDT tree with classifiers at tree leaves (uVFDTc). The uVFDTc algorithm can exploit uncertain information effectively and efficiently in both the learning and the classification phases. In the learning phase, it uses Hoeffding bound theory to learn from uncertain data streams and yield fast and reasonable decision trees. In the classification phase, at tree leaves it uses uncertain naive Bayes (UNB) classifiers to improve the classification performance. Experimental results on both synthetic and real-life datasets demonstrate the strong ability of uVFDTc to classify uncertain data streams. The use of UNB at tree leaves has improved the performance of uVFDTc, especially the any-time property, the benefit of exploiting uncertain information, and the robustness against uncertainty.

[Quantitative relationships of intra- and interspecific competition in Cryptocarya concinna].

PubMed

Zhang, Chi; Huang, Zhongliang; Li, Jiong; Shi, Junhui; Li, Lin

2006-01-01

The monsoon evergreen broad-leaved forest (MEBF) in Dinghushan Nature Reserve (DNR) has been considered as a zonal vegetation in lower subtropical China, with a history of more than 400 years. In this paper, the intra- and interspecific competition intensity in Cryptocarya concinna, one of the constructive species in MEBF in DNR was quantitatively analyzed by Hegyi single-tree competition index model. The results showed that the intraspecific competition intensity in C. concinna decreased gradually with increasing tree diameter. For C. concinna, its intraspecific competition was weaker than its interspecific competition with Aporosa yunnanensis. The competition intensity of interspecific competition with C. concinna followed the order of A. yunnanensis > Schima superba > Gironniera subaequalis > Acmena acuminatissima > Castanopsis chinensis > Syzygium rehderianum > Pygeum topengii > Blastus cochinchinensis > Sarcosperma laurinum > Pterospermum lanceaefolium > Cryptocarya chinensis. The relationship of the DBH of objective tree and the competition intensity between competitive tree and objective tree in the whole forest and C. concinna population nearly conformed to power function, while that between other competitive tree and the objective C. concinna tree conformed to logarithm function. There was a significantly negative correlation between the competition intensity and the DBH of objective tree.

A new method for separating the climatic and biological trend components from tree ring series, with implications for paleoclimate reconstructions

NASA Astrophysics Data System (ADS)

Bouldin, J.

2010-12-01

In the reconstruction of past climates from tree rings multi-decadal to multi-centennial periods, one longstanding problem is the confounding of the natural biological growth trend of the tree with any existing long term trends in the climate. No existing analytical method is capable of resolving these two change components, so it remains unclear how accurate existing ring series standardizations are, and by implication, climate reconstructions based upon them. For example, dendrochronological at the ITRDB are typically standardized by detrending, at each site, each individual tree core, using a relatively stiff deterministic function such as a negative exponential curve or smoothing spline. Another approach, referred to as RCS (Regional Curve Standardization) attempts to solve some problems of the individual series detrending, by constructing a single growth curve from the aggregated cambial ages of the rings of the cores at a site (or collection of sites). This curve is presumed to represent the “ideal” or expected growth of the trees from which it is derived. Although an improvement in some respects, this method will be degraded in direct proportion to the lack of a mixture of tree sizes or ages throughout the span of the chronology. I present a new method of removing the biological curve from tree ring series, such that temporal changes better represent the environmental variation captured by the tree rings. The method institutes several new approaches, such as the correction for the estimated number of missed rings near the pith, and the use of tree size and ring area relationships instead of the traditional tree ages and ring widths. The most important innovation is a careful extraction of the existing information on the relationship between tree size (basal area) and ring area that exists within each single year of the chronology. This information is, by definition, not contaminated by temporal climatic changes, and so when removed, leaves the climatically caused, and random error components of the chronology. A sophisticated algorithm, based on pair-wise ring comparisons in which tree size is standardized both within and between years, forms the basis of the method. Evaluations of the method are underway with both simulated and actual (ITRDB) data, to evaluate the potentials and drawbacks of the method relative to existing methods. The ITRDB test data consists of a set of about 50 primarily high elevation sites from across western North America. Most of these sites show a pronounced 20th Century warming relative to earlier centuries, in accordance with current understanding, albeit at a non-global scale. A relative minority show cooling, occasionally strongly. Current and future work emphasizes evaluation of the method with varying, simulated data, and more thorough empirical evaluations of the method in situations where the type, and intensity, of the primary environmentally limiting factor varies (e.g temperature versus soil moisture limited sites).

PHYLOGEOrec: A QGIS plugin for spatial phylogeographic reconstruction from phylogenetic tree and geographical information data

NASA Astrophysics Data System (ADS)

Nashrulloh, Maulana Malik; Kurniawan, Nia; Rahardi, Brian

2017-11-01

The increasing availability of genetic sequence data associated with explicit geographic and environment (including biotic and abiotic components) information offers new opportunities to study the processes that shape biodiversity and its patterns. Developing phylogeography reconstruction, by integrating phylogenetic and biogeographic knowledge, provides richer and deeper visualization and information on diversification events than ever before. Geographical information systems such as QGIS provide an environment for spatial modeling, analysis, and dissemination by which phylogenetic models can be explicitly linked with their associated spatial data, and subsequently, they will be integrated with other related georeferenced datasets describing the biotic and abiotic environment. We are introducing PHYLOGEOrec, a QGIS plugin for building spatial phylogeographic reconstructions constructed from phylogenetic tree and geographical information data based on QGIS2threejs. By using PHYLOGEOrec, researchers can integrate existing phylogeny and geographical information data, resulting in three-dimensional geographic visualizations of phylogenetic trees in the Keyhole Markup Language (KML) format. Such formats can be overlaid on a map using QGIS and finally, spatially viewed in QGIS by means of a QGIS2threejs engine for further analysis. KML can also be viewed in reputable geobrowsers with KML-support (i.e., Google Earth).

Tongues on the EDGE: language preservation priorities based on threat and lexical distinctiveness

PubMed Central

Davies, T. Jonathan

2017-01-01

Languages are being lost at rates exceeding the global loss of biodiversity. With the extinction of a language we lose irreplaceable dimensions of culture and the insight it provides on human history and the evolution of linguistic diversity. When setting conservation goals, biologists give higher priority to species likely to go extinct. Recent methods now integrate information on species evolutionary relationships to prioritize the conservation of those with a few close relatives. Advances in the construction of language trees allow us to use these methods to develop language preservation priorities that minimize loss of linguistic diversity. The evolutionarily distinct and globally endangered (EDGE) metric, used in conservation biology, accounts for a species’ originality (evolutionary distinctiveness—ED) and its likelihood of extinction (global endangerment—GE). Here, we use a similar framework to inform priorities for language preservation by generating rankings for 350 Austronesian languages. Kavalan, Tanibili, Waropen and Sengseng obtained the highest EDGE scores, while Xârâcùù (Canala), Nengone and Palauan are among the most linguistically distinct, but are not currently threatened. We further provide a way of dealing with incomplete trees, a common issue for both species and language trees. PMID:29308253

The application of a decision tree to establish the parameters associated with hypertension.

PubMed

Tayefi, Maryam; Esmaeili, Habibollah; Saberi Karimian, Maryam; Amirabadi Zadeh, Alireza; Ebrahimi, Mahmoud; Safarian, Mohammad; Nematy, Mohsen; Parizadeh, Seyed Mohammad Reza; Ferns, Gordon A; Ghayour-Mobarhan, Majid

2017-02-01

Hypertension is an important risk factor for cardiovascular disease (CVD). The goal of this study was to establish the factors associated with hypertension by using a decision-tree algorithm as a supervised classification method of data mining. Data from a cross-sectional study were used in this study. A total of 9078 subjects who met the inclusion criteria were recruited. 70% of these subjects (6358 cases) were randomly allocated to the training dataset for the constructing of the decision-tree. The remaining 30% (2720 cases) were used as the testing dataset to evaluate the performance of decision-tree. Two models were evaluated in this study. In model I, age, gender, body mass index, marital status, level of education, occupation status, depression and anxiety status, physical activity level, smoking status, LDL, TG, TC, FBG, uric acid and hs-CRP were considered as input variables and in model II, age, gender, WBC, RBC, HGB, HCT MCV, MCH, PLT, RDW and PDW were considered as input variables. The validation of the model was assessed by constructing a receiver operating characteristic (ROC) curve. The prevalence rates of hypertension were 32% in our population. For the decision-tree model I, the accuracy, sensitivity, specificity and area under the ROC curve (AUC) value for identifying the related risk factors of hypertension were 73%, 63%, 77% and 0.72, respectively. The corresponding values for model II were 70%, 61%, 74% and 0.68, respectively. We have developed a decision tree model to identify the risk factors associated with hypertension that maybe used to develop programs for hypertension management. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Pollution ecology of breeding great blue herons in the Columbia Basin, Oregon and Washington

USGS Publications Warehouse

Blus, L.J.; Henny, C.J.; Kaiser, T.E.

1980-01-01

Approximately 40 pairs of Great Blue Herons (Ardea herodias) formerly nested in trees on or near Blalock Island about 95 km downstream from Richland, Washington, in the Columbia River (Nehls 1972 ). In conjunction with construction of the John Day Lock and Dam and before creating Lake Umatilla in 1968, large trees along the shoreline, including those in the heronry on Blalock Island, were removed except for about six cottonwood trees (Populus sp.) that were left standing near the south bank of the river (David Lenhart, pers. comm.). As a mitigation procedure, the Umatilla National Wildlife Refuge (Umatilla) was established in 1967. The herons subsequently established a secondary heronry in the six cottonwoods; 20 pairs were present in 1971 (Nehls 1972). The inundated trees died and deteriorated; only two trees with eight nests remained in 1976 (Henny and Kurtz 1978), and we found just two nests in one tree in 1978. With a decrease in traditional nesting sites, the birds nested on islands in big sagebrush (Artemisia tridentata), on channel markers in the Columbia River, and on nesting platforms constructed for Canada Geese (Branta canadensis). The purpose of this paper is to describe the breeding biology of Great Blue Herons at Umatilla and the McNary Recreation Area (McNary) in 1978 and the relationship of organochlorine residues in eggs to eggshell thickness and reproductive success. The primary reason for conducting this study was to determine if the heptachlor seed treatment that was severely affecting Canada Geese at Umatilla (Blus et al. 1979) was also a hazard to Great Blue Herons. At the same time we also investigated possible effects of other organochlorines on the herons.

A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

PubMed Central

Keremane, Manjunath L.; Lee, Richard F.; Maureira-Butler, Ivan J.; Roose, Mikeal L.

2013-01-01

Background Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4–12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species. Methodology and Principal Findings (1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test. Conclusions We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches–gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus. PMID:23874615

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

NASA Astrophysics Data System (ADS)

Bleich, Justin

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

U.S. Air Force Environmental Assessment, Add To and Alter Type III Hydrant Fueling System, Tinker Air Force Base, Oklahoma

DTIC Science & Technology

2011-12-01

burning of fossil fuels (e.g., oil , natural gas , coal), solid waste decay, and trees and wood products and also as a result of chemical reactions...to negative GHG effects. Methane. CH4 is a GHG that is emitted during the production and transport of coal, natural gas , and oil . Methane...the pump station (Facility 486); Control Room (Facility 487); and the oil -water separator (Facility 488). • Construction of a new Type III pump house

Tree Topping Ceremony at NASA's Propulsion Research Laboratory

NASA Technical Reports Server (NTRS)

2003-01-01

A new, world-class laboratory for research into future space transportation technologies is under construction at the Marshall Space Flight Center (MSFC) in Huntsville, AL. The state-of-the-art Propulsion Research Laboratory will serve as a leading national resource for advanced space propulsion research. Its purpose is to conduct research that will lead to the creation and development of irnovative propulsion technologies for space exploration. The facility will be the epicenter of the effort to move the U.S. space program beyond the confines of conventional chemical propulsion into an era of greatly improved access to space and rapid transit throughout the solar system. The Laboratory is designed to accommodate researchers from across the United States, including scientists and engineers from NASA, the Department of Defense, the Department of Energy, universities, and industry. The facility, with 66,000 square feet of useable laboratory space, will feature a high degree of experimental capability. Its flexibility will allow it to address a broad range of propulsion technologies and concepts, such as plasma, electromagnetic, thermodynamic, and propellantless propulsion. An important area of emphasis will be development and utilization of advanced energy sources, including highly energetic chemical reactions, solar energy, and processes based on fission, fusion, and antimatter. The Propulsion Research Laboratory is vital for developing the advanced propulsion technologies needed to open up the space frontier, and will set the stage of research that could revolutionize space transportation for a broad range of applications. This photo depicts construction workers taking part in a tree topping ceremony as the the final height of the laboratory is framed. The ceremony is an old German custom of paying homage to the trees that gave their lives in preparation of the building site.

[Soft-ridged bench terrace design in hilly loess region].

PubMed

Cao, Shixiong; Chen, Li; Gao, Wangsheng

2005-08-01

Reconfiguration of hillside field into terrace is regarded as one of the key techniques for water and soil conservation in mountainous regions. On slopes exceeding 30 degrees, the traditional techniques of terracing are difficult to apply as risers (i.e., backslopes), and if not reinforced, are so abrupt and easy to collapse under gravity alone, thus damaging the terrace. To improve the reconfiguration of hillside field into terrace, holistic techniques of soft-ridged bench terrace engineering, including revegetation, with trees and planting grasses on riser slopes, were tested between 1997 and 2001 in Xiabiangou watershed of Yan' an, Shaanxi Province. A "working with Nature" engineering approach, riser slopes of 45 degrees, similar to the pre-existing slope of 35 degrees, was employed to radically reduce gravity-erosion. Based on the concepts of biodiversity and the principles of landscape ecology, terrace benches, bunds, and risers were planted with trees, shrubs, forage grasses, and crops, serving to generate a diverse array of plants, a semi-forested area, and to stabilize terrace bunds. Soft-ridged bench terrace made it possible to significantly reduce hazards arising from gravity erosion, and reduce the costs of individual bench construction and maintenance by 24.9% and 55.5% of the costs under traditional techniques, respectively. Such a construction allowed an enrichment and concentration of nutrients in the soils of terrace bunds, providing an ideal environment for a range of plants to grow and develop. The terrace riser could be planted with drought-resistant plants ranging from forage grasses to trees, and this riser vegetation would turn the exposed bunds and risers existing under traditional techniques into plant-covered belts, great green ribbons decorating farmland and contributing to the enhancement of the landscape biology.

Impact assessment of a high-speed railway line on species distribution: application to the European tree frog (Hyla arborea) in Franche-Comté.

PubMed

Clauzel, Céline; Girardet, Xavier; Foltête, Jean-Christophe

2013-09-30

The aim of the present work is to assess the potential long-distance effect of a high-speed railway line on the distribution of the European tree frog (Hyla arborea) in eastern France by combining graph-based analysis and species distribution models. This combination is a way to integrate patch-level connectivity metrics on different scales into a predictive model. The approach used is put in place before the construction of the infrastructure and allows areas potentially affected by isolation to be mapped. Through a diachronic analysis, comparing species distribution before and after the construction of the infrastructure, we identify changes in the probability of species presence and we determine the maximum distance of impact. The results show that the potential impact decreases with distance from the high-speed railway line and the largest disturbances occur within the first 500 m. Between 500 m and 3500 m, the infrastructure generates a moderate decrease in the probability of presence with maximum values close to -40%. Beyond 3500 m the average disturbance is less than -10%. The spatial extent of the impact is greater than the dispersal distance of the tree frog, confirming the assumption of the long-distance effect of the infrastructure. This predictive modelling approach appears to be a useful tool for environmental impact assessment and strategic environmental assessment. The results of the species distribution assessment may provide guidance for field surveys and support for conservation decisions by identifying the areas most affected. Copyright © 2013 Elsevier Ltd. All rights reserved.

Carbon stock estimation in the catchment of Kotli Bhel 1A hydroelectric reservoir, Uttarakhand, India.

PubMed

Kumar, Amit; Sharma, M P

2016-12-01

Constructions of dams/reservoirs all over the world are reported to emit significant amount of greenhouse gases (GHGs) and are considered as environmental polluters. Organic carbon is contributed by the forest in the catchment, part of soil organic carbon is transported through the runoffs to the reservoir and undergoes aerobic and anaerobic degradation with time to release GHGs to the atmosphere. Literature reveals that no work is available on the estimation of 'C' stock of trees of forest catchment for assessing/predicting the GHGs emissions from the reservoirs to atmosphere. To assess the GHGs emission potential of the reservoir, an attempt is made in the study to estimate the 'C' stock in the forest catchment of Kotli Bhel 1A hydroelectric reservoir located in Tehri Garhwal district of Uttarakhand, India. For this purpose, the selected area was categorized into the site-I, II and III along the Bhagirathi River based on type of forest available in the catchment. The total carbon density (TCD) of tree species of different forest types was calculated using diameter at breast height (dbh) and trees height. The results found that the TCD of forest catchment was found 76.96MgCha -1 as the highest at the site-II and 29.93MgCha -1 as lowest at site-I with mean of 51.50MgCha -1 . The estimated forest 'C' stock shall be used to know the amount of carbon present before and after construction of the dam and to predict net GHGs emissions. The results may be helpful to study the potential of a given reservoir to release GHG and its subsequent impacts on global warming/climate challenges. Copyright © 2015 Elsevier Inc. All rights reserved.

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins

PubMed Central

2013-01-01

Background The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. Results By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. Conclusions We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications. PMID:24053117

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins.

PubMed

Mühlhausen, Stefanie; Kollmar, Martin

2013-09-22

The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications.

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

NASA Astrophysics Data System (ADS)

Ferguson, Thomas A.; Lu, Lixuan

2017-09-01

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

Scattering measurements on natural and model trees

NASA Technical Reports Server (NTRS)

Rogers, James C.; Lee, Sung M.

1990-01-01

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

Random forests of interaction trees for estimating individualized treatment effects in randomized trials.

PubMed

Su, Xiaogang; Peña, Annette T; Liu, Lei; Levine, Richard A

2018-04-29

Assessing heterogeneous treatment effects is a growing interest in advancing precision medicine. Individualized treatment effects (ITEs) play a critical role in such an endeavor. Concerning experimental data collected from randomized trials, we put forward a method, termed random forests of interaction trees (RFIT), for estimating ITE on the basis of interaction trees. To this end, we propose a smooth sigmoid surrogate method, as an alternative to greedy search, to speed up tree construction. The RFIT outperforms the "separate regression" approach in estimating ITE. Furthermore, standard errors for the estimated ITE via RFIT are obtained with the infinitesimal jackknife method. We assess and illustrate the use of RFIT via both simulation and the analysis of data from an acupuncture headache trial. Copyright © 2018 John Wiley & Sons, Ltd.

The range and valence of a real Smirnov function

NASA Astrophysics Data System (ADS)

Ferguson, Timothy; Ross, William T.

2018-02-01

We give a complete description of the possible ranges of real Smirnov functions (quotients of two bounded analytic functions on the open unit disk where the denominator is outer and such that the radial boundary values are real almost everywhere on the unit circle). Our techniques use the theory of unbounded symmetric Toeplitz operators, some general theory of unbounded symmetric operators, classical Hardy spaces, and an application of the uniformization theorem. In addition, we completely characterize the possible valences for these real Smirnov functions when the valence is finite. To do so we construct Riemann surfaces we call disk trees by welding together copies of the unit disk and its complement in the Riemann sphere. We also make use of certain trees we call valence trees that mirror the structure of disk trees.

Convergence properties of halo merger trees; halo and substructure merger rates across cosmic history

NASA Astrophysics Data System (ADS)

Poole, Gregory B.; Mutch, Simon J.; Croton, Darren J.; Wyithe, Stuart

2017-12-01

We introduce GBPTREES: an algorithm for constructing merger trees from cosmological simulations, designed to identify and correct for pathological cases introduced by errors or ambiguities in the halo finding process. GBPTREES is built upon a halo matching method utilizing pseudo-radial moments constructed from radially sorted particle ID lists (no other information is required) and a scheme for classifying merger tree pathologies from networks of matches made to-and-from haloes across snapshots ranging forward-and-backward in time. Focusing on SUBFIND catalogues for this work, a sweep of parameters influencing our merger tree construction yields the optimal snapshot cadence and scanning range required for converged results. Pathologies proliferate when snapshots are spaced by ≲0.128 dynamical times; conveniently similar to that needed for convergence of semi-analytical modelling, as established by Benson et al. Total merger counts are converged at the level of ∼5 per cent for friends-of-friends (FoF) haloes of size np ≳ 75 across a factor of 512 in mass resolution, but substructure rates converge more slowly with mass resolution, reaching convergence of ∼10 per cent for np ≳ 100 and particle mass mp ≲ 109 M⊙. We present analytic fits to FoF and substructure merger rates across nearly all observed galactic history (z ≤ 8.5). While we find good agreement with the results presented by Fakhouri et al. for FoF haloes, a slightly flatter dependence on merger ratio and increased major merger rates are found, reducing previously reported discrepancies with extended Press-Schechter estimates. When appropriately defined, substructure merger rates show a similar mass ratio dependence as FoF rates, but with stronger mass and redshift dependencies for their normalization.

SALAD database: a motif-based database of protein annotations for plant comparative genomics

PubMed Central

Mihara, Motohiro; Itoh, Takeshi; Izawa, Takeshi

2010-01-01

Proteins often have several motifs with distinct evolutionary histories. Proteins with similar motifs have similar biochemical properties and thus related biological functions. We constructed a unique comparative genomics database termed the SALAD database (http://salad.dna.affrc.go.jp/salad/) from plant-genome-based proteome data sets. We extracted evolutionarily conserved motifs by MEME software from 209 529 protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available. We also developed a viewer named ‘SALAD on ARRAYs’ to view arbitrary microarray data sets of paralogous genes linked to the same dendrogram in a window. The SALAD database is a powerful tool for comparing protein sequences and can provide valuable hints for biological analysis. PMID:19854933

Mapping environmental susceptibility to Saint Louis encephalitis virus, based on a decision tree model of remotely-sensed data.

PubMed

Rotela, Camilo H; Spinsanti, Lorena I; Lamfri, Mario A; Contigiani, Marta S; Almirón, Walter R; Scavuzzo, Carlos M

2011-11-01

In response to the first human outbreak (January May 2005) of Saint Louis encephalitis (SLE) virus in Córdoba province, Argentina, we developed an environmental SLE virus risk map for the capital, i.e. Córdoba city. The aim was to provide a map capable of detecting macro-environmental factors associated with the spatial distribution of SLE cases, based on remotely sensed data and a geographical information system. Vegetation, soil brightness, humidity status, distances to water-bodies and areas covered by vegetation were assessed based on pre-outbreak images provided by the Landsat 5TM satellite. A strong inverse relationship between the number of humans infected by SLEV and distance to high-vigor vegetation was noted. A statistical non-hierarchic decision tree model was constructed, based on environmental variables representing the areas surrounding patient residences. From this point of view, 18% of the city could be classified as being at high risk for SLEV infection, while 34% carried a low risk, or none at all. Taking the whole 2005 epidemic into account, 80% of the cases came from areas classified by the model as medium-high or high risk. Almost 46% of the cases were registered in high-risk areas, while there were no cases (0%) in areas affirmed as risk free.

SALAD database: a motif-based database of protein annotations for plant comparative genomics.

PubMed

Mihara, Motohiro; Itoh, Takeshi; Izawa, Takeshi

2010-01-01

Proteins often have several motifs with distinct evolutionary histories. Proteins with similar motifs have similar biochemical properties and thus related biological functions. We constructed a unique comparative genomics database termed the SALAD database (http://salad.dna.affrc.go.jp/salad/) from plant-genome-based proteome data sets. We extracted evolutionarily conserved motifs by MEME software from 209,529 protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available. We also developed a viewer named 'SALAD on ARRAYs' to view arbitrary microarray data sets of paralogous genes linked to the same dendrogram in a window. The SALAD database is a powerful tool for comparing protein sequences and can provide valuable hints for biological analysis.

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

PubMed Central

2011-01-01

Background Species of the Fusarium genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of Fusarium species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the Fusarium genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among Fusairum species revealed the possibility that each gene in Fusarium genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of Fusarium. There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution. Results We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene (β-tub), the elongation factor 1α gene (EF-1α), and the aminoadipate reductase gene (lys2). Although incongruence of the tree topologies between lys2 and the other genes was detected, all genes supported the classification of Fusarium species into 7 major clades, I to VII. To obtain a reliable phylogeny for Fusarium species, we excluded the lys2 sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster, β-tub, and EF-1α. Our ML tree indicated some interesting relationships in the higher and lower taxa of Fusarium species and related genera. Moreover, we observed a novel evolutionary history of lys2. We suggest that the unique tree topologies of lys2 are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages. Conclusion This study showed the reliable species tree of the higher and lower taxonomy in the lineage of the Fusarium genus. Our ML tree clearly indicated 7 major clades within the Fusarium genus. Furthermore, this study reported differences in the evolutionary histories among multiple genes within this genus for the first time. PMID:22047111

Metaphors and Sense of Teaching: How These Constructs Influence Novice Teachers

ERIC Educational Resources Information Center

Massengill, Donita; Mahlios, Marc; Barry, Arlene

2005-01-01

The purpose of this study was to identify the root metaphors of secondary classroom teachers and to observe ways in which these constructs influence teachers' work with their students and their environments. Specifically, five case studies of novice teachers were presented. Results indicated that the metaphor of life as a tree was the most common…

Nonpoint Source: Forestry

EPA Pesticide Factsheets

Sources of nonpoint source (NPS) pollution associated with forestry activities include removal of streamside vegetation, road construction and use, timber harvesting, and mechanical preparation for the planting of trees. Information resources.

On metric structure of ultrametric spaces

NASA Astrophysics Data System (ADS)

Nechaev, S. K.; Vasilyev, O. A.

2004-03-01

In our work we have reconsidered the old problem of diffusion at the boundary of an ultrametric tree from a 'number theoretic' point of view. Namely, we use the modular functions (in particular, the Dedekind eegr-function) to construct the 'continuous' analogue of the Cayley tree isometrically embedded in the Poincaré upper half-plane. Later we work with this continuous Cayley tree as with a standard function of a complex variable. In the framework of our approach, the results of Ogielsky and Stein on dynamics in ultrametric spaces are reproduced semi-analytically or semi-numerically. The speculation on the new 'geometrical' interpretation of replica n rarr 0 limit is proposed.

Section-Based Tree Species Identification Using Airborne LIDAR Point Cloud

NASA Astrophysics Data System (ADS)

Yao, C.; Zhang, X.; Liu, H.

2017-09-01

The application of LiDAR data in forestry initially focused on mapping forest community, particularly and primarily intended for largescale forest management and planning. Then with the smaller footprint and higher sampling density LiDAR data available, detecting individual tree overstory, estimating crowns parameters and identifying tree species are demonstrated practicable. This paper proposes a section-based protocol of tree species identification taking palm tree as an example. Section-based method is to detect objects through certain profile among different direction, basically along X-axis or Y-axis. And this method improve the utilization of spatial information to generate accurate results. Firstly, separate the tree points from manmade-object points by decision-tree-based rules, and create Crown Height Mode (CHM) by subtracting the Digital Terrain Model (DTM) from the digital surface model (DSM). Then calculate and extract key points to locate individual trees, thus estimate specific tree parameters related to species information, such as crown height, crown radius, and cross point etc. Finally, with parameters we are able to identify certain tree species. Comparing to species information measured on ground, the portion correctly identified trees on all plots could reach up to 90.65 %. The identification result in this research demonstrate the ability to distinguish palm tree using LiDAR point cloud. Furthermore, with more prior knowledge, section-based method enable the process to classify trees into different classes.

Re-Construction of Reference Population and Generating Weights by Decision Tree

DTIC Science & Technology

2017-07-21

2017 Claflin University Orangeburg, SC 29115 DEFENSE EQUAL OPPORTUNITY MANAGEMENT INSTITUTE RESEARCH, DEVELOPMENT, AND STRATEGIC...Original Dataset 32 List of Figures in Appendix B Figure 1: Flow and Components of Project 20 Figure 2: Decision Tree 31 Figure 3: Effects of Weight...can compare the sample data. The dataset of this project has the reference population on unit level for group and gender, which is in red-dotted box

Larval microhabitats of Lutzomyia longipalpis (Diptera: Psychodidae) in an endemic focus of visceral leishmaniasis in Colombia.

PubMed

Ferro, C; Pardo, R; Torres, M; Morrison, A C

1997-11-01

An intensive search for the larval habitats of Lutzomyia longipalpis (Lutz & Neiva) was conducted from November 1992 to October 1993 at a small rural community in Colombia where American visceral leishmaniasis is endemic. Emergence traps constructed from polyvinyl chloride pipes were used to sample a variety of soil microhabitats that included edge areas of covered pigpens, cattle corrals, the base of trees, and leaf litter at sites within 40 m of a house, rocks in fields located between 50 and 500 m from houses, and sites within a patch of secondary forest (rocks, base of palm trees, and leaf litter). The teneral status of the sand flies captured in the emergence traps was confirmed by laboratory studies that determined the rate of terminalia rotation in male L. longipalpis and the rate of cuticular growth layer formation of the thoracic phragma in both sexes of this species. A total of 58 teneral sand flies was captured during the study period (49 wk). Fifteen specimens were L. longipalpis; of these 11 (5 sand flies per square meter) were captured near pigpens, 3 (1.4 sand flies per square meter) were captured near rock resting sites, and 1 (1.6 sand flies per square meter) was collected at the base of a tree. The remainder of the sand flies were either L. trinidadensis (Newstead) or L. cayennensis (Flock & Abonnenc). Our results indicate that L. longipalpis larvae were dispersed widely in sites near houses, rather than concentrated in a few optimal microhabitats.

Differences in the impacts of formal and informal recreational trails on urban forest loss and tree structure.

PubMed

Ballantyne, Mark; Pickering, Catherine Marina

2015-08-15

Recreational trails are one of the most common types of infrastructure used for nature-based activities such as hiking and mountain biking worldwide. Depending on their design, location, construction, maintenance and use, these trails differ in their environmental impacts. There are few studies, however, comparing the impacts of different trail types including between formal management-created trails and informal visitor-created trails. Although both types of trails can be found in remote natural areas, dense networks of them often occur in forests close to cities where they experience intense visitor use. To assess the relative impacts of different recreational trails in urban forests, we compared the condition of the trail surface, loss of forest strata and changes in tree structure caused by seven types of trails (total network 46.1 km) traversing 17 remnants of an endangered urban forest in Australia. After mapping and classifying all trails, we assessed their impact on the forest condition at 125 sites (15 sites per trail type, plus 15 control sites within undisturbed forest). On the trail sites, the condition of the trail surface, distance from the trail edge to four forest strata (litter, understory, midstorey and tree cover) and structure of the tree-line were assessed. Informal trails generally had poorer surface conditions and were poorly-designed and located. Per site, formal and informal trails resulted in similar loss of forest strata, with wider trails resulting in greater loss of forest. Because there were more informal trails, however, they accounted for the greatest cumulative forest loss. Structural impacts varied, with the widest informal trails and all formal hardened trails resulting in similar reductions in canopy cover and tree density but an increase in saplings. These structural impacts are likely a function of the unregulated and intense use of large informal trails, and disturbance from the construction and maintenance of formal trails. The results demonstrate that different types of recreational trails vary in the type and range of impacts they cause to forests. They highlight the importance of careful consideration towards management options when dealing with trail networks especially in areas of high conservation value. Copyright © 2015 Elsevier Ltd. All rights reserved.

Study on the Application of the Kent Index Method on the Risk Assessment of Disastrous Accidents in Subway Engineering

PubMed Central

Lu, Hao; Wang, Mingyang; Yang, Baohuai; Rong, Xiaoli

2013-01-01

With the development of subway engineering, according to uncertain factors and serious accidents involved in the construction of subways, implementing risk assessment is necessary and may bring a number of benefits for construction safety. The Kent index method extensively used in pipeline construction is improved to make risk assessment much more practical for the risk assessment of disastrous accidents in subway engineering. In the improved method, the indexes are divided into four categories, namely, basic, design, construction, and consequence indexes. In this study, a risk assessment model containing four kinds of indexes is provided. Three kinds of risk occurrence modes are listed. The probability index model which considers the relativity of the indexes is established according to the risk occurrence modes. The model provides the risk assessment process through the fault tree method and has been applied in the risk assessment of Nanjing subway's river-crossing tunnel construction. Based on the assessment results, the builders were informed of what risks should be noticed and what they should do to avoid the risks. The need for further research is discussed. Overall, this method may provide a tool for the builders, and improve the safety of the construction. PMID:23710136

[Satellite remote sensing retrieval of canopy nitrogen nutritional status of apple trees at blossom stage].

PubMed

Wang, Ling; Zhao, Geng-Xing; Zhu, Xi-Cun; Wang, Rui-Yan; Chang, Chun-Yan

2013-10-01

Taking Qixia City of Shandong, China as the study area, and based on the Landsat-5 TM and ALOS AVNIR-2 images, the canopy retrieval reflectance of apple trees at blossom stage was acquired. In combining with the measured reflectance of sample trees, the nitrogen-sensitive spectral indices were constructed and selected. By using the sensitive spectral indices as the independent variables, the nitrogen retrieval models were established, and the model with the best accuracy was used for spatial retrieve. The correlations between the spectral indices and the nitrogen nutritional status were in the order of canopy > leaf > flower. The sensitive indices were mainly composed of green, red, and near infrared bands. The accuracy of the retrieval models was in the order of support vector regression > multi-variable stepwise regression > one-variable regression. The retrieval results based on different images were similar, and showed that the leaf nitrogen content was mainly of grades 3-4 (27-33 g x kg(-1)), and the canopy nitrogen nutrient indices were mainly of grades 2-4 (TM: 38-47 g x kg(-1); ALOS: 32-41 g x kg(-1)). The spatial distribution of the retrieval nitrogen nutritional status based on different images also showed the similar trend, i. e., the nitrogen nutritional status was higher in the north and south than that in the middle part of the study area, and the areas with the high grades of leaf nitrogen and canopy nitrogen were mainly located in Sujiadian Town and Songshan subdistrict in the northwest, Zangjiazhuang Town and Tingkou Town in the northeast, and Shewopo Town in the south, which were consistent with the distribution of the key towns for apple production in Qixia City. This study provided a feasible method for the acquisition of nitrogen nutritional status of apple trees on macroscopic scale, and also, provided reference for other similar remote sensing retrievals.

Trees, chemistry, and prehistory in the American Southwest

USGS Publications Warehouse

Durand, S.R.; Shelley, P.H.; Antweiler, Ronald C.; Taylor, Howard E.

1999-01-01

At least 200 000 trees were used in the building construction in Chaco Canyon, New Mexico, from about (AD) 850-1150. A large portion of these construction timbers were transported 50 km or more and the harvesting location(s) is not known. We argue that a feasible method for determining the wood source areas is to chemically characterize the possible source areas using modern wood and then attempt to match the prehistoric timbers to the modern signatures. This paper establishes the feasibility of this method. ICP-AES was employed to obtain element concentration values for 29 elements, from 62 trees, on three bedrock types. We conclude that it is possible to isolate the variation due to lithology if one controls for wood type (bark, sapwood, heartwood). In addition, ICP-MS was used for the analysis of a small sample of ancient wood. Data from these determinations are presented and the results indicate that the elemental variation is consistent with the most current model of wood use practices in Chaco Canyon. The methods pioneered here should be broadly applicable for determining wood source areas.

The complete mitochondrial genome of the Aluterus monoceros.

PubMed

Li, Wenshen; Zhang, Guoqing; Wen, Xin; Wang, Qian; Chen, Guohua

2016-07-01

The complete mitochondrial genome of Aluterus monoceros (A. monoceros) has been sequenced. The mitochondrial genome of A. monoceros is 16,429 bp in length, consisting of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and a D-loop region (Gen Bank accession number KP637022). The base A + T of the mitochondrial genome is 63.25%, including 33.16% of A, 30.09% of T and 20.74% of C. Twelve protein-coding genes start with a standard ATG as the initiation codon, expect for the COXI, which begins with GTG. Some of the termination codons are incomplete T or TA, except for the ND1, COXI, ATP8, ND4L1, ND5 and ND6, which stop with TAA. Construction of phylogenetic trees based on the entire mitochondrial genome sequence of 14 Tetrodontiformes species constructed has suggested that A. monoceros has closer relationship with Acreichthys tomentosus and Monacanthus chinensis, and they constitute a sister group.

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

Strauss, Steve; Shevchenko, Olga; Ma, Caiping

The overall goal of this project was to develop and validate sterility systems in poplar with the ultimate goal of fulfilling the basic requirements for commercial use. For this, sterility must be complete and stable over multiple growing seasons, cause no detrimental effects on vegetative growth, and successful transformation events must be identifiable via molecular tests when trees are still juvenile. Because of the inherent difficulties in achieving and demonstrating complete sterility in trees, our approach was to study alternate sterility systems in Arabidopsis and/or early-flowering tree systems. The public benefit from this work is the capacity for containment ofmore » genes or exotic forms of trees so they can be of benefit for industry for production of wood, energy, and renewable products, while having minimal impact on wild populations of trees. We tested three methods for engineering sterility: dominant negative mutant (DNM) proteins, floral tissue ablation, and RNA interference (RNAi) to suppress the expression of several floral regulatory genes. The ultimate goal of this work was to produce a number of transgenic poplars that could be outplanted to enable future assessments of the effectiveness of these transgenic sterility methods. Our attempts to produce ablation constructs that did not interfere with tree health were partially successful. Using the poplar LEAFY gene promoter and the barnase/barstar system, we were able to regenerate plants that grew well in the greenhouse, but they showed poor health in the field. Four of seven DNM genes tested were considered promising enough, based on results in Arabidopsis, to produce transgenic poplars. Single, double, and triple RNAi genes were produced and transformed into poplar. Over all, we produced 1,964 PCR-confirmed transgenic events with 19 different kinds of sterility genes and several kinds of control genes. We propagated 5,640, 6,820, and 7,055 trees for each of three test poplar genotypes, and field plantings were begun in Spring of 2003 and will be finished in Spring 2007. Continued field studies and monitoring will be required to establish if any of the approaches we have taken will prove to be safe for tree health, stable, and provide reliable containment.« less

Detection of fraudulent financial statements using the hybrid data mining approach.

PubMed

Chen, Suduan

2016-01-01

The purpose of this study is to construct a valid and rigorous fraudulent financial statement detection model. The research objects are companies which experienced both fraudulent and non-fraudulent financial statements between the years 2002 and 2013. In the first stage, two decision tree algorithms, including the classification and regression trees (CART) and the Chi squared automatic interaction detector (CHAID) are applied in the selection of major variables. The second stage combines CART, CHAID, Bayesian belief network, support vector machine and artificial neural network in order to construct fraudulent financial statement detection models. According to the results, the detection performance of the CHAID-CART model is the most effective, with an overall accuracy of 87.97 % (the FFS detection accuracy is 92.69 %).

Signatures of microevolutionary processes in phylogenetic patterns.

PubMed

Costa, Carolina L N; Lemos-Costa, Paula; Marquitti, Flavia M D; Fernandes, Lucas D; Ramos, Marlon F; Schneider, David M; Martins, Ayana B; Aguiar, Marcus A M

2018-06-23

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Complexity Characteristics of Currency Networks

NASA Astrophysics Data System (ADS)

Gorski, A. Z.; Drozdz, S.; Kwapien, J.; Oswiecimka, P.

2006-11-01

A large set of daily FOREX time series is analyzed. The corresponding correlation matrices (CM) are constructed for USD, EUR and PLN used as the base currencies. The triangle rule is interpreted as constraints reducing the number of independent returns. The CM spectrum is computed and compared with the cases of shuffled currencies and a fictitious random currency taken as a base currency. The Minimal Spanning Tree (MST) graphs are calculated and the clustering effects for strong currencies are found. It is shown that for MSTs the node rank has power like, scale free behavior. Finally, the scaling exponents are evaluated and found in the range analogous to those identified recently for various complex networks.

Tree mortality rates and tree population projections in Baltimore, Maryland, USA

Treesearch

David J. Nowak; Miki Kuroda; Daniel E. Crane

2004-01-01

Based on re-measurements (1999 and 2001) of randomly-distributed permanent plots within the city boundaries of Baltimore, Maryland, trees are estimated to have an annual mortality rate of 6.6% with an overall annual net change in the number of live trees of -4.2%. Tree mortality rates were significantly different based on tree size, condition, species, and Land use....

Drought stress, growth and nonstructural carbohydrate dynamics of pine trees in a semi-arid forest.

PubMed

Klein, Tamir; Hoch, Günter; Yakir, Dan; Körner, Christian

2014-09-01

In trees exposed to prolonged drought, both carbon uptake (C source) and growth (C sink) typically decrease. This correlation raises two important questions: (i) to what degree is tree growth limited by C availability; and (ii) is growth limited by concurrent C storage (e.g., as nonstructural carbohydrates, NSC)? To test the relationships between drought, growth and C reserves, we monitored the changes in NSC levels and constructed stem growth chronologies of mature Pinus halepensis Miller trees of three drought stress levels growing in Yatir forest, Israel, at the dry distribution limit of forests. Moderately stressed and stressed trees showed 34 and 14% of the stem growth, 71 and 31% of the sap flux density, and 79 and 66% of the final needle length of healthy trees in 2012. In spite of these large reductions in growth and sap flow, both starch and soluble sugar concentrations in the branches of these trees were similar in all trees throughout the dry season (2-4% dry mass). At the same time, the root starch concentrations of moderately stressed and stressed trees were 47 and 58% of those of healthy trees, but never <2% dry mass. Our results show that all the studied trees maintain a fairly good coordination between C supply and demand, and even during prolonged drought there is more than one way for a tree to maintain a positive C balance. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Research on Robustness of Tree-based P2P Streaming

NASA Astrophysics Data System (ADS)

Chu, Chen; Yan, Jinyao; Ding, Kuangzheng; Wang, Xi

Research on P2P streaming media is a hot topic in the area of Internet technology. It has emerged as a promising technique. This new paradigm brings a number of unique advantages such as scalability, resilience and also effectiveness in coping with dynamics and heterogeneity. However, There are also many problems in P2P streaming media systems using traditional tree-based topology such as the bandwidth limits between parents and child nodes; node's joining or leaving has a great effect on robustness of tree-based topology. This paper will introduce a method of measuring the robustness of tree-based topology: using network measurement, we observe and record the bandwidth between all the nodes, analyses the correlation between all the sibling flows, measure the robustness of tree-based topology. And the result shows that in the Tree-based topology, the different links which have similar routing paths would share the bandwidth bottleneck, reduce the robustness of the Tree-based topology.

Privacy-Preserving Classifier Learning

NASA Astrophysics Data System (ADS)

Brickell, Justin; Shmatikov, Vitaly

We present an efficient protocol for the privacy-preserving, distributed learning of decision-tree classifiers. Our protocol allows a user to construct a classifier on a database held by a remote server without learning any additional information about the records held in the database. The server does not learn anything about the constructed classifier, not even the user’s choice of feature and class attributes.