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Sample records for parse tree apt

  1. Dependency Parsing

    CERN Document Server

    Kubler, Sandra; Nivre, Joakim

    2009-01-01

    Dependency-based methods for syntactic parsing have become increasingly popular in natural language processing in recent years. This book gives a thorough introduction to the methods that are most widely used today. After an introduction to dependency grammar and dependency parsing, followed by a formal characterization of the dependency parsing problem, the book surveys the three major classes of parsing models that are in current use: transition-based, graph-based, and grammar-based models. It continues with a chapter on evaluation and one on the comparison of different methods, and it close

  2. Inducing Head-Driven PCFGs with Latent Heads: Refining a Tree-bank Grammar for Parsing

    NARCIS (Netherlands)

    Prescher, D.; Gama, J.; Camacho, R.; Brazdil, P.; Jorge, A.; Torgo, L.

    2005-01-01

    Although state-of-the-art parsers for natural language are lexicalized, it was recently shown that an accurate unlexicalized parser for the Penn tree-bank can be simply read off a manually refined tree-bank. While lexicalized parsers often suffer from sparse data, manual mark-up is costly and

  3. Bit-coded regular expression parsing

    DEFF Research Database (Denmark)

    Nielsen, Lasse; Henglein, Fritz

    2011-01-01

    the DFA-based parsing algorithm due to Dub ´e and Feeley to emit the bits of the bit representation without explicitly materializing the parse tree itself. We furthermore show that Frisch and Cardelli’s greedy regular expression parsing algorithm can be straightforwardly modified to produce bit codings...

  4. Two-pass greedy regular expression parsing

    DEFF Research Database (Denmark)

    Grathwohl, Niels Bjørn Bugge; Henglein, Fritz; Nielsen, Lasse

    2013-01-01

    We present new algorithms for producing greedy parses for regular expressions (REs) in a semi-streaming fashion. Our lean-log algorithm executes in time O(mn) for REs of size m and input strings of size n and outputs a compact bit-coded parse tree representation. It improves on previous algorithms...... by: operating in only 2 passes; using only O(m) words of random-access memory (independent of n); requiring only kn bits of sequentially written and read log storage, where k ... and not requiring it to be stored at all. Previous RE parsing algorithms do not scale linearly with input size, or require substantially more log storage and employ 3 passes where the first consists of reversing the input, or do not or are not known to produce a greedy parse. The performance of our unoptimized C...

  5. Dual decomposition for parsing with non-projective head automata

    OpenAIRE

    Koo, Terry; Rush, Alexander Matthew; Collins, Michael; Jaakkola, Tommi S.; Sontag, David Alexander

    2010-01-01

    This paper introduces algorithms for non-projective parsing based on dual decomposition. We focus on parsing algorithms for non-projective head automata, a generalization of head-automata models to non-projective structures. The dual decomposition algorithms are simple and efficient, relying on standard dynamic programming and minimum spanning tree algorithms. They provably solve an LP relaxation of the non-projective parsing problem. Empirically the LP relaxation is very often tight: for man...

  6. Faster, Practical GLL Parsing

    NARCIS (Netherlands)

    A. Afroozeh (Ali); A. Izmaylova (Anastasia)

    2015-01-01

    htmlabstractGeneralized LL (GLL) parsing is an extension of recursive-descent (RD) parsing that supports all context-free grammars in cubic time and space. GLL parsers have the direct relationship with the grammar that RD parsers have, and therefore, compared to GLR, are easier to understand, debug,

  7. Unifying LL and LR parsing

    NARCIS (Netherlands)

    W.H.L.M. Pijls (Wim)

    1993-01-01

    textabstractIn parsing theory, LL parsing and LR parsing are regarded to be two distinct methods. In this paper the relation between these methods is clarified.As shown in literature on parsing theory, for every context-free grammar, a so-called non-deterministic LR(0) automaton can be constructed.

  8. YakYak: Parsing with Logical Side Constraints

    DEFF Research Database (Denmark)

    Hansen, Niels Damgaard; Klarlund, Nils; Schwartzbach, Michael Ignatieff

    2000-01-01

    Yak, which extends Yacc with first-order logic for specifying consteaints that are regular tree languages. Concise formulas about the parse tree replace explicit programming, and they are turned into canonical attribute grammars through tree automata calculations. YakYak is implemented as a proprocessor...

  9. Apte, Dr Shree Kumar

    Indian Academy of Sciences (India)

    Elected: 2008 Section: General Biology. Apte, Dr Shree Kumar Ph.D. (Gujarat), FNA, FNASc, FNAAS. Date of birth: 18 October 1952. Specialization: Molecular Biology & Biotechnology, Physiology and Stress Biology of Bacteria & Plants Address: Emeritus Professor, Homi Bhabha National Institute, Anushakti Nagar, ...

  10. APT: Aperture Photometry Tool

    Science.gov (United States)

    Laher, Russ

    2012-08-01

    Aperture Photometry Tool (APT) is software for astronomers and students interested in manually exploring the photometric qualities of astronomical images. It has a graphical user interface (GUI) which allows the image data associated with aperture photometry calculations for point and extended sources to be visualized and, therefore, more effectively analyzed. Mouse-clicking on a source in the displayed image draws a circular or elliptical aperture and sky annulus around the source and computes the source intensity and its uncertainty, along with several commonly used measures of the local sky background and its variability. The results are displayed and can be optionally saved to an aperture-photometry-table file and plotted on graphs in various ways using functions available in the software. APT is geared toward processing sources in a small number of images and is not suitable for bulk processing a large number of images, unlike other aperture photometry packages (e.g., SExtractor). However, APT does have a convenient source-list tool that enables calculations for a large number of detections in a given image. The source-list tool can be run either in automatic mode to generate an aperture photometry table quickly or in manual mode to permit inspection and adjustment of the calculation for each individual detection. APT displays a variety of useful graphs, including image histogram, and aperture slices, source scatter plot, sky scatter plot, sky histogram, radial profile, curve of growth, and aperture-photometry-table scatter plots and histograms. APT has functions for customizing calculations, including outlier rejection, pixel “picking” and “zapping,” and a selection of source and sky models. The radial-profile-interpolation source model, accessed via the radial-profile-plot panel, allows recovery of source intensity from pixels with missing data and can be especially beneficial in crowded fields.

  11. On Parsing CHILDES

    OpenAIRE

    Laakso, Aarre

    2005-01-01

    Research on child language acquisition would benefit from the availability of a large body of syntactically parsed utterances between parents and children. We consider the problem of generating such a ``treebank'' from the CHILDES corpus, which currently contains primarily orthographically transcribed speech tagged for lexical category.

  12. Faster scannerless GLR parsing

    NARCIS (Netherlands)

    Economopoulos, G.R.; Klint, P.; Vinju, J.J.; Moor, de O.; Schwartzbach, M.I.

    2009-01-01

    Analysis and renovation of large software portfolios requires syntax analysis of multiple, usually embedded, languages and this is beyond the capabilities of many standard parsing techniques. The traditional separation between lexer and parser falls short due to the limitations of tokenization based

  13. Faster Scannerless GLR parsing

    NARCIS (Netherlands)

    J.J. Vinju (Jurgen); G.R. Economopoulos (Giorgos Robert); P. Klint (Paul)

    2008-01-01

    textabstractAnalysis and renovation of large software portfolios requires syntax analysis of multiple, usually embedded, languages and this is beyond the capabilities of many standard parsing techniques. The traditional separation between lexer and parser falls short due to the limitations of

  14. Faster scannerless GLR parsing

    NARCIS (Netherlands)

    G.R. Economopoulos (Giorgos Robert); P. Klint (Paul); J.J. Vinju (Jurgen); O. de Moor; M.I. Schwartzbach

    2009-01-01

    textabstractAnalysis and renovation of large software portfolios requires syntax analysis of multiple, usually embedded, languages and this is beyond the capabilities of many standard parsing techniques. The traditional separation between lexer and parser falls short due to the limitations of

  15. Memory-Based Shallow Parsing

    NARCIS (Netherlands)

    Tjong Kim Sang, E.F.

    2002-01-01

    We present memory-based learning approaches to shallow parsing and apply these to five tasks: base noun phrase identification, arbitrary base phrase recognition, clause detection, noun phrase parsing and full parsing. We use feature selection techniques and system combination methods for improving

  16. APT accelerator. Topical report

    International Nuclear Information System (INIS)

    Lawrence, G.; Rusthoi, D.

    1995-03-01

    The Accelerator Production of Tritium (APT) project, sponsored by Department of Energy Defense Programs (DOE/DP), involves the preconceptual design of an accelerator system to produce tritium for the nation's stockpile of nuclear weapons. Tritium is an isotope of hydrogen used in nuclear weapons, and must be replenished because of radioactive decay (its half-life is approximately 12 years). Because the annual production requirements for tritium has greatly decreased since the end of the Cold War, an alternative approach to reactors for tritium production, based on a linear accelerator, is now being seriously considered. The annual tritium requirement at the time this study was undertaken (1992-1993) was 3/8 that of the 1988 goal, usually stated as 3/8-Goal. Continued reduction in the number of weapons in the stockpile has led to a revised (lower) production requirement today (March, 1995). The production requirement needed to maintain the reduced stockpile, as stated in the recent Nuclear Posture Review (summer 1994) is approximately 3/16-Goal, half the previous level. The Nuclear Posture Review also requires that the production plant be designed to accomodate a production increase (surge) to 3/8-Goal capability within five years, to allow recovery from a possible extended outage of the tritium plant. A multi-laboratory team, collaborating with several industrial partners, has developed a preconceptual APT design for the 3/8-Goal, operating at 75% capacity. The team has presented APT as a promising alternative to the reactor concepts proposed for Complex-21. Given the requirements of a reduced weapons stockpile, APT offers both significant safety, environmental, and production-fexibility advantages in comparison with reactor systems, and the prospect of successful development in time to meet the US defense requirements of the 21st Century

  17. APT accelerator. Topical report

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, G.; Rusthoi, D. [comp.] [ed.

    1995-03-01

    The Accelerator Production of Tritium (APT) project, sponsored by Department of Energy Defense Programs (DOE/DP), involves the preconceptual design of an accelerator system to produce tritium for the nation`s stockpile of nuclear weapons. Tritium is an isotope of hydrogen used in nuclear weapons, and must be replenished because of radioactive decay (its half-life is approximately 12 years). Because the annual production requirements for tritium has greatly decreased since the end of the Cold War, an alternative approach to reactors for tritium production, based on a linear accelerator, is now being seriously considered. The annual tritium requirement at the time this study was undertaken (1992-1993) was 3/8 that of the 1988 goal, usually stated as 3/8-Goal. Continued reduction in the number of weapons in the stockpile has led to a revised (lower) production requirement today (March, 1995). The production requirement needed to maintain the reduced stockpile, as stated in the recent Nuclear Posture Review (summer 1994) is approximately 3/16-Goal, half the previous level. The Nuclear Posture Review also requires that the production plant be designed to accomodate a production increase (surge) to 3/8-Goal capability within five years, to allow recovery from a possible extended outage of the tritium plant. A multi-laboratory team, collaborating with several industrial partners, has developed a preconceptual APT design for the 3/8-Goal, operating at 75% capacity. The team has presented APT as a promising alternative to the reactor concepts proposed for Complex-21. Given the requirements of a reduced weapons stockpile, APT offers both significant safety, environmental, and production-fexibility advantages in comparison with reactor systems, and the prospect of successful development in time to meet the US defense requirements of the 21st Century.

  18. Parse Journal #2: Introduction

    OpenAIRE

    Bowman, Jason; Malik, Suhail; Phillips, Andrea

    2015-01-01

    As a periodical concerned with the critical potential of artistic research, this edition of the PARSE journal mobilises the multiple perspectives of artists, thinkers, critics and curators on the problematics, discontents and possibilities of private capital as an unregulated yet assumptive producer of art’s value, including its integration with state-funding. We have put emphasis on how this conditioning of art’s production, circulation, reception and sale can be put to task. In particular, ...

  19. APT accelerator technology

    International Nuclear Information System (INIS)

    Schneider, J. David

    1996-01-01

    The proposed accelerator production of tritium (APT) project requires an accelerator that provides a cw proton beam of 100 m A at 1300 MeV. Since the majority of the technical risk of a high-current cw (continuous-wave, 100% DF) accelerator resides in the low-energy section, Los Alamos is building a 20 MeV duplicate of the accelerator front end to confirm design codes, beam performance, and demonstrate operational reliability. We report on design details of this low-energy demonstration accelerator (LEDA) and discuss the integrated design of the full accelerator for the APT plant. LEDA's proton injector is under test and has produced more than 130 mA at 75 keV. Fabrication is proceeding on a 6.7- MeV, 8-meter-long RFQ, and detailed design is underway on coupled-cavity drift-tube linac (CCDTL) structures. In addition, detailed design and technology experiments are underway on medium-beta superconducting cavities to assess the feasibility of replacing the conventional (room-temperature copper) high-energy linac with a linac made of niobium superconducting RF cavities. (author)

  20. Memory-Based Shallow Parsing

    OpenAIRE

    Sang, Erik F. Tjong Kim

    2002-01-01

    We present memory-based learning approaches to shallow parsing and apply these to five tasks: base noun phrase identification, arbitrary base phrase recognition, clause detection, noun phrase parsing and full parsing. We use feature selection techniques and system combination methods for improving the performance of the memory-based learner. Our approach is evaluated on standard data sets and the results are compared with that of other systems. This reveals that our approach works well for ba...

  1. Parsing Heterogeneous Striatal Activity

    Directory of Open Access Journals (Sweden)

    Kae Nakamura

    2017-05-01

    Full Text Available The striatum is an input channel of the basal ganglia and is well known to be involved in reward-based decision making and learning. At the macroscopic level, the striatum has been postulated to contain parallel functional modules, each of which includes neurons that perform similar computations to support selection of appropriate actions for different task contexts. At the single-neuron level, however, recent studies in monkeys and rodents have revealed heterogeneity in neuronal activity even within restricted modules of the striatum. Looking for generality in the complex striatal activity patterns, here we briefly survey several types of striatal activity, focusing on their usefulness for mediating behaviors. In particular, we focus on two types of behavioral tasks: reward-based tasks that use salient sensory cues and manipulate outcomes associated with the cues; and perceptual decision tasks that manipulate the quality of noisy sensory cues and associate all correct decisions with the same outcome. Guided by previous insights on the modular organization and general selection-related functions of the basal ganglia, we relate striatal activity patterns on these tasks to two types of computations: implementation of selection and evaluation. We suggest that a parsing with the selection/evaluation categories encourages a focus on the functional commonalities revealed by studies with different animal models and behavioral tasks, instead of a focus on aspects of striatal activity that may be specific to a particular task setting. We then highlight several questions in the selection-evaluation framework for future explorations.

  2. Video Scene Parsing with Predictive Feature Learning

    OpenAIRE

    Jin, Xiaojie; Li, Xin; Xiao, Huaxin; Shen, Xiaohui; Lin, Zhe; Yang, Jimei; Chen, Yunpeng; Dong, Jian; Liu, Luoqi; Jie, Zequn; Feng, Jiashi; Yan, Shuicheng

    2016-01-01

    In this work, we address the challenging video scene parsing problem by developing effective representation learning methods given limited parsing annotations. In particular, we contribute two novel methods that constitute a unified parsing framework. (1) \\textbf{Predictive feature learning}} from nearly unlimited unlabeled video data. Different from existing methods learning features from single frame parsing, we learn spatiotemporal discriminative features by enforcing a parsing network to ...

  3. Dependency Parsing with Transformed Feature

    Directory of Open Access Journals (Sweden)

    Fuxiang Wu

    2017-01-01

    Full Text Available Dependency parsing is an important subtask of natural language processing. In this paper, we propose an embedding feature transforming method for graph-based parsing, transform-based parsing, which directly utilizes the inner similarity of the features to extract information from all feature strings including the un-indexed strings and alleviate the feature sparse problem. The model transforms the extracted features to transformed features via applying a feature weight matrix, which consists of similarities between the feature strings. Since the matrix is usually rank-deficient because of similar feature strings, it would influence the strength of constraints. However, it is proven that the duplicate transformed features do not degrade the optimization algorithm: the margin infused relaxed algorithm. Moreover, this problem can be alleviated by reducing the number of the nearest transformed features of a feature. In addition, to further improve the parsing accuracy, a fusion parser is introduced to integrate transformed and original features. Our experiments verify that both transform-based and fusion parser improve the parsing accuracy compared to the corresponding feature-based parser.

  4. Contextual Semantic Parsing using Crowdsourced Spatial Descriptions

    OpenAIRE

    Dukes, Kais

    2014-01-01

    We describe a contextual parser for the Robot Commands Treebank, a new crowdsourced resource. In contrast to previous semantic parsers that select the most-probable parse, we consider the different problem of parsing using additional situational context to disambiguate between different readings of a sentence. We show that multiple semantic analyses can be searched using dynamic programming via interaction with a spatial planner, to guide the parsing process. We are able to parse sentences in...

  5. Amtrak performance tracking (APT) system : methodology summary

    Science.gov (United States)

    2017-09-15

    The Volpe Center collaborated with Amtrak and the Federal Railroad Administration (FRA) to develop a cost accounting system named Amtrak Performance Tracking (APT) used by Amtrak to manage, allocate, and report its costs. APTs initial development ...

  6. Waste management plan for the APT

    International Nuclear Information System (INIS)

    England, J.L.

    1997-01-01

    This revision of the APT Waste Management Plan details the waste management requirements and issues specific to the APT plant for design considerations, construction, and operation. The APT Waste Management Plan is by its nature a living document and will be reviewed at least annually and revised as required

  7. Parsing Universal Dependencies without training

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Agic, Zeljko; Plank, Barbara

    2017-01-01

    We present UDP, the first training-free parser for Universal Dependencies (UD). Our algorithm is based on PageRank and a small set of specific dependency head rules. UDP features two-step decoding to guarantee that function words are attached as leaf nodes. The parser requires no training......, and it is competitive with a delexicalized transfer system. UDP offers a linguistically sound unsupervised alternative to cross-lingual parsing for UD. The parser has very few parameters and distinctly robust to domain change across languages....

  8. Automated prototyping tool-kit (APT)

    OpenAIRE

    Nada, Nader; Shing, M.; Berzins, V.; Luqi

    2002-01-01

    Automated prototyping tool-kit (APT) is an integrated set of software tools that generate source programs directly from real-time requirements. The APT system uses a fifth-generation prototyping language to model the communication structure, timing constraints, 1/0 control, and data buffering that comprise the requirements for an embedded software system. The language supports the specification of hard real-time systems with reusable components from domain specific component libraries. APT ha...

  9. Toward the Soundness of Sense Structure Definitions in Thesaurus-Dictionaries. Parsing Problems and Solutions

    Directory of Open Access Journals (Sweden)

    Neculai Curteanu

    2012-10-01

    Full Text Available In this paper we point out some difficult problems of thesaurus-dictionary entry parsing, relying on the parsing technology of SCD (Segmentation-Cohesion-Dependency configurations, successfully applied on six largest thesauri -- Romanian (2, French, German (2, and Russian. \\textbf{Challenging Problems:} \\textbf{(a}~Intricate and~/~or recursive structures of the lexicographic segments met in the entries of certain thesauri; \\textbf{(b}~Cyclicity (recursive calls of some sense marker classes on marker sequences; \\textbf{(c}~Establishing the hypergraph-driven dependencies between all the atomic and non-atomic sense definitions. Classical approach to solve these parsing problems is hard mainly because of depth-first search of sense definitions and markers, the substantial complexity of entries, and the sense tree dynamic construction embodied within these parsers. \\textbf{SCD-based Parsing Solutions:} \\textbf{(a}~The SCD parsing method is a procedural tool, completely formal grammar-free, handling the recursive structure of the lexicographic segments by procedural non-recursive calls performed on the SCD parsing configurations of the entry structure. \\textbf{(b}~For dealing with cyclicity (recursive calls between secondary sense markers and the sense enumeration markers, we proposed the Enumeration Closing Condition, sometimes coupled with New{\\_}Paragraphs typographic markers transformed into numeral sense enumeration. \\textbf{(c}~These problems, their lexicographic modeling and parsing solutions are addressed to both dictionary parser programmers to experience the SCD-based parsing method, as well as to lexicographers and thesauri designers for tailoring balanced lexical-semantics granularities and sounder sense tree definitions of the dictionary entries.

  10. Technical memorandum: instrumentation for APT and LTPP

    CSIR Research Space (South Africa)

    Steyn, WJvdM

    2006-01-01

    Full Text Available . In these phases, the parameters to be monitored on APT and LTPP sections have been identified, appropriate instruments and sensors for monitoring these parameters have been identified, and recommendations made regarding new developments, required upgrading...

  11. Probabilistic lexical generalization for French dependency parsing

    OpenAIRE

    Henestroza Anguiano , Enrique; Candito , Marie

    2012-01-01

    International audience; This paper investigates the impact on French dependency parsing of lexical generalization methods beyond lemmatization and morphological analysis. A distributional thesaurus is created from a large text corpus and used for distributional clustering and WordNet automatic sense ranking. The standard approach for lexical generalization in parsing is to map a word to a single generalized class, either replacing the word with the class or adding a new feature for the class....

  12. Context-free parsing with connectionist networks

    Science.gov (United States)

    Fanty, M. A.

    1986-08-01

    This paper presents a simple algorithm which converts any context-free grammar into a connectionist network which parses strings (of arbitrary but fixed maximum length) in the language defined by that grammar. The network is fast, O(n), and deterministicd. It consists of binary units which compute a simple function of their input. When the grammar is put in Chomsky normal form, O(n3) units needed to parse inputs of length up to n.

  13. Interrogation of duplicitous stars with an APT

    Science.gov (United States)

    Bopp, Bernard W.

    1992-01-01

    Preliminary results from intensive spectroscopic and APT monitoring of two interacting binary systems are presented. Both V644 Mon (Be + K:) and HD 37453 (F5 II + B) show complex, composite, and variable spectral. APT observations extending over three years show both stars to vary by 0.1-0.2 mag in V. The photometric variability of V644 Mon appears to be irregular, though there is some evidence for periodic behavior in the 50-60 day range. HD 37453 has an orbital period of 66.75 days; the best-fit photometric period is not quite half this value, indicating the star is an ellipsoidal variable.

  14. APT and CEST Techniques for Clinical MRI

    NARCIS (Netherlands)

    Keupp, J.

    2011-01-01

    Chemical exchange saturation transfer (CEST) based in vivo detectionand quantification of endogenous macro-molecules (i.e., amide proton transfer, APT) or exogenous contrast agents is a highly sensitivemolecular MRI technique bearing a substantial clinical potential forexample in oncology or for

  15. Application development with Parse using iOS SDK

    CERN Document Server

    Birani, Bhanu

    2013-01-01

    A practical guide, featuring step-by-step instructions showing you how to use Parse iOS, and handle your data on cloud.If you are a developer who wants to build your applications instantly using Parse iOS as a back end application development, this book is ideal for you. This book will help you to understand Parse, featuring examples to help you get familiar with the concepts of Parse iOS.

  16. A Semantic Constraint on Syntactic Parsing.

    Science.gov (United States)

    Crain, Stephen; Coker, Pamela L.

    This research examines how semantic information influences syntactic parsing decisions during sentence processing. In the first experiment, subjects were presented lexical strings having syntactically identical surface structures but with two possible underlying structures: "The children taught by the Berlitz method," and "The…

  17. Sequence distance via parsing complexity: Heartbeat signals

    International Nuclear Information System (INIS)

    Degli Esposti, M.; Farinelli, C.; Menconi, G.

    2009-01-01

    We compare and discuss the use of different symbolic codings of electrocardiogram (ECG) signals in order to distinguish healthy patients from hospitalized ones. To this aim, we recall a parsing-based similarity distance and compare the performances of several methods of classification of data.

  18. Perceiving Event Dynamics and Parsing Hollywood Films

    Science.gov (United States)

    Cutting, James E.; Brunick, Kaitlin L.; Candan, Ayse

    2012-01-01

    We selected 24 Hollywood movies released from 1940 through 2010 to serve as a film corpus. Eight viewers, three per film, parsed them into events, which are best termed subscenes. While watching a film a second time, viewers scrolled through frames and recorded the frame number where each event began. Viewers agreed about 90% of the time. We then…

  19. Parsing polarization squeezing into Fock layers

    DEFF Research Database (Denmark)

    Mueller, Christian R.; Madsen, Lars Skovgaard; Klimov, Andrei B.

    2016-01-01

    photon number do the methods coincide; when the photon number is indefinite, we parse the state in Fock layers, finding that substantially higher squeezing can be observed in some of the single layers. By capitalizing on the properties of the Husimi Q function, we map this notion onto the Poincare space......, providing a full account of the measured squeezing....

  20. Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture

    Science.gov (United States)

    Lassahn, Gordon D.; Lancaster, Gregory D.; Apel, William A.; Thompson, Vicki S.

    2013-01-08

    Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.

  1. A structural SVM approach for reference parsing.

    Science.gov (United States)

    Zhang, Xiaoli; Zou, Jie; Le, Daniel X; Thoma, George R

    2011-06-09

    Automated extraction of bibliographic data, such as article titles, author names, abstracts, and references is essential to the affordable creation of large citation databases. References, typically appearing at the end of journal articles, can also provide valuable information for extracting other bibliographic data. Therefore, parsing individual reference to extract author, title, journal, year, etc. is sometimes a necessary preprocessing step in building citation-indexing systems. The regular structure in references enables us to consider reference parsing a sequence learning problem and to study structural Support Vector Machine (structural SVM), a newly developed structured learning algorithm on parsing references. In this study, we implemented structural SVM and used two types of contextual features to compare structural SVM with conventional SVM. Both methods achieve above 98% token classification accuracy and above 95% overall chunk-level accuracy for reference parsing. We also compared SVM and structural SVM to Conditional Random Field (CRF). The experimental results show that structural SVM and CRF achieve similar accuracies at token- and chunk-levels. When only basic observation features are used for each token, structural SVM achieves higher performance compared to SVM since it utilizes the contextual label features. However, when the contextual observation features from neighboring tokens are combined, SVM performance improves greatly, and is close to that of structural SVM after adding the second order contextual observation features. The comparison of these two methods with CRF using the same set of binary features show that both structural SVM and CRF perform better than SVM, indicating their stronger sequence learning ability in reference parsing.

  2. Telugu dependency parsing using different statistical parsers

    Directory of Open Access Journals (Sweden)

    B. Venkata Seshu Kumari

    2017-01-01

    Full Text Available In this paper we explore different statistical dependency parsers for parsing Telugu. We consider five popular dependency parsers namely, MaltParser, MSTParser, TurboParser, ZPar and Easy-First Parser. We experiment with different parser and feature settings and show the impact of different settings. We also provide a detailed analysis of the performance of all the parsers on major dependency labels. We report our results on test data of Telugu dependency treebank provided in the ICON 2010 tools contest on Indian languages dependency parsing. We obtain state-of-the art performance of 91.8% in unlabeled attachment score and 70.0% in labeled attachment score. To the best of our knowledge ours is the only work which explored all the five popular dependency parsers and compared the performance under different feature settings for Telugu.

  3. Fast Parsing using Pruning and Grammar Specialization

    OpenAIRE

    Rayner, Manny; Carter, David

    1996-01-01

    We show how a general grammar may be automatically adapted for fast parsing of utterances from a specific domain by means of constituent pruning and grammar specialization based on explanation-based learning. These methods together give an order of magnitude increase in speed, and the coverage loss entailed by grammar specialization is reduced to approximately half that reported in previous work. Experiments described here suggest that the loss of coverage has been reduced to the point where ...

  4. Trees

    Science.gov (United States)

    Al-Khaja, Nawal

    2007-01-01

    This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

  5. Error Parsing: An alternative method of implementing social judgment theory

    OpenAIRE

    Crystal C. Hall; Daniel M. Oppenheimer

    2015-01-01

    We present a novel method of judgment analysis called Error Parsing, based upon an alternative method of implementing Social Judgment Theory (SJT). SJT and Error Parsing both posit the same three components of error in human judgment: error due to noise, error due to cue weighting, and error due to inconsistency. In that sense, the broad theory and framework are the same. However, SJT and Error Parsing were developed to answer different questions, and thus use different m...

  6. Superconducting cavities for the APT accelerator

    International Nuclear Information System (INIS)

    Krawczyk, F.L.; Gentzlinger, R.C.; Haynes, B.; Montoya, D.I.; Rusnak, B.; Shapiro, A.H.

    1997-01-01

    The design of an Accelerator Production of Tritium (APT) facility being investigated at Los Alamos includes a linear accelerator using superconducting rf-cavities for the acceleration of a high-current cw proton beam. For electron accelerators with particles moving at the speed of light (β ∼ 1.0), resonators with a rounded shape, consisting of ellipsoidal and cylindrical sections, are well established. They are referred to as elliptical cavities. For the APT-design, this shape has been adapted for much slower proton beams with β ranging from 0.60 to 0.94. This is a new energy range, in which resonators of an elliptical type have never been used before. Simulations with the well-proven electromagnetic modeling tools MAFIA and SUPERFISH were performed. The structures have been optimized for their rf and mechanical properties as well as for beam dynamics requirements. The TRAK-RF simulation code is used to investigate potential multipacting in these structures. All the simulations will be put to a final test in experiments performed on single cell cavities that have started in the structures laboratory

  7. A Parse Tree Model for Analyzing And Detecting SQL Injection ...

    African Journals Online (AJOL)

    2013-03-01

    Mar 1, 2013 ... a difficult task as it requires lots of hard ... additional cost to any organization that may ... change the logic, syntax, or semantic of a .... language (quest language, e.g., MySQL, ..... A Classification of SQL Injection Attacks and.

  8. Conceptual Design of an APT Reusable Spaceplane

    Science.gov (United States)

    Corpino, S.; Viola, N.

    This paper concerns the conceptual design of an Aerial Propellant Transfer reusable spaceplane carried out during our PhD course under the supervision of prof. Chiesa. The new conceptual design methodology employed in order to develop the APT concept and the main characteristics of the spaceplane itself will be presented and discussed. The methodology for conceptual design has been worked out during the last three years. It was originally thought for atmospheric vehicle design but, thanks to its modular structure which makes it very flexible, it has been possible to convert it to space transportation systems design by adding and/or modifying a few modules. One of the major improvements has been for example the conception and development of the mission simulation and trajectory optimisation module. The methodology includes as main characteristics and innovations the latest techniques of geometric modelling and logistic, operational and cost aspects since the first stages of the project. Computer aided design techniques are used to obtain a better definition of the product at the end of the conceptual design phase and virtual reality concepts are employed to visualise three-dimensional installation and operational aspects, at least in part replacing full-scale mock- ups. The introduction of parametric three-dimensional CAD software integrated into the conceptual design methodology represents a great improvement because it allows to carry out different layouts and to assess them immediately. It is also possible to link the CAD system to a digital prototyping software which combines 3D visualisation and assembly analysis, useful to define the so-called Digital Mock-Up at Conceptual Level (DMUCL) which studies the integration between the on board systems, sized with simulation algorithms, and the airframe. DMUCL represents a very good means to integrate the conceptual design with a methodology turned towards dealing with Reliability, Availability, Maintainability and

  9. Incremental Learning of Context Free Grammars by Parsing-Based Rule Generation and Rule Set Search

    Science.gov (United States)

    Nakamura, Katsuhiko; Hoshina, Akemi

    This paper discusses recent improvements and extensions in Synapse system for inductive inference of context free grammars (CFGs) from sample strings. Synapse uses incremental learning, rule generation based on bottom-up parsing, and the search for rule sets. The form of production rules in the previous system is extended from Revised Chomsky Normal Form A→βγ to Extended Chomsky Normal Form, which also includes A→B, where each of β and γ is either a terminal or nonterminal symbol. From the result of bottom-up parsing, a rule generation mechanism synthesizes minimum production rules required for parsing positive samples. Instead of inductive CYK algorithm in the previous version of Synapse, the improved version uses a novel rule generation method, called ``bridging,'' which bridges the lacked part of the derivation tree for the positive string. The improved version also employs a novel search strategy, called serial search in addition to minimum rule set search. The synthesis of grammars by the serial search is faster than the minimum set search in most cases. On the other hand, the size of the generated CFGs is generally larger than that by the minimum set search, and the system can find no appropriate grammar for some CFL by the serial search. The paper shows experimental results of incremental learning of several fundamental CFGs and compares the methods of rule generation and search strategies.

  10. Simulation of temperature conditions on APT of HMA mixes

    CSIR Research Space (South Africa)

    Steyn, WJVDM

    2008-10-01

    Full Text Available between these APT data and practical application of the outcomes of the tests. The paper starts with general background on the effect of temperature on the loading conditions and response of HMA materials, methods to manage it during APT testing...

  11. The APT model as reduced-rank regression

    NARCIS (Netherlands)

    Bekker, P.A.; Dobbelstein, P.; Wansbeek, T.J.

    Integrating the two steps of an arbitrage pricing theory (APT) model leads to a reduced-rank regression (RRR) model. So the results on RRR can be used to estimate APT models, making estimation very simple. We give a succinct derivation of estimation of RRR, derive the asymptotic variance of RRR

  12. Tree Notation: an antifragile program notation

    OpenAIRE

    Yunits, Breck

    2017-01-01

    This paper presents Tree Notation, a new simple, universal syntax. Language designers can invent new programming languages, called Tree Languages, on top of Tree Notation. Tree Languages have a number of advantages over traditional programming languages. We include a Visual Abstract to succinctly display the problem and discovery. Then we describe the problem--the BNF to abstract syntax tree (AST) parse step--and introduce the novel solution we discovered: a new family of 2D programming langu...

  13. APT LLRF control system functionality and architecture

    International Nuclear Information System (INIS)

    Regan, A.H.; Rohlev, A.S.; Ziomek, C.D.

    1996-01-01

    1% amplitude and l degree phase. The feedback control system requires a phase-stable RF reference subsystem signal to correctly phase each cavity. Also, instead of a single klystron RF source for individual accelerating cavities, multiple klystrons will drive a string of resonantly coupled cavities, based on input from a single LLRF feedback control system. To achieve maximum source efficiency, we will be employing single fast feedback controls around individual klystrons such that the gain and phase characteristics of each will be ''identical.'' In addition, resonance control is performed by providing a proper drive signal to structure cooling water valves in order to keep the cavity resonant during operation. To quickly respond to RF shutdowns, and hence rapid accelerating cavity cool- down, due to RF fault conditions, drive frequency agility in the main feedback control subsystem will also be incorporated. Top level block diagrams will be presented and described for each of the aforementioned subsystems as they will first be developed and demonstrated on the Low Energy Demonstrator Accelerator (LEDA) The low-level RF (LLRF) control system for the Accelerator Production of Tritium (APT) will perform various functions. Foremost is the feedback control of the accelerating fields within the cavity in order to maintain field stability within

  14. APT LLRF control system functionality and architecture

    International Nuclear Information System (INIS)

    Regan, A.H.; Rohlev, A.S.; Ziomek, C.D.

    1996-01-01

    The low-level RF (LLRF) control system for the Accelerator Production of Tritium (APT) will perform various functions. Foremost is the feedback control of the accelerating fields within the cavity in order to maintain field stability within ± 1% amplitude and 1 degree phase. The feedback control system requires a phase-stable RF reference subsystem signal to correctly phase each cavity. Also, instead of a single klystron RF source for individual accelerating cavities, multiple klystrons will drive a string of resonantly coupled cavities, based on input from a single LLRF feedback control system. To achieve maximum source efficiency, we will be employing single fast feedback controls around individual klystrons such that the gain and phase characteristics of each will be 'identical'. In addition, the resonance condition of the cavities is monitored and maintained. To quickly respond to RF shutdowns, and hence rapid accelerating cavity cool-down, due to RF fault conditions, drive frequency agility in the main feedback control subsystem will also be incorporated. Top level block diagrams will be presented and described as they will first be developed and demonstrated on the Low Energy Demonstrator Accelerator (LEDA). (author)

  15. Forest FIRE and FIRE wood : tools for tree automata and tree algorithms

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Piskorski, J.; Watson, B.W.; Yli-Jyrä, A.

    2009-01-01

    Pattern matching, acceptance, and parsing algorithms on node-labeled, ordered, ranked trees ('tree algorithms') are important for applications such as instruction selection and tree transformation/term rewriting. Many such algorithms have been developed. They often are based on results from such

  16. From LL-regular to LL(1) grammars: Transformations, covers and parsing

    NARCIS (Netherlands)

    Nijholt, Antinus

    1982-01-01

    In this paper it is shown that it is possible to transform any LL-regular grammar G into an LL(1) grammar G' in such a way that parsing G' is as good as parsing G. That is, a parse of a sentence of grammar G can be obtained with a simple string homomorphism from the parse of a corresponding sentence

  17. Chinese Unknown Word Recognition for PCFG-LA Parsing

    Directory of Open Access Journals (Sweden)

    Qiuping Huang

    2014-01-01

    Full Text Available This paper investigates the recognition of unknown words in Chinese parsing. Two methods are proposed to handle this problem. One is the modification of a character-based model. We model the emission probability of an unknown word using the first and last characters in the word. It aims to reduce the POS tag ambiguities of unknown words to improve the parsing performance. In addition, a novel method, using graph-based semisupervised learning (SSL, is proposed to improve the syntax parsing of unknown words. Its goal is to discover additional lexical knowledge from a large amount of unlabeled data to help the syntax parsing. The method is mainly to propagate lexical emission probabilities to unknown words by building the similarity graphs over the words of labeled and unlabeled data. The derived distributions are incorporated into the parsing process. The proposed methods are effective in dealing with the unknown words to improve the parsing. Empirical results for Penn Chinese Treebank and TCT Treebank revealed its effectiveness.

  18. Assessment of Alternative RF Linac Structures for APT

    Energy Technology Data Exchange (ETDEWEB)

    None

    1997-03-26

    The APT program has been examining both normal and superconducting variants of the APT linac for the past two years. A decision on which of the two will be the selected technology will depend upon several considerations including the results of ongoing feasibility experiments, the performance and overall attractiveness of each of the design concepts, and an assessment of the system-level features of both alternatives. The primary objective of the Assessment of Alternative RF Linac Structures for APT study reported herein was to assess and compare, at the system-level, the performance, capital and life cycle costs, reliability/availability/maintainability (RAM) and manufacturing schedules of APT RF linear accelerators based upon both superconducting and normal conducting technologies. A secondary objective was to perform trade studies to explore opportunities for system optimization, technology substitution and alternative growth pathways and to identify sensitivities to design uncertainties.

  19. Assessment of Alternative RF Linac Structures for APT

    International Nuclear Information System (INIS)

    None

    1997-01-01

    The APT program has been examining both normal and superconducting variants of the APT linac for the past two years. A decision on which of the two will be the selected technology will depend upon several considerations including the results of ongoing feasibility experiments, the performance and overall attractiveness of each of the design concepts, and an assessment of the system-level features of both alternatives. The primary objective of the Assessment of Alternative RF Linac Structures for APT study reported herein was to assess and compare, at the system-level, the performance, capital and life cycle costs, reliability/availability/maintainability (RAM) and manufacturing schedules of APT RF linear accelerators based upon both superconducting and normal conducting technologies. A secondary objective was to perform trade studies to explore opportunities for system optimization, technology substitution and alternative growth pathways and to identify sensitivities to design uncertainties

  20. ASEAN plus Three (APT) As a Socializing Environment

    DEFF Research Database (Denmark)

    Zhang, Jiuan

    2012-01-01

    In East Asia, several formal and informal regional institutions have been established in the last several decades to promote regional integration. However, it is difficult to identify which is the dominant institution and determine how it is working. ASEAN Plus Three (APT), representing the first...... institutionalized effort to combine Northeast and Southeast Asia and further promote integration in this institutionally undeveloped region, is central to the regionalist view of international relations. 1 Moreover, China’ s approach to the establishment of APT and changes in its regional behavior have attracted...... scholarly attention. This article combines an empirical analysis of China’s approach to APT with a theoretical discussion of APT’ s institutional design in order to illustrate how APT is working as an environment of socialization in the context of regional integration....

  1. Breaking the Resource Bottleneck for Multilingual Parsing

    National Research Council Canada - National Science Library

    Hwa, Rebecca; Resnik, Philip; Weinberg, Amy

    2005-01-01

    ...-quality English resources. We present a large-scale experiment showing that Chinese dependency trees can be induced by using an English parser, a word alignment package, and a large corpus of sentence-aligned bilingual text...

  2. Confinement and Tritium Stripping Systems for APT Tritium Processing

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, R.H. [Westinghouse Savannah River Company, AIKEN, SC (United States); Heung, L.K.

    1997-10-20

    This report identifies functions and requirements for the tritium process confinement and clean-up system (PCCS) and provides supporting technical information for the selection and design of tritium confinement, clean-up (stripping) and recovery technologies for new tritium processing facilities in the Accelerator for the Production of Tritium (APT). The results of a survey of tritium confinement and clean-up systems for large-scale tritium handling facilities and recommendations for the APT are also presented.

  3. Confinement and Tritium Stripping Systems for APT Tritium Processing

    International Nuclear Information System (INIS)

    Hsu, R.H.; Heung, L.K.

    1997-01-01

    This report identifies functions and requirements for the tritium process confinement and clean-up system (PCCS) and provides supporting technical information for the selection and design of tritium confinement, clean-up (stripping) and recovery technologies for new tritium processing facilities in the Accelerator for the Production of Tritium (APT). The results of a survey of tritium confinement and clean-up systems for large-scale tritium handling facilities and recommendations for the APT are also presented

  4. Associated Particle Tagging (APT) in Magnetic Spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, David V.; Baciak, James E.; Stave, Sean C.; Chichester, David; Dale, Daniel; Kim, Yujong; Harmon, Frank

    2012-10-16

    Summary In Brief The Associated Particle Tagging (APT) project, a collaboration of Pacific Northwest National Laboratory (PNNL), Idaho National Laboratory (INL) and the Idaho State University (ISU)/Idaho Accelerator Center (IAC), has completed an exploratory study to assess the role of magnetic spectrometers as the linchpin technology in next-generation tagged-neutron and tagged-photon active interrogation (AI). The computational study considered two principle concepts: (1) the application of a solenoidal alpha-particle spectrometer to a next-generation, large-emittance neutron generator for use in the associated particle imaging technique, and (2) the application of tagged photon beams to the detection of fissile material via active interrogation. In both cases, a magnetic spectrometer momentum-analyzes charged particles (in the neutron case, alpha particles accompanying neutron generation in the D-T reaction; in the tagged photon case, post-bremsstrahlung electrons) to define kinematic properties of the relevant neutral interrogation probe particle (i.e. neutron or photon). The main conclusions of the study can be briefly summarized as follows: Neutron generator: • For the solenoidal spectrometer concept, magnetic field strengths of order 1 Tesla or greater are required to keep the transverse size of the spectrometer smaller than 1 meter. The notional magnetic spectrometer design evaluated in this feasibility study uses a 5-T magnetic field and a borehole radius of 18 cm. • The design shows a potential for 4.5 Sr tagged neutron solid angle, a factor of 4.5 larger than achievable with current API neutron-generator designs. • The potential angular resolution for such a tagged neutron beam can be less than 0.5o for modest Si-detector position resolution (3 mm). Further improvement in angular resolution can be made by using Si-detectors with better position resolution. • The report documents several features of a notional generator design incorporating the

  5. On Collocations and Their Interaction with Parsing and Translation

    Directory of Open Access Journals (Sweden)

    Violeta Seretan

    2013-10-01

    Full Text Available We address the problem of automatically processing collocations—a subclass of multi-word expressions characterized by a high degree of morphosyntactic flexibility—in the context of two major applications, namely, syntactic parsing and machine translation. We show that parsing and collocation identification are processes that are interrelated and that benefit from each other, inasmuch as syntactic information is crucial for acquiring collocations from corpora and, vice versa, collocational information can be used to improve parsing performance. Similarly, we focus on the interrelation between collocations and machine translation, highlighting the use of translation information for multilingual collocation identification, as well as the use of collocational knowledge for improving translation. We give a panorama of the existing relevant work, and we parallel the literature surveys with our own experiments involving a symbolic parser and a rule-based translation system. The results show a significant improvement over approaches in which the corresponding tasks are decoupled.

  6. Recursive Neural Networks Based on PSO for Image Parsing

    Directory of Open Access Journals (Sweden)

    Guo-Rong Cai

    2013-01-01

    Full Text Available This paper presents an image parsing algorithm which is based on Particle Swarm Optimization (PSO and Recursive Neural Networks (RNNs. State-of-the-art method such as traditional RNN-based parsing strategy uses L-BFGS over the complete data for learning the parameters. However, this could cause problems due to the nondifferentiable objective function. In order to solve this problem, the PSO algorithm has been employed to tune the weights of RNN for minimizing the objective. Experimental results obtained on the Stanford background dataset show that our PSO-based training algorithm outperforms traditional RNN, Pixel CRF, region-based energy, simultaneous MRF, and superpixel MRF.

  7. Radiation damage calculations for the APT materials test program

    International Nuclear Information System (INIS)

    Corzine, R.K.; Wechsler, M.S.; Dudziak, D.J.; Ferguson, P.D.; James, M.R.

    1999-01-01

    A materials irradiation was performed at the Los Alamos Neutron Science Center (LANSCE) in the fall of 1996 and spring of 1997 in support of the Accelerator Production of Tritium (APT) program. Testing of the irradiated materials is underway. In the proposed APT design, materials in the target and blanket are to be exposed to protons and neutrons over a wide range of energies. The irradiation and testing program was undertaken to enlarge the very limited direct knowledge presently available of the effects of medium-energy protons (∼1 GeV) on the properties of engineering materials. APT candidate materials were placed in or near the LANSCE accelerator 800-MeV, 1-mA proton beam and received roughly the same proton current density in the center of the beam as would be the case for the APT facility. As a result, the proton fluences achieved in the irradiation were expected to approach the APT prototypic full-power-year values. To predict accurately the performance of materials in APT, radiation damage parameters for the materials experiment must be determined. By modeling the experiment, calculations for atomic displacement, helium and hydrogen cross sections and for proton and neutron fluences were done for representative samples in the 17A, 18A, and 18C areas. The LAHET code system (LCS) was used to model the irradiation program, LAHET 2.82 within LCS transports protons > 1 MeV, and neutrons >20 MeV. A modified version of MCNP for use in LCS, HMCNP 4A, was employed to tally neutrons of energies <20 MeV

  8. Testing APT Model upon a BVB Stocks’ Portfolio

    Directory of Open Access Journals (Sweden)

    Alexandra BONTAŞ

    2011-01-01

    Full Text Available Applying the Arbitrage Pricing Theory model (APT, there can be identified the major factors of influence for a BVB’ portfolio stocks' trend. There were taken into consideration two of the APT theory models, establishing influences upon portfolio's yield: given to macroeconomic environment and to some stochastic factors. The researchs results certify that, on the long term, what influences the stocks’ movement in the stock market is mostly the action of specific short-term factors, without general covering, like the ones that are classified in the research area of behavioral finance (investors’ preference towards risk and towards time.

  9. Deep PDF parsing to extract features for detecting embedded malware.

    Energy Technology Data Exchange (ETDEWEB)

    Munson, Miles Arthur; Cross, Jesse S. (Missouri University of Science and Technology, Rolla, MO)

    2011-09-01

    The number of PDF files with embedded malicious code has risen significantly in the past few years. This is due to the portability of the file format, the ways Adobe Reader recovers from corrupt PDF files, the addition of many multimedia and scripting extensions to the file format, and many format properties the malware author may use to disguise the presence of malware. Current research focuses on executable, MS Office, and HTML formats. In this paper, several features and properties of PDF Files are identified. Features are extracted using an instrumented open source PDF viewer. The feature descriptions of benign and malicious PDFs can be used to construct a machine learning model for detecting possible malware in future PDF files. The detection rate of PDF malware by current antivirus software is very low. A PDF file is easy to edit and manipulate because it is a text format, providing a low barrier to malware authors. Analyzing PDF files for malware is nonetheless difficult because of (a) the complexity of the formatting language, (b) the parsing idiosyncrasies in Adobe Reader, and (c) undocumented correction techniques employed in Adobe Reader. In May 2011, Esparza demonstrated that PDF malware could be hidden from 42 of 43 antivirus packages by combining multiple obfuscation techniques [4]. One reason current antivirus software fails is the ease of varying byte sequences in PDF malware, thereby rendering conventional signature-based virus detection useless. The compression and encryption functions produce sequences of bytes that are each functions of multiple input bytes. As a result, padding the malware payload with some whitespace before compression/encryption can change many of the bytes in the final payload. In this study we analyzed a corpus of 2591 benign and 87 malicious PDF files. While this corpus is admittedly small, it allowed us to test a system for collecting indicators of embedded PDF malware. We will call these indicators features throughout

  10. Parsing the Dictionary of Modern Literary Russian Language with the Method of SCD Configurations. The Lexicographic Modeling

    Directory of Open Access Journals (Sweden)

    Neculai Curteanu

    2012-05-01

    Full Text Available This paper extends the experience of parsing other five, sensibly different, Romanian, French, and German largest dictionaries, to \\textbf{\\textit{DMLRL}} (Dictionary of Modern Literary Russian Language [18], using the optimal and portable parsing method of SCD (Segmentation-Cohesion-Dependency configurations [7], [11], [15]. The purpose of the present paper is to elaborate the lexicographic modeling of \\textbf{\\textit{DMLRL}}, which necessarily precedes the sense tree parsing dictionary entries. The following \\textbf{\\textit{three}} SCD configurations are described: the \\textbf{\\textit{first one}} has to separate the lexicographic segments in a \\textbf{\\textit{DMLRL}} entry, the \\textbf{\\textit{second}} SCD-configuration concentrates on the SCD marker classes and their hypergraph hierarchy for \\textbf{\\textit{DMLRL}} primary and secondary senses, while the \\textbf{\\textit{third}} SCD configuration hands down the same modeling process to the atomic sense definitions and their examples-to-definitions. The dependency hypergraph of the third SCD configuration, interconnected to the one of the second SCD configuration, is specified completely at the atomic sense level for the first time, exceeding the SCD configuration modeling for other five dictionaries [15], [14]. Numerous examples from \\textbf{\\textit{DMLRL}} and comparison to \\textbf{\\textit{DLR-DAR}} Romanian thesaurus-dictionary support the proposed \\textbf{\\textit{DMLRL}} lexicographic modeling.

  11. Parsing with subdomain instance weighting from raw corpora

    NARCIS (Netherlands)

    Plank, B.; Sima'an, K.

    2008-01-01

    The treebanks that are used for training statistical parsers consist of hand-parsed sentences from a single source/domain like newspaper text. However, newspaper text concerns different subdomains of language use (e.g. finance, sports, politics, music), which implies that the statistics gathered by

  12. Parsing with Subdomain Instance Weighting from Raw Corpora

    NARCIS (Netherlands)

    Plank, Barbara; Sima'an, Khalil

    2008-01-01

    The treebanks that are used for training statistical parsers consist of hand-parsed sentences from a single source/domain like newspaper text. However, newspaper text concerns different subdomains of language use (e.g. finance, sports, politics, music), which implies that the statistics gathered by

  13. A simple DOP model for constituency parsing of Italian sentences

    NARCIS (Netherlands)

    Sangati, F.

    2009-01-01

    We present a simplified Data-Oriented Parsing (DOP) formalism for learning the constituency structure of Italian sentences. In our approach we try to simplify the original DOP methodology by constraining the number and type of fragments we extract from the training corpus. We provide some examples

  14. On the Approximation Ratio of Lempel-Ziv Parsing

    DEFF Research Database (Denmark)

    Gagie, Travis; Navarro, Gonzalo; Prezza, Nicola

    2018-01-01

    in the text. Since computing b is NP-complete, a popular gold standard is z, the number of phrases in the Lempel-Ziv parse of the text, where phrases can be copied only from the left. While z can be computed in linear time, almost nothing has been known for decades about its approximation ratio with respect...

  15. Finding EL+ justifications using the Earley parsing algorithm

    CSIR Research Space (South Africa)

    Nortje, R

    2009-12-01

    Full Text Available into a reachability preserving context free grammar (CFG). The well known earley algorithm for parsing strings, given some CFG, is then applied to the problem of extracting minimal reachability-based axiom sets for subsumption entailments. The author has...

  16. Advanced programming concepts in a course on grammars and parsing

    NARCIS (Netherlands)

    Jeuring, J.T.; Swierstra, S.D.

    1999-01-01

    One of the important goals of the Computer Science curriculum at Utrecht University is to familiarize students with abstract programming concepts such as, for example, partial evaluation and deforestation. A course on grammars and parsing offers excellent possibilities for exemplifying and

  17. Time-Driven Effects on Parsing during Reading

    Science.gov (United States)

    Roll, Mikael; Lindgren, Magnus; Alter, Kai; Horne, Merle

    2012-01-01

    The phonological trace of perceived words starts fading away in short-term memory after a few seconds. Spoken utterances are usually 2-3 s long, possibly to allow the listener to parse the words into coherent prosodic phrases while they still have a clear representation. Results from this brain potential study suggest that even during silent…

  18. Fuzzy Context- Free Languages. Part 2: Recognition and Parsing Algorithms

    NARCIS (Netherlands)

    Asveld, P.R.J.

    2000-01-01

    In a companion paper \\cite{Asv:FCF1} we used fuzzy context-free grammars in order to model grammatical errors resulting in erroneous inputs for robust recognizing and parsing algorithms for fuzzy context-free languages. In particular, this approach enables us to distinguish between small errors

  19. The aptness of knowledge related metaphors: a research agenda

    NARCIS (Netherlands)

    Dr. Daan Andriessen

    2010-01-01

    Metaphors are common phenomena intellectual capital and knowledge management theories and practice. An important question to ask is: what are the ‗best‘ metaphors we can use in our theorizing on intellectual capital and knowledge management? This paper addresses the question of the aptness of

  20. Identifying APT Malware Domain Based on Mobile DNS Logging

    Directory of Open Access Journals (Sweden)

    Weina Niu

    2017-01-01

    Full Text Available Advanced Persistent Threat (APT is a serious threat against sensitive information. Current detection approaches are time-consuming since they detect APT attack by in-depth analysis of massive amounts of data after data breaches. Specifically, APT attackers make use of DNS to locate their command and control (C&C servers and victims’ machines. In this paper, we propose an efficient approach to detect APT malware C&C domain with high accuracy by analyzing DNS logs. We first extract 15 features from DNS logs of mobile devices. According to Alexa ranking and the VirusTotal’s judgement result, we give each domain a score. Then, we select the most normal domains by the score metric. Finally, we utilize our anomaly detection algorithm, called Global Abnormal Forest (GAF, to identify malware C&C domains. We conduct a performance analysis to demonstrate that our approach is more efficient than other existing works in terms of calculation efficiency and recognition accuracy. Compared with Local Outlier Factor (LOF, k-Nearest Neighbor (KNN, and Isolation Forest (iForest, our approach obtains more than 99% F-M and R for the detection of C&C domains. Our approach not only can reduce data volume that needs to be recorded and analyzed but also can be applicable to unsupervised learning.

  1. BAIK– PROGRAMMING LANGUAGE BASED ON INDONESIAN LEXICAL PARSING FOR MULTITIER WEB DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Haris Hasanudin

    2012-05-01

    Full Text Available Business software development with global team is increasing rapidly and the programming language as development tool takes the important role in the global web development. The real user friendly programming language should be written in local language for programmer who has native language is not in English. This paper presents our design of BAIK (Bahasa Anak Indonesia untuk Komputerscripting language which syntax is modeled with Bahasa Indonesian for multitier web development. Researcher propose the implementation of Indonesian Parsing Engine and Binary Search Tree structure for memory allocation of variable and compose the language features that support basic Object Oriented Programming, Common Gateway Interface, HTML style manipulation and database connection. Our goal is to build real programming language from simple structure design for web development using Indonesian lexical words. Pengembangan bisnis perangkat lunak dalam tim berskala global meningkat dengan cepat dan bahasa pemrograman berperan penting dalam pengembangan web secara global. Bahasa pemrograman yang benar-benar ramah terhadap pengguna harus ditulis dalam bahasa lokal programmer yang bahasa ibunya bukan Bahasa Inggris. Paper ini menyajikan desain dari bahasa penulisan BAIK (Bahasa Anak Indonesia untuk Komputer, yang sintaksisnya dimodelkan dengan Bahasa Indonesia untuk pengembangan web multitier. Peneliti mengusulkan implementasi dari parsing engine Bahasa Indonesia dan struktur binary search tree untuk alokasi memori terhadap variabel, serta membuat fitur bahasa yang mendukung dasar pemrograman berbasis objek, common gateway interface, manipulasi gaya HTML, dan koneksi basis data. Tujuan penelitian ini adalah untuk menciptakan bahasa pemrograman yang sesungguhnya dan menggunakan desain struktur sederhana untuk pengembangan web dengan menggunakan kata-kata dari Bahasa Indonesia.

  2. Pseudocode Interpreter (Pseudocode Integrated Development Environment with Lexical Analyzer and Syntax Analyzer using Recursive Descent Parsing Algorithm

    Directory of Open Access Journals (Sweden)

    Christian Lester D. Gimeno

    2017-11-01

    Full Text Available –This research study focused on the development of a software that helps students design, write, validate and run their pseudocode in a semi Integrated Development Environment (IDE instead of manually writing it on a piece of paper.Specifically, the study aimed to develop lexical analyzer or lexer, syntax analyzer or parser using recursive descent parsing algorithm and an interpreter. The lexical analyzer reads pseudocodesource in a sequence of symbols or characters as lexemes.The lexemes are then analyzed by the lexer that matches a pattern for valid tokens and passes to the syntax analyzer or parser. The syntax analyzer or parser takes those valid tokens and builds meaningful commands using recursive descent parsing algorithm in a form of an abstract syntax tree. The generation of an abstract syntax tree is based on the specified grammar rule created by the researcher expressed in Extended Backus-Naur Form. The Interpreter takes the generated abstract syntax tree and starts the evaluation or interpretation to produce pseudocode output. The software was evaluated using white-box testing by several ICT professionals and black-box testing by several computer science students based on the International Organization for Standardization (ISO 9126 software quality standards. The overall results of the evaluation both for white-box and black-box were described as “Excellent in terms of functionality, reliability, usability, efficiency, maintainability and portability”.

  3. Towards Understanding Tyre-Pavement Contact in APT Research on Flexible Pavements

    CSIR Research Space (South Africa)

    De Beer, Morris

    2016-09-01

    Full Text Available An important element of Accelerated Pavement Testing (APT) is the selection of appropriate test tyre(s) to be used for APT testing. By far the majority of full scale (or scaled) APT devices uses pneumatic rubber tyres. Tyres differ not only in size...

  4. APT/LEDA RFQ and support frame structural analysis

    International Nuclear Information System (INIS)

    Ellis, S.

    1997-01-01

    This report documents structural analysis of the Accelerator Production of Tritium Low Energy Demonstration Accelerator (APT/LEDA) Radio Frequency Quadrupole (RFQ) accelerator structure and its associated support frame. This work was conducted for the Department of Energy in support of the APT/LEDA. Structural analysis of the RFQ was performed to quantify stress levels and deflections due to both vacuum loading and gravity loading. This analysis also verified the proposed support scheme geometry and quantified interface loads. This analysis also determined the necessary stiffness and strength requirements of the RFQ support frame verifying the conceptual design geometry and allowing specification of individual frame elements. Complete structural analysis of the frame was completed subsequently. This report details structural analysis of the RFQ assembly with regard to gravity and vacuum loads only. Thermally induced stresses from the Radio Frequency (RF) surface resistance heating were not considered

  5. Miniaturization of the atmospheric laser communication APT system

    Science.gov (United States)

    Sun, Wei; Ai, Yong; Yang, Jinling; Huang, Haibo

    2003-09-01

    The paper presents a scheme of the miniaturization of APT system and the design of the system based on the investigation of status in quo. It deals with the infrared image of the other terminal's beacon from the Charge Coupled Device (CCD) by the Complex Programmable Logic Device (CPLD). The result of the transaction is delivered to Single Chip Microcomputer (SCM), which controls the micro-servomotor. Subsequently, the precision drive system drives the optical system that uses only one light axis for signal beam and beacon to finish the acquisition, pointing, and tracking of the communication terminals. The anlayses of the APT system's error indicate that the tracking error limits in 70uRad with the weight of the system lighter than 8-kilogram.

  6. Development of a commissioning plan for the APT linac

    International Nuclear Information System (INIS)

    Funk, L.W.; Crandall, K.R.; Gilpatrick, J.D.; Gray, E.R.; Regan, A.H.; Rohlev, A.; Rybarcyk, L.J.; Wangler, T.P.

    1998-01-01

    The Accelerator Production of Tritium (APT) facility is based on a linac which incorporates both normal-conducting and superconducting RF technology and accelerates a 100-mA cw proton beam to an energy of 1,030 MeV or higher, depending on the desired production rate. Commissioning plans to achieve full power operation with minimum beam-induced activation of components have been evolving. This paper presents the main issues and the basic approaches that are now being discussed

  7. Thermal analysis of the APT materials irradiation samples

    International Nuclear Information System (INIS)

    Maloy, S.A.; Willcutt, G.J.; James, M.R.; Teague, J.; Diebe, D.A.; Sommer, W.F.; Ferguson, P.D.

    1998-01-01

    The accelerator production of tritium (APT) project proposes to use a 1.7 GeV, 100 mA proton beam to produce neutrons from an Inconel 718 clad tungsten target. The neutrons are multiplied and moderated in a lead/water blanket before being captured in He 3 to form tritium. In this process, the materials in the target and blanket region are exposed to a wide range of different fluxes comprised of protons and neutrons with energies into the GeV range. To investigate the effect of irradiation on the mechanical properties of candidate APT materials (Inconel 718, 316L stainless steel, Al 6061-T6, Mod 9Cr-1Mo, 304L stainless steel and Al5052-0), the APT Engineering Design and Development group fielded an extensive materials irradiation using the LANSCE (Los Alamos Neutron Science Center) accelerator, which operates at an energy of 800 MeV and a current of 1 mA. The test set-up was designed to place mechanical test specimens in locations in and near the proton beam where the environment of proton and neutron fluxes and temperatures are prototypic to those expected in the APT target/blanket (50--170 C). After irradiating for about 3,600 hours, the maximum achieved proton fluence was 4--5 x 10 21 p/cm 2 for the materials in the center of the beam. To obtain relevant data on the change in the mechanical properties with fluence, it is essential to know the temperature at which the materials were irradiated. This paper explains the method of determining the specimen temperature and reports some specific examples

  8. Creating Parsing Lexicons from Semantic Lexicons Automatically and Its Applications

    National Research Council Canada - National Science Library

    Ayan, Necip F; Dorr, Bonnie

    2002-01-01

    ...). We also present the effects of using such a lexicon on the parser performance. The advantage of automating the process is that the same technique can be applied directly to lexicons we have for other languages, for example, Arabic, Chinese, and Spanish. The results indicate that our method will help us generate parsing lexicons which can be used by a broad-coverage parser that runs on different languages.

  9. Extending TF1: Argument parsing, function composition, and vectorization

    CERN Document Server

    Tsang Mang Kin, Arthur Leonard

    2017-01-01

    In this project, we extend the functionality of the TF1 function class in root. We add argument parsing, making it possible to freely pass variables and parameters into pre-defined and user-defined functions. We also introduce a syntax to use certain compositions of functions, namely normalized sums and convolutions, directly in TF1. Finally, we introduce some simple vectorization functionality to TF1 and demonstrate the potential to speed up parallelizable computations.

  10. Investigation and Prediction of RF Window Performance in APT Accelerators

    International Nuclear Information System (INIS)

    Humphries, S. Jr.

    1997-01-01

    The work described in this report was performed between November 1996 and May 1997 in support of the APT (Accelerator Production of Tritium) Program at Los Alamos National Laboratory. The goal was to write and to test computer programs for charged particle orbits in RF fields. The well-documented programs were written in portable form and compiled for standard personal computers for easy distribution to LANL researchers. They will be used in several APT applications including the following. Minimization of multipactor effects in the moderate β superconducting linac cavities under design for the APT accelerator. Investigation of suppression techniques for electron multipactoring in high-power RF feedthroughs. Modeling of the response of electron detectors for the protection of high power RF vacuum windows. In the contract period two new codes, Trak-RF and WaveSim, were completed and several critical benchmark etests were carried out. Trak-RF numerically tracks charged particle orbits in combined electrostatic, magnetostatic and electromagnetic fields. WaveSim determines frequency-domain RF field solutions and provides a key input to Trak-RF. The two-dimensional programs handle planar or cylindrical geometries. They have several unique characteristics

  11. APT, The Phase I tool for HST Cycle 12

    Science.gov (United States)

    Blacker, Brett S.; Bertch, Maria; Curtis, Gary; Douglas, Robert E., Jr.; Krueger, Anthony P.

    2002-12-01

    In the continuing effort to streamline our systems and improve service to the science community, the Space Telescope Science Institute (STScI) is developing and releasing, APT The Astronomer’s Proposal Tool as the new interface for Hubble Space Telescope (HST) Phase I and Phase II proposal submissions for HST Cycle 12. APT, was formerly called the Scientist’s Expert Assistant (SEA), which started as a prototype effort to try and bring state of the art technology, more visual tools and power into the hands of proposers so that they can optimize the scientific return of their programs as well as HST. Proposing for HST and other missions, consists of requesting observing time and/or archival research funding. This step is called Phase I, where the scientific merit of a proposal is considered by a community based peer-review process. Accepted proposals then proceed thru Phase II, where the observations are specified in sufficient detail to enable scheduling on the telescope. In this paper, we will present our concept and implementation plans for our Phase I development and submission tool, APT. More importantly, we will go behind the scenes and discuss why it’s important for the Science Policies Division (SPD) and other groups at the STScI to have a new submission tool and submission output products. This paper is an update of the status of the HST Phase I Proposal Processing System that was described in the published paper “A New Era for HST Phase I Development and Submission.”

  12. Locating and parsing bibliographic references in HTML medical articles.

    Science.gov (United States)

    Zou, Jie; Le, Daniel; Thoma, George R

    2010-06-01

    The set of references that typically appear toward the end of journal articles is sometimes, though not always, a field in bibliographic (citation) databases. But even if references do not constitute such a field, they can be useful as a preprocessing step in the automated extraction of other bibliographic data from articles, as well as in computer-assisted indexing of articles. Automation in data extraction and indexing to minimize human labor is key to the affordable creation and maintenance of large bibliographic databases. Extracting the components of references, such as author names, article title, journal name, publication date and other entities, is therefore a valuable and sometimes necessary task. This paper describes a two-step process using statistical machine learning algorithms, to first locate the references in HTML medical articles and then to parse them. Reference locating identifies the reference section in an article and then decomposes it into individual references. We formulate this step as a two-class classification problem based on text and geometric features. An evaluation conducted on 500 articles drawn from 100 medical journals achieves near-perfect precision and recall rates for locating references. Reference parsing identifies the components of each reference. For this second step, we implement and compare two algorithms. One relies on sequence statistics and trains a Conditional Random Field. The other focuses on local feature statistics and trains a Support Vector Machine to classify each individual word, followed by a search algorithm that systematically corrects low confidence labels if the label sequence violates a set of predefined rules. The overall performance of these two reference-parsing algorithms is about the same: above 99% accuracy at the word level, and over 97% accuracy at the chunk level.

  13. KEGGParser: parsing and editing KEGG pathway maps in Matlab.

    Science.gov (United States)

    Arakelyan, Arsen; Nersisyan, Lilit

    2013-02-15

    KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab. The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

  14. Defining clusters in APT reconstructions of ODS steels.

    Science.gov (United States)

    Williams, Ceri A; Haley, Daniel; Marquis, Emmanuelle A; Smith, George D W; Moody, Michael P

    2013-09-01

    Oxide nanoclusters in a consolidated Fe-14Cr-2W-0.3Ti-0.3Y₂O₃ ODS steel and in the alloy powder after mechanical alloying (but before consolidation) are investigated by atom probe tomography (APT). The maximum separation method is a standard method to define and characterise clusters from within APT data, but this work shows that the extent of clustering between the two materials is sufficiently different that the nanoclusters in the mechanically alloyed powder and in the consolidated material cannot be compared directly using the same cluster selection parameters. As the cluster selection parameters influence the size and composition of the clusters significantly, a procedure to optimise the input parameters for the maximum separation method is proposed by sweeping the d(max) and N(min) parameter space. By applying this method of cluster parameter selection combined with a 'matrix correction' to account for trajectory aberrations, differences in the oxide nanoclusters can then be reliably quantified. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Analysis of Azari Language based on Parsing using Link Gram

    Directory of Open Access Journals (Sweden)

    Maryam Arabzadeh

    2014-09-01

    Full Text Available There are different classes of theories for the natural lanuguage syntactic parsing problem and for creating the related grammars .This paper presents a syntactic grammar developed in the link grammar formalism for Turkish which is an agglutinative language. In the link grammar formalism, the words of a sentence are linked with each other depending on their syntactic roles. Turkish has complex derivational and inflectional morphology, and derivational and inflection morphemes play important syntactic roles in the sentences. In order to develop a link grammar for Turkish, the lexical parts in the morphological representations of Turkish words are removed, and the links are created depending on the part of speech tags and inflectional morphemes in words. Furthermore, a derived word is separated at the derivational boundaries in order to treat each derivation morpheme as a special distinct word, and allow it to be linked with the rest of the sentence. The derivational morphemes of a word are also linked with each other with special links to indicate that they are parts of the same word. Finally the adapted unique link grammar formalism for Turkish provides flexibility for the linkage construction, and similar methods can be used for other languages with complex morphology. Finally, using the Delphi programming language, the link grammar related to the Azeri language was developed and implemented and then by selecting 250 random sentences, this grammar is evaluated and then tested. For 84.31% of the sentences, the result set of the parser contains the correct parse.

  16. Automated vocabulary discovery for geo-parsing online epidemic intelligence.

    Science.gov (United States)

    Keller, Mikaela; Freifeld, Clark C; Brownstein, John S

    2009-11-24

    Automated surveillance of the Internet provides a timely and sensitive method for alerting on global emerging infectious disease threats. HealthMap is part of a new generation of online systems designed to monitor and visualize, on a real-time basis, disease outbreak alerts as reported by online news media and public health sources. HealthMap is of specific interest for national and international public health organizations and international travelers. A particular task that makes such a surveillance useful is the automated discovery of the geographic references contained in the retrieved outbreak alerts. This task is sometimes referred to as "geo-parsing". A typical approach to geo-parsing would demand an expensive training corpus of alerts manually tagged by a human. Given that human readers perform this kind of task by using both their lexical and contextual knowledge, we developed an approach which relies on a relatively small expert-built gazetteer, thus limiting the need of human input, but focuses on learning the context in which geographic references appear. We show in a set of experiments, that this approach exhibits a substantial capacity to discover geographic locations outside of its initial lexicon. The results of this analysis provide a framework for future automated global surveillance efforts that reduce manual input and improve timeliness of reporting.

  17. Automated vocabulary discovery for geo-parsing online epidemic intelligence

    Directory of Open Access Journals (Sweden)

    Freifeld Clark C

    2009-11-01

    Full Text Available Abstract Background Automated surveillance of the Internet provides a timely and sensitive method for alerting on global emerging infectious disease threats. HealthMap is part of a new generation of online systems designed to monitor and visualize, on a real-time basis, disease outbreak alerts as reported by online news media and public health sources. HealthMap is of specific interest for national and international public health organizations and international travelers. A particular task that makes such a surveillance useful is the automated discovery of the geographic references contained in the retrieved outbreak alerts. This task is sometimes referred to as "geo-parsing". A typical approach to geo-parsing would demand an expensive training corpus of alerts manually tagged by a human. Results Given that human readers perform this kind of task by using both their lexical and contextual knowledge, we developed an approach which relies on a relatively small expert-built gazetteer, thus limiting the need of human input, but focuses on learning the context in which geographic references appear. We show in a set of experiments, that this approach exhibits a substantial capacity to discover geographic locations outside of its initial lexicon. Conclusion The results of this analysis provide a framework for future automated global surveillance efforts that reduce manual input and improve timeliness of reporting.

  18. Parsing a cognitive task: a characterization of the mind's bottleneck.

    Directory of Open Access Journals (Sweden)

    Mariano Sigman

    2005-02-01

    Full Text Available Parsing a mental operation into components, characterizing the parallel or serial nature of this flow, and understanding what each process ultimately contributes to response time are fundamental questions in cognitive neuroscience. Here we show how a simple theoretical model leads to an extended set of predictions concerning the distribution of response time and its alteration by simultaneous performance of another task. The model provides a synthesis of psychological refractory period and random-walk models of response time. It merely assumes that a task consists of three consecutive stages-perception, decision based on noisy integration of evidence, and response-and that the perceptual and motor stages can operate simultaneously with stages of another task, while the central decision process constitutes a bottleneck. We designed a number-comparison task that provided a thorough test of the model by allowing independent variations in number notation, numerical distance, response complexity, and temporal asynchrony relative to an interfering probe task of tone discrimination. The results revealed a parsing of the comparison task in which each variable affects only one stage. Numerical distance affects the integration process, which is the only step that cannot proceed in parallel and has a major contribution to response time variability. The other stages, mapping the numeral to an internal quantity and executing the motor response, can be carried out in parallel with another task. Changing the duration of these processes has no significant effect on the variance.

  19. Constructing APT Attack Scenarios Based on Intrusion Kill Chain and Fuzzy Clustering

    Directory of Open Access Journals (Sweden)

    Ru Zhang

    2017-01-01

    Full Text Available The APT attack on the Internet is becoming more serious, and most of intrusion detection systems can only generate alarms to some steps of APT attack and cannot identify the pattern of the APT attack. To detect APT attack, many researchers established attack models and then correlated IDS logs with the attack models. However, the accuracy of detection deeply relied on the integrity of models. In this paper, we propose a new method to construct APT attack scenarios by mining IDS security logs. These APT attack scenarios can be further used for the APT detection. First, we classify all the attack events by purpose of phase of the intrusion kill chain. Then we add the attack event dimension to fuzzy clustering, correlate IDS alarm logs with fuzzy clustering, and generate the attack sequence set. Next, we delete the bug attack sequences to clean the set. Finally, we use the nonaftereffect property of probability transfer matrix to construct attack scenarios by mining the attack sequence set. Experiments show that the proposed method can construct the APT attack scenarios by mining IDS alarm logs, and the constructed scenarios match the actual situation so that they can be used for APT attack detection.

  20. The APT program plan: Providing an assured tritium production capability

    International Nuclear Information System (INIS)

    Lisowski, P.W.; Anderson, J.L.; Bishop, W.P.; Boggs, B.; Hall, K.

    1996-01-01

    Tritium is a radioactive hydrogen isotope used in all U.S. nuclear weapons. Because the half-life of tritium is short, 12.3 yr, it must be periodically replenished. To provide a new source, the U.S. Department of Energy (DOE) is sponsoring conceptual design and engineering development and demonstration activities for a plant that will use a high-power proton linear accelerator to produce tritium and will go on-line no later than 2007. The APT project is in the process of completing the conceptual design for a tritium production plant. In addition, there are several important areas under engineering development and demonstration that will ensure an efficient, cost-effective plant design and provide an adequate margin of tritium production. Information provided from this work will be used by the DOE in its 1998 choice of production technology implementation

  1. Micah 1, an apt introduction to power talks

    Directory of Open Access Journals (Sweden)

    W.J. Wessels

    1998-08-01

    Full Text Available Power and the abuse of it, is often an integral part of discussions in any society. The prophets of the Old Testament felt strongly about this issue and often spoke out against the abuse of power and the suffering caused by it. Micah particularly addresses this issue in chapters 2 and 3. He blames the leaders in society, who should look out for the ordinary people, that they in particular are guilty of this transgression. In chapter 1 Micah proclaims Yahweh as the sovereign power who they should take note off. On the very basis of Yahweh's sovereign power he then proclaims oracles of judgment on the people of Judah. Micah 1 seems to form an apt introduction to the talks of the abuse of power in the society of Judah.

  2. Relative clauses as a benchmark for Minimalist parsing

    Directory of Open Access Journals (Sweden)

    Thomas Graf

    2017-07-01

    Full Text Available Minimalist grammars have been used recently in a series of papers to explain well-known contrasts in human sentence processing in terms of subtle structural differences. These proposals combine a top-down parser with complexity metrics that relate parsing difficulty to memory usage. So far, though, there has been no large-scale exploration of the space of viable metrics. Building on this earlier work, we compare the ability of 1600 metrics to derive several processing effects observed with relative clauses, many of which have been proven difficult to unify. We show that among those 1600 candidates, a few metrics (and only a few can provide a unified account of all these contrasts. This is a welcome result for two reasons: First, it provides a novel account of extensively studied psycholinguistic data. Second, it significantly limits the number of viable metrics that may be applied to other phenomena, thus reducing theoretical indeterminacy.

  3. Motion based parsing for video from observational psychology

    Science.gov (United States)

    Kokaram, Anil; Doyle, Erika; Lennon, Daire; Joyeux, Laurent; Fuller, Ray

    2006-01-01

    In Psychology it is common to conduct studies involving the observation of humans undertaking some task. The sessions are typically recorded on video and used for subjective visual analysis. The subjective analysis is tedious and time consuming, not only because much useless video material is recorded but also because subjective measures of human behaviour are not necessarily repeatable. This paper presents tools using content based video analysis that allow automated parsing of video from one such study involving Dyslexia. The tools rely on implicit measures of human motion that can be generalised to other applications in the domain of human observation. Results comparing quantitative assessment of human motion with subjective assessment are also presented, illustrating that the system is a useful scientific tool.

  4. Machine learning to parse breast pathology reports in Chinese.

    Science.gov (United States)

    Tang, Rong; Ouyang, Lizhi; Li, Clara; He, Yue; Griffin, Molly; Taghian, Alphonse; Smith, Barbara; Yala, Adam; Barzilay, Regina; Hughes, Kevin

    2018-01-29

    Large structured databases of pathology findings are valuable in deriving new clinical insights. However, they are labor intensive to create and generally require manual annotation. There has been some work in the bioinformatics community to support automating this work via machine learning in English. Our contribution is to provide an automated approach to construct such structured databases in Chinese, and to set the stage for extraction from other languages. We collected 2104 de-identified Chinese benign and malignant breast pathology reports from Hunan Cancer Hospital. Physicians with native Chinese proficiency reviewed the reports and annotated a variety of binary and numerical pathologic entities. After excluding 78 cases with a bilateral lesion in the same report, 1216 cases were used as a training set for the algorithm, which was then refined by 405 development cases. The Natural language processing algorithm was tested by using the remaining 405 cases to evaluate the machine learning outcome. The model was used to extract 13 binary entities and 8 numerical entities. When compared to physicians with native Chinese proficiency, the model showed a per-entity accuracy from 91 to 100% for all common diagnoses on the test set. The overall accuracy of binary entities was 98% and of numerical entities was 95%. In a per-report evaluation for binary entities with more than 100 training cases, 85% of all the testing reports were completely correct and 11% had an error in 1 out of 22 entities. We have demonstrated that Chinese breast pathology reports can be automatically parsed into structured data using standard machine learning approaches. The results of our study demonstrate that techniques effective in parsing English reports can be scaled to other languages.

  5. Using machine learning to parse breast pathology reports.

    Science.gov (United States)

    Yala, Adam; Barzilay, Regina; Salama, Laura; Griffin, Molly; Sollender, Grace; Bardia, Aditya; Lehman, Constance; Buckley, Julliette M; Coopey, Suzanne B; Polubriaginof, Fernanda; Garber, Judy E; Smith, Barbara L; Gadd, Michele A; Specht, Michelle C; Gudewicz, Thomas M; Guidi, Anthony J; Taghian, Alphonse; Hughes, Kevin S

    2017-01-01

    Extracting information from electronic medical record is a time-consuming and expensive process when done manually. Rule-based and machine learning techniques are two approaches to solving this problem. In this study, we trained a machine learning model on pathology reports to extract pertinent tumor characteristics, which enabled us to create a large database of attribute searchable pathology reports. This database can be used to identify cohorts of patients with characteristics of interest. We collected a total of 91,505 breast pathology reports from three Partners hospitals: Massachusetts General Hospital, Brigham and Women's Hospital, and Newton-Wellesley Hospital, covering the period from 1978 to 2016. We trained our system with annotations from two datasets, consisting of 6295 and 10,841 manually annotated reports. The system extracts 20 separate categories of information, including atypia types and various tumor characteristics such as receptors. We also report a learning curve analysis to show how much annotation our model needs to perform reasonably. The model accuracy was tested on 500 reports that did not overlap with the training set. The model achieved accuracy of 90% for correctly parsing all carcinoma and atypia categories for a given patient. The average accuracy for individual categories was 97%. Using this classifier, we created a database of 91,505 parsed pathology reports. Our learning curve analysis shows that the model can achieve reasonable results even when trained on a few annotations. We developed a user-friendly interface to the database that allows physicians to easily identify patients with target characteristics and export the matching cohort. This model has the potential to reduce the effort required for analyzing large amounts of data from medical records, and to minimize the cost and time required to glean scientific insight from these data.

  6. Potassium hydroxide: an alternative reagent to perform the modified apt test.

    Science.gov (United States)

    Chicaiza, Henry; Hellstrand, Karl; Lerer, Trudy; Smith, Sharon; Sylvester, Francisco

    2014-09-01

    We tested the performance of potassium hydroxide (KOH) in the modified Apt test under different experimental conditions using sodium hydroxide as a positive control. Like sodium hydroxide, KOH differentiated fresh fetal and adult blood stains on a cloth but not dried blood. KOH may be used to perform the Apt test at the bedside. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Design of 250-MW CW RF system for APT

    International Nuclear Information System (INIS)

    Rees, D.

    1997-01-01

    The design for the RF systems for the APT (Accelerator Production of Tritium) proton linac will be presented. The linac produces a continuous beam power of 130 MW at 1300 MeV with the installed capability to produce up to a 170 MW beam at 1700 MeV. The linac is comprised of a 350 MHz RFQ to 7 MeV followed in sequence by a 700 MHz coupled-cavity drift tube linac, coupled-cavity linac, and superconducting (SC) linac to 1700 MeV. At the 1700 MeV, 100 mA level the linac requires 213 MW of continuous-wave (CW) RF power. This power will be supplied by klystrons with a nominal output power of 1.0 MW. 237 kystrons are required with all but three of these klystrons operating at 700 MHz. The klystron count includes redundancy provisions that will be described which allow the RF systems to meet an operational availability in excess of 95 percent. The approach to achieve this redundancy will be presented for both the normal conducting (NC) and SC accelerators. Because of the large amount of CW RF power required for the APT linac, efficiency is very important to minimize operating cost. Operation and the RF system design, including in-progress advanced technology developments which improve efficiency, will be discussed. RF system performance will also be predicted. Because of the simultaneous pressures to increase RF system reliability, reduce tunnel envelope, and minimize RF system cost, the design of the RF vacuum windows has become an important issue. The power from a klystron will be divided into four equal parts to minimize the stress on the RF vacuum windows. Even with this reduction, the RF power level at the window is at the upper boundary of the power levels employed at other CW accelerator facilities. The design of a 350 MHz, coaxial vacuum window will be presented as well as test results and high power conditioning profiles. The transmission of 950 kW, CW, power through this window has been demonstrated with only minimal high power conditioning

  8. Advanced buck converter power supply ABCPS for APT

    International Nuclear Information System (INIS)

    Street, R.; Overett, T.; Bowles, E.

    1998-01-01

    The United States Department of Energy (DOE) is planning to fabricate an Accelerator for the Production of Tritium (APT) at their Savannah River Site, to provide Tritium for national defense. The 1700 million electron volt (MeV) proton beam accelerator will be powered by radio frequency (RF) klystrons. A direct current (DC) power supply is required for each of the approximately two hundred and fifty 1-megawatt (MW) continuous wave klystrons in the RF power system. The requirements are that the power supply meet output performance specifications, provide fault protection for the klystron, have high efficiency, high reliability, good maintainability, and be readily manufacturable. As the power supplies are one of the largest cost elements in the accelerator, a technology review was made to determine the most economical approach to satisfy the requirements. A switch-mode power supply employing a buck-regulator was identified as being potentially the lowest cost approach. As the switch represents a certain development risk, a small-scale prototype has been constructed for evaluation, and has resulted in the decision to fabricate a full-scale prototype power supply. A description of the hardware will be presented

  9. Development of the SCRF Power Coupler for the APT Accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Schmierer, E.N.; Lujan, R.E.; Rusnak, B.; Smith, B.; Haynes, W.B.; Gautier, C.; Waynert, J.A.; Krawczyk, F.; Gioia, J.

    1999-03-01

    The team responsible for the design of the Accelerator Production of Tritium (APT) superconducting (SC) radio frequency (RF) power coupler has developed two 700-MHz, helium gas-cooled power couplers. One has a fixed inner conductor and the other has an adjustable inner conductor (gamma prototype and alpha prototype). The power couplers will be performance tested in the near future. This paper discusses the mechanical design and fabrication techniques employed in the development of each power coupler. This includes material selection, copper coating, assembly sequences, and metal joining procedures, as well as the engineering analyses performed to determine the dynamic response of the inner conductors due to environmental excitations. A bellows is used in both prototype inner conductors in the area near the ceramic RF window, to compensate for thermal expansion and mechanical tolerance build-up. In addition, a bellows is used near the tip of the inner conductor of the alpha prototype for running the power coupler after it is installed on the accelerator. Extensive analytical work has been performed to determine the static loads transmitted by the bellows due to thermally induced expansion on the inner conductor and on the RF window. This paper also discusses this analysis, as well as the mechanical analysis performed to determine the final geometric shape of the bellows. Finally, a discussion of the electromagnetic analysis used to optimize the performance of the power couplers is included.

  10. Chomsky-Schützenberger parsing for weighted multiple context-free languages

    Directory of Open Access Journals (Sweden)

    Tobias Denkinger

    2017-07-01

    Full Text Available We prove a Chomsky-Schützenberger representation theorem for multiple context-free languages weighted over complete commutative strong bimonoids. Using this representation we devise a parsing algorithm for a restricted form of those devices.

  11. Basis for low beam loss in the high-current APT linac

    International Nuclear Information System (INIS)

    Wangler, T.P.; Gray, E.R.; Krawczyk, F.L.; Kurennoy, S.S.; Lawrence, G.P.; Ryne, R.D.; Crandall, K.R.

    1998-01-01

    The present evidence that the APT proton linac design will meet its goal of low beam loss operation. The conclusion has three main bases: (1) extrapolation from the understanding of the performance of the 800-MeV LANSCE proton linac at Los Alamos, (2) the theoretical understanding of the dominant halo-forming mechanism in the APT accelerator from physics models and multiparticle simulations, and (3) the conservative approach and key principles underlying the design of the APT linac, which are aimed at minimizing beam halo and providing large apertures to reduce beam loss to a very low value

  12. Grammar-Based Specification and Parsing of Binary File Formats

    Directory of Open Access Journals (Sweden)

    William Underwood

    2012-03-01

    Full Text Available The capability to validate and view or play binary file formats, as well as to convert binary file formats to standard or current file formats, is critically important to the preservation of digital data and records. This paper describes the extension of context-free grammars from strings to binary files. Binary files are arrays of data types, such as long and short integers, floating-point numbers and pointers, as well as characters. The concept of an attribute grammar is extended to these context-free array grammars. This attribute grammar has been used to define a number of chunk-based and directory-based binary file formats. A parser generator has been used with some of these grammars to generate syntax checkers (recognizers for validating binary file formats. Among the potential benefits of an attribute grammar-based approach to specification and parsing of binary file formats is that attribute grammars not only support format validation, but support generation of error messages during validation of format, validation of semantic constraints, attribute value extraction (characterization, generation of viewers or players for file formats, and conversion to current or standard file formats. The significance of these results is that with these extensions to core computer science concepts, traditional parser/compiler technologies can potentially be used as a part of a general, cost effective curation strategy for binary file formats.

  13. Parsing (malicious pleasures: Schadenfreude and gloating at others’ adversity

    Directory of Open Access Journals (Sweden)

    Colin Wayne Leach

    2015-02-01

    Full Text Available We offer the first empirical comparison of the pleasure in seeing (i.e., schadenfreude and in causing (i.e., gloating others’ adversity. In Study 1, we asked participants to recall and report on an (individual or group episode of pleasure that conformed to our formal definition of schadenfreude, gloating, pride, or joy, without reference to an emotion word. Schadenfreude and gloating were distinct in the situational features of the episode, participants’ appraisals of it, and their expressions of pleasure (e.g., smiling, boasting. In Study 2, we had participants imagine being in an (individual or group emotion episode designed to fit our conceptualization of schadenfreude or gloating. Individual and group versions of the emotions did not differ much in either study. However, the two pleasures differed greatly in their situational features, appraisals, experience, and expression. This parsing of the particular pleasures of schadenfreude and gloating brings nuance to the study of (malicious pleasure, which tends to be less finely conceptualized and examined than displeasure despite its importance to social relations.

  14. Simulation of dynamic traffic loading based on accelerated pavement testing (APT)

    CSIR Research Space (South Africa)

    Steyn, WJvdM

    2004-03-01

    Full Text Available The objective of this paper is to introduce the latest Heavy Vehicle Simulator (HVS) technology as part of the South African Accelerated Pavement Testing (APT) efforts, its capabilities and expected impact on road pavement analysis....

  15. A New Framework for Textual Information Mining over Parse Trees. CRESST Report 805

    Science.gov (United States)

    Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

    2011-01-01

    Textual information mining is a challenging problem that has resulted in the creation of many different rule-based linguistic query languages. However, these languages generally are not optimized for the purpose of text mining. In other words, they usually consider queries as individuals and only return raw results for each query. Moreover they…

  16. APT - NASA ENHANCED VERSION OF AUTOMATICALLY PROGRAMMED TOOL SOFTWARE - STAND-ALONE VERSION

    Science.gov (United States)

    Premo, D. A.

    1994-01-01

    The APT code is one of the most widely used software tools for complex numerically controlled (N/C) machining. APT is an acronym for Automatically Programmed Tools and is used to denote both a language and the computer software that processes that language. Development of the APT language and software system was begun over twenty years ago as a U. S. government sponsored industry and university research effort. APT is a "problem oriented" language that was developed for the explicit purpose of aiding the N/C machine tools. Machine-tool instructions and geometry definitions are written in the APT language to constitute a "part program." The APT part program is processed by the APT software to produce a cutter location (CL) file. This CL file may then be processed by user supplied post processors to convert the CL data into a form suitable for a particular N/C machine tool. This June, 1989 offering of the APT system represents an adaptation, with enhancements, of the public domain version of APT IV/SSX8 to the DEC VAX-11/780 for use by the Engineering Services Division of the NASA Goddard Space Flight Center. Enhancements include the super pocket feature which allows concave and convex polygon shapes of up to 40 points including shapes that overlap, that leave islands of material within the pocket, and that have one or more arcs as part of the pocket boundary. Recent modifications to APT include a rework of the POCKET subroutine and correction of an error that prevented the use within a macro of a macro variable cutter move statement combined with macro variable double check surfaces. Former modifications included the expansion of array and buffer sizes to accommodate larger part programs, and the insertion of a few user friendly error messages. The APT system software on the DEC VAX-11/780 is organized into two separate programs: the load complex and the APT processor. The load complex handles the table initiation phase and is usually only run when changes to the

  17. Evaluation of medical isotope production with the accelerator production of tritium (APT) facility

    International Nuclear Information System (INIS)

    Benjamin, R.W.; Frey, G.D.; McLean, D.C., Jr; Spicer, K.M.; Davis, S.E.; Baron, S.; Frysinger, J.R.; Blanpied, G.; Adcock, D.

    1997-01-01

    The accelerator production of tritium (APT) facility, with its high beam current and high beam energy, would be an ideal supplier of radioisotopes for medical research, imaging, and therapy. By-product radioisotopes will be produced in the APT window and target cooling systems and in the tungsten target through spallation, neutron, and proton interactions. High intensity proton fluxes are potentially available at three different energies for the production of proton- rich radioisotopes. Isotope production targets can be inserted into the blanket for production of neutron-rich isotopes. Currently, the major production sources of radioisotopes are either aging or abroad, or both. The use of radionuclides in nuclear medicine is growing and changing, both in terms of the number of nuclear medicine procedures being performed and in the rapidly expanding range of procedures and radioisotopes used. A large and varied demand is forecast, and the APT would be an ideal facility to satisfy that demand

  18. Study of surface functionalization on IDE by using 3-aminopropyl triethoxysilane (APTES) for cervical cancer detection

    Science.gov (United States)

    Raqeema, S.; Hashim, U.; Azizah, N.

    2016-07-01

    This paper presented the study of surface functionalization on IDE by using 3-Aminopropyl triethoxysilane (APTES). The DNA nanochip based interdigitated (IDE) has been proposed to optimized the sensitivity of the device due to the cervical cancer detection. The DNA nanochip will be more efficient using surface modification of TiO2 nanoparticles with 3-Aminopropyl triethoxysilane (APTES). Furthermore, APTES gain the better functionalization of the adsorption mechanism on IDE. The combination of the DNA probe and the HPV target will produce more sensitivity and speed of the DNA nanochip due to their properties. The IDE has been characterized using current-voltage (IV) measurement. This functionalization of the surface would be applicable, sensitive, selective and low cost for cervical cancer detection.

  19. The Analysis of Income Per Capita Convergence on ASEAN Plus Three (APT) Countries

    OpenAIRE

    Fatiwetunusa, Any; Syamsurijal, Syamsurijal; Yuliana, Sa’adah

    2017-01-01

    The main objective of this study is to test the convergence of income per capita in APT countries through three models: absolute convergence, conditional convergence and sigma convergence. Regression analysis of panel data from 13 APT countries during the period of 2001-2014 is used to analysed to study problem. In absolute convergence model, the growth of real GDP per capita and initial real GDP are used as the variables, meanwhile, 8 variables such as the growth of real GPD per capita, init...

  20. Generative re-ranking model for dependency parsing of Italian sentences

    NARCIS (Netherlands)

    Sangati, F.

    2009-01-01

    We present a general framework for dependency parsing of Italian sentences based on a combination of discriminative and generative models. We use a state-of-the-art discriminative model to obtain a k-best list of candidate structures for the test sentences, and use the generative model to compute

  1. Towards a Robuster Interpretive Parsing: learning from overt forms in Optimality Theory

    NARCIS (Netherlands)

    Biró, T.

    2013-01-01

    The input data to grammar learning algorithms often consist of overt forms that do not contain full structural descriptions. This lack of information may contribute to the failure of learning. Past work on Optimality Theory introduced Robust Interpretive Parsing (RIP) as a partial solution to this

  2. Single-View 3D Scene Reconstruction and Parsing by Attribute Grammar.

    Science.gov (United States)

    Liu, Xiaobai; Zhao, Yibiao; Zhu, Song-Chun

    2018-03-01

    In this paper, we present an attribute grammar for solving two coupled tasks: i) parsing a 2D image into semantic regions; and ii) recovering the 3D scene structures of all regions. The proposed grammar consists of a set of production rules, each describing a kind of spatial relation between planar surfaces in 3D scenes. These production rules are used to decompose an input image into a hierarchical parse graph representation where each graph node indicates a planar surface or a composite surface. Different from other stochastic image grammars, the proposed grammar augments each graph node with a set of attribute variables to depict scene-level global geometry, e.g., camera focal length, or local geometry, e.g., surface normal, contact lines between surfaces. These geometric attributes impose constraints between a node and its off-springs in the parse graph. Under a probabilistic framework, we develop a Markov Chain Monte Carlo method to construct a parse graph that optimizes the 2D image recognition and 3D scene reconstruction purposes simultaneously. We evaluated our method on both public benchmarks and newly collected datasets. Experiments demonstrate that the proposed method is capable of achieving state-of-the-art scene reconstruction of a single image.

  3. Neural Semantic Parsing by Character-based Translation: Experiments with Abstract Meaning Representations

    NARCIS (Netherlands)

    van Noord, Rik; Bos, Johannes

    2017-01-01

    We evaluate the character-level translation method for neural semantic parsing on a large corpus of sentences annotated with Abstract Meaning Representations (AMRs). Using a sequence-to-sequence model, and some trivial preprocessing and postprocessing of AMRs, we obtain a baseline accuracy of 53.1

  4. ParseCNV integrative copy number variation association software with quality tracking.

    Science.gov (United States)

    Glessner, Joseph T; Li, Jin; Hakonarson, Hakon

    2013-03-01

    A number of copy number variation (CNV) calling algorithms exist; however, comprehensive software tools for CNV association studies are lacking. We describe ParseCNV, unique software that takes CNV calls and creates probe-based statistics for CNV occurrence in both case-control design and in family based studies addressing both de novo and inheritance events, which are then summarized based on CNV regions (CNVRs). CNVRs are defined in a dynamic manner to allow for a complex CNV overlap while maintaining precise association region. Using this approach, we avoid failure to converge and non-monotonic curve fitting weaknesses of programs, such as CNVtools and CNVassoc, and although Plink is easy to use, it only provides combined CNV state probe-based statistics, not state-specific CNVRs. Existing CNV association methods do not provide any quality tracking information to filter confident associations, a key issue which is fully addressed by ParseCNV. In addition, uncertainty in CNV calls underlying CNV associations is evaluated to verify significant results, including CNV overlap profiles, genomic context, number of probes supporting the CNV and single-probe intensities. When optimal quality control parameters are followed using ParseCNV, 90% of CNVs validate by polymerase chain reaction, an often problematic stage because of inadequate significant association review. ParseCNV is freely available at http://parsecnv.sourceforge.net.

  5. Introduction to special issue on machine learning approaches to shallow parsing

    NARCIS (Netherlands)

    Hammerton, J; Osborne, M; Armstrong, S; Daelemans, W

    2002-01-01

    This article introduces the problem of partial or shallow parsing (assigning partial syntactic structure to sentences) and explains why it is an important natural language processing (NLP) task. The complexity of the task makes Machine Learning an attractive option in comparison to the handcrafting

  6. Tackling Error Propagation through Reinforcement Learning: A Case of Greedy Dependency Parsing

    NARCIS (Netherlands)

    Le, M.N.; Fokkens, A.S.

    Error propagation is a common problem in NLP. Reinforcement learning explores erroneous states during training and can therefore be more robust when mistakes are made early in a process. In this paper, we apply reinforcement learning to greedy dependency parsing which is known to suffer from error

  7. Fuzzy context-free languages - Part 2: Recognition and parsing algorithms

    NARCIS (Netherlands)

    Asveld, P.R.J.

    2005-01-01

    In a companion paper [P.R.J. Asveld, Fuzzy context-free languages---Part 1: Generalized fuzzy context-free grammars, Theoret. Comp. Sci. (2005)] we used fuzzy context-free grammars in order to model grammatical errors resulting in erroneous inputs for robust recognizing and parsing algorithms for

  8. Integrating high dimensional bi-directional parsing models for gene mention tagging.

    Science.gov (United States)

    Hsu, Chun-Nan; Chang, Yu-Ming; Kuo, Cheng-Ju; Lin, Yu-Shi; Huang, Han-Shen; Chung, I-Fang

    2008-07-01

    Tagging gene and gene product mentions in scientific text is an important initial step of literature mining. In this article, we describe in detail our gene mention tagger participated in BioCreative 2 challenge and analyze what contributes to its good performance. Our tagger is based on the conditional random fields model (CRF), the most prevailing method for the gene mention tagging task in BioCreative 2. Our tagger is interesting because it accomplished the highest F-scores among CRF-based methods and second over all. Moreover, we obtained our results by mostly applying open source packages, making it easy to duplicate our results. We first describe in detail how we developed our CRF-based tagger. We designed a very high dimensional feature set that includes most of information that may be relevant. We trained bi-directional CRF models with the same set of features, one applies forward parsing and the other backward, and integrated two models based on the output scores and dictionary filtering. One of the most prominent factors that contributes to the good performance of our tagger is the integration of an additional backward parsing model. However, from the definition of CRF, it appears that a CRF model is symmetric and bi-directional parsing models will produce the same results. We show that due to different feature settings, a CRF model can be asymmetric and the feature setting for our tagger in BioCreative 2 not only produces different results but also gives backward parsing models slight but constant advantage over forward parsing model. To fully explore the potential of integrating bi-directional parsing models, we applied different asymmetric feature settings to generate many bi-directional parsing models and integrate them based on the output scores. Experimental results show that this integrated model can achieve even higher F-score solely based on the training corpus for gene mention tagging. Data sets, programs and an on-line service of our gene

  9. Modification of silicon nitride surfaces with GOPES and APTES for antibody immobilization: computational and experimental studies

    International Nuclear Information System (INIS)

    To, Thien Dien; Nguyen, Anh Tuan; Phan, Khoa Nhat Thanh; Truong, An Thu Thi; Doan, Tin Chanh Duc; Dang, Chien Mau

    2015-01-01

    Chemical modification of silicon nitride (SiN) surfaces by silanization has been widely studied especially with 3-(aminopropyl)triethoxysilane (APTES) and 3-(glycidyloxypropyl) dimethylethoxysilane (GOPES). However few reports performed the experimental and computational studies together. In this study, surface modification of SiN surfaces with GOPES and APTES covalently bound with glutaraldehyde (GTA) was investigated for antibody immobilization. The monoclonal anti-cytokeratin-FITC (MACF) antibody was immobilized on the modified SiN surfaces. The modified surfaces were characterized by water contact angle measurements, atomic force microscopy and fluorescence microscopy. The FITC-fluorescent label indicated the existence of MACF antibody on the SiN surfaces and the efficiency of the silanization reaction. Absorption of APTES and GOPES on the oxidized SiN surfaces was computationally modeled and calculated by Materials Studio software. The computational and experimental results showed that modification of the SiN surfaces with APTES and GTA was more effective than the modification with GOPES. (paper)

  10. Amide Proton Transfer (APT) MR imaging and Magnetization Transfer (MT) MR imaging of pediatric brain development

    International Nuclear Information System (INIS)

    Zhang, Hong; Kang, Huiying; Peng, Yun; Zhao, Xuna; Jiang, Shanshan; Zhang, Yi; Zhou, Jinyuan

    2016-01-01

    To quantify the brain maturation process during childhood using combined amide proton transfer (APT) and conventional magnetization transfer (MT) imaging at 3 Tesla. Eighty-two neurodevelopmentally normal children (44 males and 38 females; age range, 2-190 months) were imaged using an APT/MT imaging protocol with multiple saturation frequency offsets. The APT-weighted (APTW) and MT ratio (MTR) signals were quantitatively analyzed in multiple brain areas. Age-related changes in MTR and APTW were evaluated with a non-linear regression analysis. The APTW signals followed a decreasing exponential curve with age in all brain regions measured (R"2 = 0.7-0.8 for the corpus callosum, frontal and occipital white matter, and centrum semiovale). The most significant changes appeared within the first year. At maturation, larger decreases in APTW and lower APTW values were found in the white matter. On the contrary, the MTR signals followed an increasing exponential curve with age in the same brain regions measured, with the most significant changes appearing within the initial 2 years. There was an inverse correlation between the MTR and APTW signal intensities during brain maturation. Together with MT imaging, protein-based APT imaging can provide additional information in assessing brain myelination in the paediatric population. (orig.)

  11. Medical Isotope Production With The Accelerator Production of Tritium (APT) Facility

    International Nuclear Information System (INIS)

    Buckner, M.; Cappiello, M.; Pitcher, E.; O'Brien, H.

    1998-01-01

    In order to meet US tritium needs to maintain the nuclear weapons deterrent, the Department of Energy (DOE) is pursuing a dual track program to provide a new tritium source. A record of decision is planned for late in 1998 to select either the Accelerator Production of Tritium (APT) or the Commercial Light Water Reactor (CLWR) as the technology for new tritium production in the next century. To support this decision, an APT Project was undertaken to develop an accelerator design capable of producing 3 kg of tritium per year by 2007 (START I requirements). The Los Alamos National Laboratory (LANL) was selected to lead this effort with Burns and Roe Enterprises, Inc. (BREI) / General Atomics (GA) as the prime contractor for design, construction, and commissioning of the facility. If chosen in the downselect, the facility will be built at the Savannah River Site (SRS) and operated by the SRS Maintenance and Operations (M ampersand O) contractor, the Westinghouse Savannah River Company (WSRC), with long-term technology support from LANL. These three organizations (LANL, BREI/GA, and WSRC) are working together under the direction of the APT National Project Office which reports directly to the DOE Office of Accelerator Production which has program authority and responsibility for the APT Project

  12. Amide Proton Transfer (APT) MR imaging and Magnetization Transfer (MT) MR imaging of pediatric brain development

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hong; Kang, Huiying; Peng, Yun [Beijing Children' s Hospital, Capital Medical University, Imaging Center, Department of Radiology, Beijing (China); Zhao, Xuna [Philips Healthcare, Beijing (China); Jiang, Shanshan; Zhang, Yi; Zhou, Jinyuan [Johns Hopkins University, Division of MR Research, Department of Radiology, Baltimore, MD (United States)

    2016-10-15

    To quantify the brain maturation process during childhood using combined amide proton transfer (APT) and conventional magnetization transfer (MT) imaging at 3 Tesla. Eighty-two neurodevelopmentally normal children (44 males and 38 females; age range, 2-190 months) were imaged using an APT/MT imaging protocol with multiple saturation frequency offsets. The APT-weighted (APTW) and MT ratio (MTR) signals were quantitatively analyzed in multiple brain areas. Age-related changes in MTR and APTW were evaluated with a non-linear regression analysis. The APTW signals followed a decreasing exponential curve with age in all brain regions measured (R{sup 2} = 0.7-0.8 for the corpus callosum, frontal and occipital white matter, and centrum semiovale). The most significant changes appeared within the first year. At maturation, larger decreases in APTW and lower APTW values were found in the white matter. On the contrary, the MTR signals followed an increasing exponential curve with age in the same brain regions measured, with the most significant changes appearing within the initial 2 years. There was an inverse correlation between the MTR and APTW signal intensities during brain maturation. Together with MT imaging, protein-based APT imaging can provide additional information in assessing brain myelination in the paediatric population. (orig.)

  13. APT Blanket Detailed Bin Model Based on Initial Plate-Type Design -3D FLOWTRAN-TF Model

    International Nuclear Information System (INIS)

    Hamm, L.L.

    1998-01-01

    This report provides background information for a series of reports documenting accident scenario simulations for the Accelerator Production of Tritium (APT) blanket heat removal systems. The simulations were performed in support of the Preliminary Safety Analysis Report for the APT. This report gives a brief description of the FLOWTRAN-TF code which was used for detailed blanket bin modeling

  14. Update on the methodology for Amtrak cost accounting Amtrak performance tracking (APT) : volume 2, appendices A-F.

    Science.gov (United States)

    2016-04-22

    Each table below represents the list of Cost Centers associated with each APT Subfamily at the time the data for this report was gathered from APT in April 2016. The #701 Capital Family is not included as it does not have Cost Centers in a traditiona...

  15. Amide proton transfer (APT) imaging of brain tumors at 7 T : The role of tissue water T1 -Relaxation properties

    NARCIS (Netherlands)

    Khlebnikov, V; Polders, Daniel; Hendrikse, J; Robe, Pierre A.; Voormolen, Eduard H; Luijten, Peter R; Klomp, DWJ; Hoogduin, Hans

    PURPOSE: To provide insight into the effect of water T1 relaxation (T1wat ) on amide proton transfer (APT) contrast in tumors. Three different metrics of APT contrast-magnetization transfer ratio (MTRRex ), relaxation-compensated MTRRex (AREX), and traditional asymmetry (MTRasym )-were compared in

  16. Molecular layer deposition of APTES on silicon nanowire biosensors: Surface characterization, stability and pH response

    International Nuclear Information System (INIS)

    Liang, Yuchen; Huang, Jie; Zang, Pengyuan; Kim, Jiyoung; Hu, Walter

    2014-01-01

    Graphical abstract: - Abstract: We report the use of molecular layer deposition (MLD) for depositing 3-aminopropyltriethoxysilane (APTES) on a silicon dioxide surface. The APTES monolayer was characterized using spectroscopic ellipsometry, contact angle goniometry, and atomic force microscopy. Effects of reaction time of repeating pulses and simultaneous feeding of water vapor with APTES were tested. The results indicate that the synergistic effects of water vapor and reaction time are significant for the formation of a stable monolayer. Additionally, increasing the number of repeating pulses improved the APTES surface coverage but led to saturation after 10 pulses. In comparing MLD with solution-phase deposition, the APTES surface coverage and the surface quality were nearly equivalent. The hydrolytic stability of the resulting films was also studied. The results confirmed that the hydrolysis process was necessary for MLD to obtain stable surface chemistry. Furthermore, we compared the pH sensing results of Si nanowire field effect transistors (Si NWFETs) modified by both the MLD and solution methods. The highly repeatable pH sensing results reflected the stability of APTES monolayers. The results also showed an improved pH response of the sensor prepared by MLD compared to the one prepared by the solution treatment, which indicated higher surface coverage of APTES

  17. Molecular layer deposition of APTES on silicon nanowire biosensors: Surface characterization, stability and pH response

    Science.gov (United States)

    Liang, Yuchen; Huang, Jie; Zang, Pengyuan; Kim, Jiyoung; Hu, Walter

    2014-12-01

    We report the use of molecular layer deposition (MLD) for depositing 3-aminopropyltriethoxysilane (APTES) on a silicon dioxide surface. The APTES monolayer was characterized using spectroscopic ellipsometry, contact angle goniometry, and atomic force microscopy. Effects of reaction time of repeating pulses and simultaneous feeding of water vapor with APTES were tested. The results indicate that the synergistic effects of water vapor and reaction time are significant for the formation of a stable monolayer. Additionally, increasing the number of repeating pulses improved the APTES surface coverage but led to saturation after 10 pulses. In comparing MLD with solution-phase deposition, the APTES surface coverage and the surface quality were nearly equivalent. The hydrolytic stability of the resulting films was also studied. The results confirmed that the hydrolysis process was necessary for MLD to obtain stable surface chemistry. Furthermore, we compared the pH sensing results of Si nanowire field effect transistors (Si NWFETs) modified by both the MLD and solution methods. The highly repeatable pH sensing results reflected the stability of APTES monolayers. The results also showed an improved pH response of the sensor prepared by MLD compared to the one prepared by the solution treatment, which indicated higher surface coverage of APTES.

  18. Pippi — Painless parsing, post-processing and plotting of posterior and likelihood samples

    Science.gov (United States)

    Scott, Pat

    2012-11-01

    Interpreting samples from likelihood or posterior probability density functions is rarely as straightforward as it seems it should be. Producing publication-quality graphics of these distributions is often similarly painful. In this short note I describe pippi, a simple, publicly available package for parsing and post-processing such samples, as well as generating high-quality PDF graphics of the results. Pippi is easily and extensively configurable and customisable, both in its options for parsing and post-processing samples, and in the visual aspects of the figures it produces. I illustrate some of these using an existing supersymmetric global fit, performed in the context of a gamma-ray search for dark matter. Pippi can be downloaded and followed at http://github.com/patscott/pippi.

  19. Fetching and Parsing Data from the Web with OpenRefine

    Directory of Open Access Journals (Sweden)

    Evan Peter Williamson

    2017-08-01

    Full Text Available OpenRefine is a powerful tool for exploring, cleaning, and transforming data. An earlier Programming Historian lesson, “Cleaning Data with OpenRefine”, introduced the basic functionality of Refine to efficiently discover and correct inconsistency in a data set. Building on those essential data wrangling skills, this lesson focuses on Refine’s ability to fetch URLs and parse web content. Examples introduce some of the advanced features to transform and enhance a data set including: - fetch URLs using Refine - construct URL queries to retrieve information from a simple web API - parse HTML and JSON responses to extract relevant data - use array functions to manipulate string values - use Jython to extend Refine’s functionality It will be helpful to have basic familiarity with OpenRefine, HTML, and programming concepts such as variables and loops to complete this lesson.

  20. Tackling Error Propagation through Reinforcement Learning: A Case of Greedy Dependency Parsing

    OpenAIRE

    Le, Minh; Fokkens, Antske

    2017-01-01

    Error propagation is a common problem in NLP. Reinforcement learning explores erroneous states during training and can therefore be more robust when mistakes are made early in a process. In this paper, we apply reinforcement learning to greedy dependency parsing which is known to suffer from error propagation. Reinforcement learning improves accuracy of both labeled and unlabeled dependencies of the Stanford Neural Dependency Parser, a high performance greedy parser, while maintaining its eff...

  1. Cross-Lingual Dependency Parsing with Late Decoding for Truly Low-Resource Languages

    OpenAIRE

    Schlichtkrull, Michael Sejr; Søgaard, Anders

    2017-01-01

    In cross-lingual dependency annotation projection, information is often lost during transfer because of early decoding. We present an end-to-end graph-based neural network dependency parser that can be trained to reproduce matrices of edge scores, which can be directly projected across word alignments. We show that our approach to cross-lingual dependency parsing is not only simpler, but also achieves an absolute improvement of 2.25% averaged across 10 languages compared to the previous state...

  2. Is human sentence parsing serial or parallel? Evidence from event-related brain potentials.

    Science.gov (United States)

    Hopf, Jens-Max; Bader, Markus; Meng, Michael; Bayer, Josef

    2003-01-01

    In this ERP study we investigate the processes that occur in syntactically ambiguous German sentences at the point of disambiguation. Whereas most psycholinguistic theories agree on the view that processing difficulties arise when parsing preferences are disconfirmed (so-called garden-path effects), important differences exist with respect to theoretical assumptions about the parser's recovery from a misparse. A key distinction can be made between parsers that compute all alternative syntactic structures in parallel (parallel parsers) and parsers that compute only a single preferred analysis (serial parsers). To distinguish empirically between parallel and serial parsing models, we compare ERP responses to garden-path sentences with ERP responses to truly ungrammatical sentences. Garden-path sentences contain a temporary and ultimately curable ungrammaticality, whereas truly ungrammatical sentences remain so permanently--a difference which gives rise to different predictions in the two classes of parsing architectures. At the disambiguating word, ERPs in both sentence types show negative shifts of similar onset latency, amplitude, and scalp distribution in an initial time window between 300 and 500 ms. In a following time window (500-700 ms), the negative shift to garden-path sentences disappears at right central parietal sites, while it continues in permanently ungrammatical sentences. These data are taken as evidence for a strictly serial parser. The absence of a difference in the early time window indicates that temporary and permanent ungrammaticalities trigger the same kind of parsing responses. Later differences can be related to successful reanalysis in garden-path but not in ungrammatical sentences. Copyright 2003 Elsevier Science B.V.

  3. Learning for Semantic Parsing with Kernels under Various Forms of Supervision

    Science.gov (United States)

    2007-08-01

    natural language sentences to their formal executable meaning representations. This is a challenging problem and is critical for developing computing...sentences are semantically tractable. This indi- cates that Geoquery is more challenging domain for semantic parsing than ATIS. In the past, there have been a...Combining parsers. In Proceedings of the Conference on Em- pirical Methods in Natural Language Processing and Very Large Corpora (EMNLP/ VLC -99), pp. 187–194

  4. Kinetics of (3-aminopropyl)triethoxylsilane (APTES) silanization of superparamagnetic iron oxide nanoparticles.

    Science.gov (United States)

    Liu, Yue; Li, Yueming; Li, Xue-Mei; He, Tao

    2013-12-10

    Silanization of magnetic ironoxide nanoparticles with (3-aminopropyl)triethoxylsilane (APTES) is reported. The kinetics of silanization toward saturation was investigated using different solvents including water, water/ethanol (1/1), and toluene/methanol (1/1) at different reaction temperature with different APTES loading. The nanoparticles were characterized by Fourier transform infrared spectroscopy, vibrating sample magnetometry, transmission electron microscopy, and thermal gravimetric analysis (TGA). Grafting density data based on TGA were used for the kinetic modeling. It is shown that initial silanization takes place very fast but the progress toward saturation is very slow, and the mechanism may involve adsorption, chemical sorption, and chemical diffusion processes. The highest equilibrium grafting density of 301 mg/g was yielded when using toluene/methanol mixture as the solvent at a reaction temperature of 70 °C.

  5. APT cost scaling: Preliminary indications from a Parametric Costing Model (PCM)

    International Nuclear Information System (INIS)

    Krakowski, R.A.

    1995-01-01

    A Parametric Costing Model has been created and evaluate as a first step in quantitatively understanding important design options for the Accelerator Production of Tritium (APT) concept. This model couples key economic and technical elements of APT in a two-parameter search of beam energy and beam power that minimizes costs within a range of operating constraints. The costing and engineering depth of the Parametric Costing Model is minimal at the present open-quotes entry levelclose quotes, and is intended only to demonstrate a potential for a more-detailed, cost-based integrating design tool. After describing the present basis of the Parametric Costing Model and giving an example of a single parametric scaling run derived therefrom, the impacts of choices related to resistive versus superconducting accelerator structures and cost of electricity versus plant availability (open-quotes load curveclose quotes) are reported. Areas of further development and application are suggested

  6. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis

    DEFF Research Database (Denmark)

    Siegel, Gabriele; Obernosterer, Gregor; Fiore, Roberto

    2009-01-01

    of acyl protein thioesterase 1 (APT1), an enzyme regulating the palmitoylation status of proteins that are known to function at the synapse, including the alpha(13) subunits of G proteins (Galpha(13)). RNA-interference-mediated knockdown of APT1 and the expression of membrane-localized Galpha(13) both...... suppress spine enlargement caused by inhibition of miR-138, suggesting that APT1-regulated depalmitoylation of Galpha(13) might be an important downstream event of miR-138 function. Our results uncover a previously unknown miRNA-dependent mechanism in neurons and demonstrate a previously unrecognized...

  7. The Analysis of Income per Capita Convergence on ASEAN Plus Three (APT Countries

    Directory of Open Access Journals (Sweden)

    Any Fatiwetunusa

    2017-09-01

    Full Text Available The main objective of this study is to test the convergence of income per capita in APT countries through three models: absolute convergence, conditional convergence and sigma convergence. Regression analysis of panel data from 13 APT countries during the period of 2001-2014 is used to analysed to study problem. In absolute convergence model, the growth of real GDP per capita and initial real GDP are used as the variables, meanwhile, 8 variables such as the growth of real GPD per capita, initial real GDP per capita, labor force ratio, value added in agricultural sector, value added in industrial sector, terms of trade, foreign direct investment and internet users ratio are analyzed in conditional convergence model. According to the Solow model, the economies of the countries will converge in which the growth of income per capita of developing countries will be higher than those of developed countries. The economies will be convergent if the countries tend to move to a similar steady state resulting in smaller gap between the countries. Based on the results of absolute convergence and conditional convergence models, APT countries is converging with the rate of 2% and 2.2%. This is consistent with the results of sigma convergence model that shows a declining trend in the dispersion of real GDP per capita in APT regions. The growth of real GDP per capita is influenced by initial GDP per capita, labor force ratio, value added in agricultural sector, value added in industrial sector, terms of trade, foreign direct investment and internet users ratio. Developed countries such as Singapore, Brunei Darussalam and South Korea experience the impact of high real GDP per capita growth. On the contrary, Indonesia, Laos, Vietnam and The Phillipines undergo the impact of low GDP per capita growth.

  8. The mediation as an apt tool for the prevention of crime as result of gender violence

    OpenAIRE

    Yaíma Águila Gutiérrez; Marileydis Pino Rosa

    2017-01-01

    Violence based in gender is an actual, social, historical and cultural matter. It affects to million persons around the world in the personal, familiar and social ambit. Violence based in gender could damage relationships and also could become in a crime. Mediation is an apt tool to use before the intervention of law for solving gender violence´s conflicts which could need the intervention of criminal law. Those reasons show that is necessary the prevention of gender violence so is important ...

  9. Scientific and engineering services for the LANCE/ER accelerator production of tritium (APT) project

    International Nuclear Information System (INIS)

    1994-01-01

    The APT project office is conducting a preconceptual design study for an accelerator driven concept to produce tritium. The facility will require new technology in many areas, since the scale of this accelerator is significantly larger then any in operation to date. The facility is composed of four subsystems: accelerator, target ampersand blanket, balance of plant, and tritium purification system (TPS). New physics realms will be entered in order for the concept to be feasible; for example, extremely high energy levels of the entering protons that induce (multiplicative) spallation of the neutrons from the high Z target will occur. These are complex and require advance codes (MCNP) to predict the physics interactions and as well as deleterious material effects in the surrounding structures. Other issues include component cooling and complex thermal-hydraulics effects within the blanket and the beam open-quotes window.close quotes In order to support a DOE mandated fast ROD schedule, Los Alamos APT staff will be provided with senior, engineering technical support staff with direct APT technology experience and whom are open-quotes on siteclose quotes. This report contains resumes of the staff

  10. "gnparser": a powerful parser for scientific names based on Parsing Expression Grammar.

    Science.gov (United States)

    Mozzherin, Dmitry Y; Myltsev, Alexander A; Patterson, David J

    2017-05-26

    Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role. We refer to this as 'parsing' the name. Parsing categorizes name's elements into those that are stable and those that are prone to change. Names are matched first by combining them according to their stable elements. Matches are then refined by examining their varying elements. This two stage process dramatically improves the number and quality of matches. It is especially useful for the automatic data exchange within the context of "Big Data" in biology. We introduce Global Names Parser (gnparser). It is a Java tool written in Scala language (a language for Java Virtual Machine) to parse scientific names. It is based on a Parsing Expression Grammar. The parser can be applied to scientific names of any complexity. It assigns a semantic meaning (such as genus name, species epithet, rank, year of publication, authorship, annotations, etc.) to all elements of a name. It is able to work with nested structures as in the names of hybrids. gnparser performs with ≈99% accuracy and processes 30 million name-strings/hour per CPU thread. The gnparser library is compatible with Scala, Java, R, Jython, and JRuby. The parser can be used as a command line application, as a socket server, a web-app or as a RESTful HTTP-service. It is released under an Open source MIT license. Global Names Parser (gnparser) is a fast, high precision tool for biodiversity informaticians and biologists working with large numbers of scientific names. It can replace expensive and error

  11. TRAINING TREE ADJOINING GRAMMARS WITH HUGE TEXT CORPUS USING SPARK MAP REDUCE

    Directory of Open Access Journals (Sweden)

    Vijay Krishna Menon

    2015-07-01

    Full Text Available Tree adjoining grammars (TAGs are mildly context sensitive formalisms used mainly in modelling natural languages. Usage and research on these psycho linguistic formalisms have been erratic in the past decade, due to its demanding construction and difficulty to parse. However, they represent promising future for formalism based NLP in multilingual scenarios. In this paper we demonstrate basic synchronous Tree adjoining grammar for English-Tamil language pair that can be used readily for machine translation. We have also developed a multithreaded chart parser that gives ambiguous deep structures and a par dependency structure known as TAG derivation. Furthermore we then focus on a model for training this TAG for each language using a large corpus of text through a map reduce frequency count model in spark and estimation of various probabilistic parameters for the grammar trees thereafter; these parameters can be used to perform statistical parsing on the trained grammar.

  12. Biomedical applications of SPION@APTES@PEG-folic acid@carboxylated quercetin nanodrug on various cancer cells

    International Nuclear Information System (INIS)

    Akal, Z.Ü.; Alpsoy, L.; Baykal, A.

    2016-01-01

    Highlights: • SPION has been synthesized via Reflux synthesis route. • SPION@APTES@FA-PEG@CQ nanodrug has super paramagnetic property. • SPION@APTES@FA-PEG@CQ nanodrug has cytotoxic, apoptotic and necrotic effects on HeLa and MCF-7 cells. • SPION@APTES@FA-PEG@CQ nanodrug can be potentially used for the delivery of quercetin to cervical and breast cancer cells. - Abstract: In this study, carboxylated quercetin (CQ) was conjugated to superparamagnetic iron oxide nanoparticles (SPIONs) which were modified by (3-aminopropyl) triethoxysilane (APTES), Folic acid (FA) and carboxylated Polyethylene glycol (PEG); (SPION@APTES@FA-PEG@CQ), nanodrug has been synthesized via polyol and accompanying by various chemical synthesis routes. The characterization of the final product was done via X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Thermal gravimetric analysis (TGA), Transmission electron spectroscopy (TEM) and Vibrating sample magnetometer (VSM). Its cytotoxic and apoptotic activities on over expressed folic acid receptor (FR + ) (MCF-7, HeLa) and none expressed folic acid receptor (FR-) (A549) cancer cell lines were determined by using MTT assay, Real-Time Cell Analysis, TUNEL assay, Annexin assay and RT-PCR analysis for Caspase3/7 respectively. SPION@APTES@FA-PEG@CQ nanodrug showed higher cytotoxicity against HeLa and MCF-7 cell lines as compared with A549 cell line. Moreover, SPION@APTES@FA-PEG@CQ nanodrug also caused higher apoptotic and necrotic effects in 100 μg/mL HeLa and MCF-7 cells than A549 cells. The findings showed that SPION@APTES@FA-PEG@CQ nanodrug has cytotoxic, apoptotic and necrotic effects on HeLa and MCF-7 which are FR over expressed cell lines and can be potentially used for the delivery of quercetin to cervical and breast cancer cells.

  13. Biomedical applications of SPION@APTES@PEG-folic acid@carboxylated quercetin nanodrug on various cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Akal, Z.Ü., E-mail: zulker@fatih.edu.tr [Department of Biology, 34500 Büyükçekmece, Istanbul (Turkey); Alpsoy, L. [Department of Biology, 34500 Büyükçekmece, Istanbul (Turkey); Department of Medical Biology, 34500 Büyükçekmece, Istanbul (Turkey); Baykal, A. [Department of Chemistry, Fatih University, 34500 Büyükçekmece, Istanbul (Turkey)

    2016-08-15

    Highlights: • SPION has been synthesized via Reflux synthesis route. • SPION@APTES@FA-PEG@CQ nanodrug has super paramagnetic property. • SPION@APTES@FA-PEG@CQ nanodrug has cytotoxic, apoptotic and necrotic effects on HeLa and MCF-7 cells. • SPION@APTES@FA-PEG@CQ nanodrug can be potentially used for the delivery of quercetin to cervical and breast cancer cells. - Abstract: In this study, carboxylated quercetin (CQ) was conjugated to superparamagnetic iron oxide nanoparticles (SPIONs) which were modified by (3-aminopropyl) triethoxysilane (APTES), Folic acid (FA) and carboxylated Polyethylene glycol (PEG); (SPION@APTES@FA-PEG@CQ), nanodrug has been synthesized via polyol and accompanying by various chemical synthesis routes. The characterization of the final product was done via X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Thermal gravimetric analysis (TGA), Transmission electron spectroscopy (TEM) and Vibrating sample magnetometer (VSM). Its cytotoxic and apoptotic activities on over expressed folic acid receptor (FR + ) (MCF-7, HeLa) and none expressed folic acid receptor (FR-) (A549) cancer cell lines were determined by using MTT assay, Real-Time Cell Analysis, TUNEL assay, Annexin assay and RT-PCR analysis for Caspase3/7 respectively. SPION@APTES@FA-PEG@CQ nanodrug showed higher cytotoxicity against HeLa and MCF-7 cell lines as compared with A549 cell line. Moreover, SPION@APTES@FA-PEG@CQ nanodrug also caused higher apoptotic and necrotic effects in 100 μg/mL HeLa and MCF-7 cells than A549 cells. The findings showed that SPION@APTES@FA-PEG@CQ nanodrug has cytotoxic, apoptotic and necrotic effects on HeLa and MCF-7 which are FR over expressed cell lines and can be potentially used for the delivery of quercetin to cervical and breast cancer cells.

  14. Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant.

    Science.gov (United States)

    Kovalchik, Kevin A; Moggridge, Sophie; Chen, David D Y; Morin, Gregg B; Hughes, Christopher S

    2018-06-01

    Effective analysis of protein samples by mass spectrometry (MS) requires careful selection and optimization of a range of experimental parameters. As the output from the primary detection device, the "raw" MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To ease and increase the range of analyses possible, the RawQuant tool was developed to enable parsing of raw MS files derived from Thermo Orbitrap instruments to yield meta and scan data in an openly readable text format. RawQuant can be commanded to export user-friendly files containing MS 1 , MS 2 , and MS 3 metadata as well as matrices of quantification values based on isobaric tagging approaches. In this study, the utility of RawQuant is demonstrated in several scenarios: (1) reanalysis of shotgun proteomics data for the identification of the human proteome, (2) reanalysis of experiments utilizing isobaric tagging for whole-proteome quantification, and (3) analysis of a novel bacterial proteome and synthetic peptide mixture for assessing quantification accuracy when using isobaric tags. Together, these analyses successfully demonstrate RawQuant for the efficient parsing and quantification of data from raw Thermo Orbitrap MS files acquired in a range of common proteomics experiments. In addition, the individual analyses using RawQuant highlights parametric considerations in the different experimental sets and suggests targetable areas to improve depth of coverage in identification-focused studies and quantification accuracy when using isobaric tags.

  15. A hierarchical methodology for urban facade parsing from TLS point clouds

    Science.gov (United States)

    Li, Zhuqiang; Zhang, Liqiang; Mathiopoulos, P. Takis; Liu, Fangyu; Zhang, Liang; Li, Shuaipeng; Liu, Hao

    2017-01-01

    The effective and automated parsing of building facades from terrestrial laser scanning (TLS) point clouds of urban environments is an important research topic in the GIS and remote sensing fields. It is also challenging because of the complexity and great variety of the available 3D building facade layouts as well as the noise and data missing of the input TLS point clouds. In this paper, we introduce a novel methodology for the accurate and computationally efficient parsing of urban building facades from TLS point clouds. The main novelty of the proposed methodology is that it is a systematic and hierarchical approach that considers, in an adaptive way, the semantic and underlying structures of the urban facades for segmentation and subsequent accurate modeling. Firstly, the available input point cloud is decomposed into depth planes based on a data-driven method; such layer decomposition enables similarity detection in each depth plane layer. Secondly, the labeling of the facade elements is performed using the SVM classifier in combination with our proposed BieS-ScSPM algorithm. The labeling outcome is then augmented with weak architectural knowledge. Thirdly, least-squares fitted normalized gray accumulative curves are applied to detect regular structures, and a binarization dilation extraction algorithm is used to partition facade elements. A dynamic line-by-line division is further applied to extract the boundaries of the elements. The 3D geometrical façade models are then reconstructed by optimizing facade elements across depth plane layers. We have evaluated the performance of the proposed method using several TLS facade datasets. Qualitative and quantitative performance comparisons with several other state-of-the-art methods dealing with the same facade parsing problem have demonstrated its superiority in performance and its effectiveness in improving segmentation accuracy.

  16. The mediation as an apt tool for the prevention of crime as result of gender violence

    Directory of Open Access Journals (Sweden)

    Yaíma Águila Gutiérrez

    2017-07-01

    Full Text Available Violence based in gender is an actual, social, historical and cultural matter. It affects to million persons around the world in the personal, familiar and social ambit. Violence based in gender could damage relationships and also could become in a crime. Mediation is an apt tool to use before the intervention of law for solving gender violence´s conflicts which could need the intervention of criminal law. Those reasons show that is necessary the prevention of gender violence so is important the intervention of criminology.

  17. Los Modelos CAPM y APT para la valuacion de empresas de Telecomunicaciones con parametros operativos

    Directory of Open Access Journals (Sweden)

    Saldaña, J.

    2007-07-01

    Full Text Available One of the most important research topics in the financial area during de the last years has been the capital assets appraisal or the appraise of shares. This seeks two determine the explanatory factor of the rate of return for a specific portfolio. The CAPM (Capital Asset Pricing Model and the APT (Arbitrage Pricing Theory, both capital asset evaluation models, are hereby presented. The main characteristics of both models are the essential assumptions for their for there development, their statement and the practical test on the telecommunications portfolio using operational, financial and macroeconomics variable, and carried on with the purpose to be compare with reality.

  18. PyParse: a semiautomated system for scoring spoken recall data.

    Science.gov (United States)

    Solway, Alec; Geller, Aaron S; Sederberg, Per B; Kahana, Michael J

    2010-02-01

    Studies of human memory often generate data on the sequence and timing of recalled items, but scoring such data using conventional methods is difficult or impossible. We describe a Python-based semiautomated system that greatly simplifies this task. This software, called PyParse, can easily be used in conjunction with many common experiment authoring systems. Scored data is output in a simple ASCII format and can be accessed with the programming language of choice, allowing for the identification of features such as correct responses, prior-list intrusions, extra-list intrusions, and repetitions.

  19. Mobile Backend as a Service: the pros and cons of parse

    OpenAIRE

    Nguyen, Phu

    2016-01-01

    Using a pre-built backend for an application is an affordable and swift approach to prototyping new application ideas. Mobile Backend as a Service (MBaaS) is the term for pre-built backend systems that developers can use. However, it is advisable to understand the pros and the cons of an MBaaS before deciding to use it. The aim of the thesis was to determine the advantages and disadvantages of using Parse, a provider of mobile backend as a service, in application development. Parse’s defin...

  20. Development of a RAMI model for LANSCE and high power APT accelerators

    International Nuclear Information System (INIS)

    Tallerico, P.J.

    1994-01-01

    Assessment of the reliability, availability, maintainability and inspectability (RAMI) of all high power, high cost systems is important to justify and improve the cost effectiveness of these systems. For the very large (over 100 MW) accelerator systems associated with APT, a RAMI model is very valuable in guiding the design and allocation of resources. A RAMI model of an existing machine is also valuable, since machine improvement funds must be allocated to increase the availability by the largest amount. The authors have developed a RAMI model using the critical subsystems of the LANSCE accelerator and beam delivery complex as an example and to evaluate the effectiveness for estimating reliability and beam availability. LAMPF and LANSCE together provide most of the features required for the accelerator and beam delivery part of a high-power APT machine, but LANSCE is pulsed, rather than CW. This complex is capable of a 1-MW average power H - beam, and it is the most powerful proton accelerator in the US built to date

  1. APT analyses of deuterium-loaded Fe/V multi-layered films

    KAUST Repository

    Gemma, R.

    2009-04-01

    Interaction of hydrogen with metallic multi-layered thin films remains as a hot topic in recent days Detailed knowledge on such chemically modulated systems is required if they are desired for application in hydrogen energy system as storage media. In this study, the deuterium concentration profile of Fe/V multi-layer was investigated by atom probe tomography (APT) at 60 and 30 K. It is firstly shown that deuterium-loaded sample can easily react with oxygen at the Pd capping layer on Fe/V and therefore, it is highly desired to avoid any oxygen exposure after D(2) loading before APT analysis. The analysis temperature also has an impact on D concentration profile. The result taken at 60 K shows clear traces of surface segregation of D atoms towards analysis surface. The observed diffusion profile of D allows us to estimate an apparent diffusion coefficient D. The calculated D at 60 K is in the order of 10(-17) cm(2)/s, deviating 6 orders of magnitude from an extrapolated value. This was interpreted with alloying, D-trapping at defects and effects of the large extension to which the extrapolation was done. A D concentration profile taken at 30 K shows nosegregation anymore and a homogeneous distribution at C(D) = 0.05(2) D/Me, which is in good accordance with that measured in the corresponding pressure-composition isotherm. (C) 2008 Elsevier B.V. All rights reserved.

  2. APT analyses of deuterium-loaded Fe/V multi-layered films

    KAUST Repository

    Gemma, R.; Al-Kassab, Talaat; Kirchheim, R.; Pundt, A.

    2009-01-01

    Interaction of hydrogen with metallic multi-layered thin films remains as a hot topic in recent days Detailed knowledge on such chemically modulated systems is required if they are desired for application in hydrogen energy system as storage media. In this study, the deuterium concentration profile of Fe/V multi-layer was investigated by atom probe tomography (APT) at 60 and 30 K. It is firstly shown that deuterium-loaded sample can easily react with oxygen at the Pd capping layer on Fe/V and therefore, it is highly desired to avoid any oxygen exposure after D(2) loading before APT analysis. The analysis temperature also has an impact on D concentration profile. The result taken at 60 K shows clear traces of surface segregation of D atoms towards analysis surface. The observed diffusion profile of D allows us to estimate an apparent diffusion coefficient D. The calculated D at 60 K is in the order of 10(-17) cm(2)/s, deviating 6 orders of magnitude from an extrapolated value. This was interpreted with alloying, D-trapping at defects and effects of the large extension to which the extrapolation was done. A D concentration profile taken at 30 K shows nosegregation anymore and a homogeneous distribution at C(D) = 0.05(2) D/Me, which is in good accordance with that measured in the corresponding pressure-composition isotherm. (C) 2008 Elsevier B.V. All rights reserved.

  3. (Invariability in the Samoan syntax/prosody interface and consequences for syntactic parsing

    Directory of Open Access Journals (Sweden)

    Kristine M. Yu

    2017-10-01

    Full Text Available While it has long been clear that prosody should be part of the grammar influencing the action of the syntactic parser, how to bring prosody into computational models of syntactic parsing has remained unclear. The challenge is that prosodic information in the speech signal is the result of the interaction of a multitude of conditioning factors. From this output, how can we factor out the contribution of syntax to conditioning prosodic events? And if we are able to do that factorization and define a production model from the syntactic grammar to a prosodified utterance, how can we then define a comprehension model based on that production model? In this case study of the Samoan morphosyntax-prosody interface, we show how to factor out the influence of syntax on prosody in empirical work and confirm there is invariable morphosyntactic conditioning of high edge tones. Then, we show how this invariability can be precisely characterized and used by a parsing model that factors the various influences of morphosyntax on tonal events. We expect that models of these kinds can be extended to more comprehensive perspectives on Samoan and to languages where the syntax/prosody coupling is more complex.

  4. FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences.

    Science.gov (United States)

    Waldmann, Jost; Gerken, Jan; Hankeln, Wolfgang; Schweer, Timmy; Glöckner, Frank Oliver

    2014-06-14

    Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data.

  5. Parsing partial molar volumes of small molecules: a molecular dynamics study.

    Science.gov (United States)

    Patel, Nisha; Dubins, David N; Pomès, Régis; Chalikian, Tigran V

    2011-04-28

    We used molecular dynamics (MD) simulations in conjunction with the Kirkwood-Buff theory to compute the partial molar volumes for a number of small solutes of various chemical natures. We repeated our computations using modified pair potentials, first, in the absence of the Coulombic term and, second, in the absence of the Coulombic and the attractive Lennard-Jones terms. Comparison of our results with experimental data and the volumetric results of Monte Carlo simulation with hard sphere potentials and scaled particle theory-based computations led us to conclude that, for small solutes, the partial molar volume computed with the Lennard-Jones potential in the absence of the Coulombic term nearly coincides with the cavity volume. On the other hand, MD simulations carried out with the pair interaction potentials containing only the repulsive Lennard-Jones term produce unrealistically large partial molar volumes of solutes that are close to their excluded volumes. Our simulation results are in good agreement with the reported schemes for parsing partial molar volume data on small solutes. In particular, our determined interaction volumes() and the thickness of the thermal volume for individual compounds are in good agreement with empirical estimates. This work is the first computational study that supports and lends credence to the practical algorithms of parsing partial molar volume data that are currently in use for molecular interpretations of volumetric data.

  6. Process of 3D wireless decentralized sensor deployment using parsing crossover scheme

    Directory of Open Access Journals (Sweden)

    Albert H.R. Ko

    2015-07-01

    Full Text Available A Wireless Sensor Networks (WSN usually consists of numerous wireless devices deployed in a region of interest, each able to collect and process environmental information and communicate with neighboring devices. It can thus be regarded as a Multi-Agent System for territorial security, where individual agents cooperate with each other to avoid duplication of effort and to exploit other agent’s capacities. The problem of sensor deployment becomes non-trivial when we consider environmental factors, such as terrain elevations. Due to the fact that all sensors are homogeneous, the chromosomes that encode sensor positions are actually interchangeable, and conventional crossover schemes such as uniform crossover would cause some redundancy as well as over-concentration in certain specific geographical area. We propose a Parsing Crossover Scheme that intends to reduce redundancy and ease geographical concentration pattern in an effort to facilitate the search. The proposed parsing crossover method demonstrates better performances than those of uniform crossover under different terrain irregularities.

  7. Attribute And-Or Grammar for Joint Parsing of Human Pose, Parts and Attributes.

    Science.gov (United States)

    Park, Seyoung; Nie, Xiaohan; Zhu, Song-Chun

    2017-07-25

    This paper presents an attribute and-or grammar (A-AOG) model for jointly inferring human body pose and human attributes in a parse graph with attributes augmented to nodes in the hierarchical representation. In contrast to other popular methods in the current literature that train separate classifiers for poses and individual attributes, our method explicitly represents the decomposition and articulation of body parts, and account for the correlations between poses and attributes. The A-AOG model is an amalgamation of three traditional grammar formulations: (i)Phrase structure grammar representing the hierarchical decomposition of the human body from whole to parts; (ii)Dependency grammar modeling the geometric articulation by a kinematic graph of the body pose; and (iii)Attribute grammar accounting for the compatibility relations between different parts in the hierarchy so that their appearances follow a consistent style. The parse graph outputs human detection, pose estimation, and attribute prediction simultaneously, which are intuitive and interpretable. We conduct experiments on two tasks on two datasets, and experimental results demonstrate the advantage of joint modeling in comparison with computing poses and attributes independently. Furthermore, our model obtains better performance over existing methods for both pose estimation and attribute prediction tasks.

  8. RAMI modeling of selected balance of plant systems for the proposed Accelerator Production of Tritium (APT) project

    International Nuclear Information System (INIS)

    Radder, J.A.; Cramer, D.S.

    1997-01-01

    In order to meet Department of Energy (DOE) Defense Program requirements for tritium in the 2005-2007 time frame, new production capability must be made available. The Accelerator Production of Tritium (APT) Plant is being considered as an alternative to nuclear reactor production of tritium, which has been the preferred method in the past. The proposed APT plant will use a high-power proton accelerator to generate thermal neutrons that will be captured in 3 He to produce tritium (3H). It is expected that the APT Plant will be built and operated at the DOE's Savannah River Site (SRS) in Aiken, South Carolina. Discussion is focused on Reliability, Availability, Maintainability, and Inspectability (RAMI) modeling of recent conceptual designs for balance of plant (BOP) systems in the proposed APT Plant. In the conceptual designs for balance of plant (BOP) systems in the proposed APT Plant. In the conceptual design phase, system RAMI estimates are necessary to identify the best possible system alternative and to provide a valid picture of the cost effectiveness of the proposed system for comparison with other system alternatives. RAMI estimates in the phase must necessarily be based on generic data. The objective of the RAMI analyses at the conceptual design stage is to assist the designers in achieving an optimum design which balances the reliability and maintainability requirements among the subsystems and components

  9. Aptámeros: agentes diagnósticos y terapéuticos = Aptamers: diagnostic and therapeutic agents

    Directory of Open Access Journals (Sweden)

    Frank J Hernandez

    2012-04-01

    Full Text Available Los aptámeros son ácidos nucleicos de cadena sencilla, ADN o ARN, que reconocen una gran variedad de moléculas. Cada aptámero posee una estructura tridimensional particular que le permite unirse con afinidad y especificidad altas a la molécula diana. Los aptámeros tienen propiedades de reconocimiento equiparables a las de los anticuerpos; sin embargo, por la naturaleza de su composición tienen ventajas significativas en cuanto a su tamaño, producción y modificación. Estas características los hacen excelentes candidatos para el desarrollo de nuevas plataformas biotecnológicas. Se han identificado aptámeros con propiedades terapéuticas que han sido evaluados exitosamente en modelos animales; entre ellos, algunos se encuentran en fase clínica y uno ya fue aprobado para tratamiento por la FDA (Food and Drug Administration. Todos estos avances ocurridos durante las dos últimas décadas permiten anticipar el protagonismo que tendrán los aptámeros como agentes diagnósticos y terapéuticos en un futuro cercano.

  10. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Boswellia serrata Roxb. ex Colebr. (Indian Frankincense tree) of Burseraceae is a large-sized deciduous tree that is native to India. Bark is thin, greenish-ash-coloured that exfoliates into smooth papery flakes. Stem exudes pinkish resin ... Fruit is a three-valved capsule. A green gum-resin exudes from the ...

  11. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Flowering Trees. Ailanthus excelsa Roxb. (INDIAN TREE OF. HEAVEN) of Simaroubaceae is a lofty tree with large pinnately compound alternate leaves, which are ... inflorescences, unisexual and greenish-yellow. Fruits are winged, wings many-nerved. Wood is used in making match sticks. 1. Male flower; 2. Female flower.

  12. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Gyrocarpus americanus Jacq. (Helicopter Tree) of Hernandiaceae is a moderate size deciduous tree that grows to about 12 m in height with a smooth, shining, greenish-white bark. The leaves are ovate, rarely irregularly ... flowers which are unpleasant smelling. Fruit is a woody nut with two long thin wings.

  13. Flowering Trees

    Indian Academy of Sciences (India)

    More Details Fulltext PDF. Volume 8 Issue 8 August 2003 pp 112-112 Flowering Trees. Zizyphus jujuba Lam. of Rhamnaceae · More Details Fulltext PDF. Volume 8 Issue 9 September 2003 pp 97-97 Flowering Trees. Moringa oleifera · More Details Fulltext PDF. Volume 8 Issue 10 October 2003 pp 100-100 Flowering Trees.

  14. Corrosion measurements on apt prototypic materials in the Lansce high-power proton beam and applicability to other systems

    International Nuclear Information System (INIS)

    Lillard, R.S.; Gac, F.D.; James, M.R.; Maloy, S.A.; Paciotti, M.A.; Waters, L.S.; Willcutt, G.J.; Chandler, G.T.; Ferguson, P.D.

    2003-01-01

    The corrosion rates of several corrosion resistant materials behave in a similar manner even under the intense radiation of the LANSCE high-power beam. A second observation was made, showing that the corrosion rates saturated under high instantaneous radiation intensity in corrosion experiments conducted for the accelerator production of tritium (APT) programme. The LANSCE H + beam is not prototypic of the proposed APT production plant in several respects. The instantaneous proton flux in the APT production plant beam is about 10 times that of the LANSCE beam. The small transverse APT beam spot is rastered to spread the power density over the area of the target, and as the beam rasters, it creates a pulsed character to the beam at a specific location. In order to develop correlations that would enable extrapolation of the corrosion data to the proposed APT production plant, the experimental programme included measurements over a range of average beam currents, measurements at high and low instantaneous beam current, and measurements at various combinations of pulse width and repetition rate. The correlations that were developed are based on an approximately linear dependence of corrosion rate on average beam current (average radiation intensity) and the saturation effect observed at high instantaneous radiation intensity. For a given transverse beam profile and for the same average beam current, the correlations predict the highest corrosion rate in a do beam and the lowest corrosion rate in the lowest duty cycle beams. In the case of the APT extrapolation, the predicted corrosion rates were a factor of 5 lower than for a do beam depositing the same average power density. The measured corrosion rates and the formulated extrapolations are applicable to water-cooled targets and components in proton beams. (authors)

  15. Sleep Disrupts High-Level Speech Parsing Despite Significant Basic Auditory Processing.

    Science.gov (United States)

    Makov, Shiri; Sharon, Omer; Ding, Nai; Ben-Shachar, Michal; Nir, Yuval; Zion Golumbic, Elana

    2017-08-09

    The extent to which the sleeping brain processes sensory information remains unclear. This is particularly true for continuous and complex stimuli such as speech, in which information is organized into hierarchically embedded structures. Recently, novel metrics for assessing the neural representation of continuous speech have been developed using noninvasive brain recordings that have thus far only been tested during wakefulness. Here we investigated, for the first time, the sleeping brain's capacity to process continuous speech at different hierarchical levels using a newly developed Concurrent Hierarchical Tracking (CHT) approach that allows monitoring the neural representation and processing-depth of continuous speech online. Speech sequences were compiled with syllables, words, phrases, and sentences occurring at fixed time intervals such that different linguistic levels correspond to distinct frequencies. This enabled us to distinguish their neural signatures in brain activity. We compared the neural tracking of intelligible versus unintelligible (scrambled and foreign) speech across states of wakefulness and sleep using high-density EEG in humans. We found that neural tracking of stimulus acoustics was comparable across wakefulness and sleep and similar across all conditions regardless of speech intelligibility. In contrast, neural tracking of higher-order linguistic constructs (words, phrases, and sentences) was only observed for intelligible speech during wakefulness and could not be detected at all during nonrapid eye movement or rapid eye movement sleep. These results suggest that, whereas low-level auditory processing is relatively preserved during sleep, higher-level hierarchical linguistic parsing is severely disrupted, thereby revealing the capacity and limits of language processing during sleep. SIGNIFICANCE STATEMENT Despite the persistence of some sensory processing during sleep, it is unclear whether high-level cognitive processes such as speech

  16. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2013-01-01

    We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  17. Tree compression with top trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

    2015-01-01

    We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

  18. Cuidado de enfermagem a pessoas com hipertensão fundamentado na teoria de Parse Atención de enfermería a personas con hipertensión basada en la teoría de Parse Nursing care to people with hypertension based on Parse's theory

    Directory of Open Access Journals (Sweden)

    Fabíola Vládia Freire da Silva

    2013-03-01

    Full Text Available Este estudo propõe o cuidado de enfermagem, baseado nos princípios de Parse, a pessoas com hipertensão consultadas na Estratégia Saúde da Família. Estudo descritivo, de cunho qualitativo, realizado de março a maio de 2011, com quatorze enfermeiros no município de Itapajé-Ceará. Para coleta das informações utilizou-se a entrevista semiestruturada e, para análise, o discurso dos sujeitos. Emergiram três categorias baseadas nos princípios de Parse: Multidimensão dos significados - o enfermeiro conduz ao relato dos significados; Sincronização de ritmos - o enfermeiro ajuda a identificar harmonia e desarmonia; Mobilização da transcendência - o enfermeiro guia o plano de mudanças. Notou-se aproximação dos discursos ao teorizado por Parse quando citaram buscar um cuidado humanizado, com a participação da família, valorização da autonomia, utilização da educação em saúde, com orientações individuais. Percebeu-se a viabilidade na implementação do cuidado de enfermagem fundamentado na Teoria de Parse a pessoas com hipertensão.Este estudio propone la atención de enfermería, basada en los principios de Parse, para personas con hipertensión en la Estrategia de Salud Familiar. Estudio descriptivo, cualitativo, realizado de marzo a mayo/2011, con catorce enfermeros en Itapajé, Ceará. Para la recolección de las informaciones, se utilizó la entrevista semiestructurada y para análisis, el discurso de los sujetos. Emergieron tres categorías: Multidimensiones de los significados - el enfermero conduce al relato de los significados; Sincronización de los ritmos - el enfermero ayuda a identificar armonía y desarmonía; Movilización de la trascendencia - el enfermero guía el plan de cambios. Se observó semejanzas entre el enfoque de los discursos y la Teoría de Parse, cuando citaron la búsqueda de atención humanizada, con participación de la familia, valoración de la autonomía, uso de la educación en salud

  19. Development of a raster electronics system for expanding the APT proton beam

    Energy Technology Data Exchange (ETDEWEB)

    Chapelle, S.; Hubbard, E.L.; Smith, T.L. [General Atomics, San Diego, CA (United States); Schulze, M.E.; Shafer, R.E. [General Atomics, Los Alamos, NM (United States)

    1998-12-31

    A 1700 MeV, 100 mA proton linear accelerator is being designed for Accelerator Production of Tritium (APT). A beam expansion system is required to uniformly irradiate a 19 x 190 cm tritium production target. This paper describes a beam expansion system consisting of eight ferrite dipole magnets to raster the beam in the x- and y-planes and also describes the salient features of the design of the electronics that are unique to the expander. Eight Insulated Gate Bipolar Transistor (IGBT)-based modulators drive the raster magnets with triangular current waveforms that are synchronized using phase-locked loops (PLLs) and voltage controlled crystal oscillators (VCXOs). Fault detection circuitry shuts down the beam before the target can be damaged by a failure of the raster system. Test data are presented for the prototype system.

  20. Beam dynamics design of the 211 MeV APT normal conducting linac

    International Nuclear Information System (INIS)

    Young, L.M.; Billen, J.H.; Takeda, H.; Wood, R.L.

    1998-01-01

    This paper describes the normal conducting linac design that is part of the Accelerator for Production of Tritium (APT) project. The new version of PARMILA designed this linac. This linac accepts the beam from the 6.7 MeV radio frequency quadrupole without a separate matching section. At about 10 MeV, it has a smooth transition in the length of period from 8βλ to 9βλ in quadrupole focusing lattice. This adjustment of the period was needed to provide sufficient space for the quadrupole focusing magnets and beam diagnostic equipment. The linac consists of the coupled cavity drift tube linac up to 97 MeV and coupled cavity linac above 97 MeV

  1. Overview of the APT high-energy beam transport and beam expanders

    International Nuclear Information System (INIS)

    Shafer, R.E.; Blind, B.; Gray, E.R.

    1997-01-01

    The APT high energy beam transport (HEBT) and beam expanders convey the 1700-MeV, 100-mA cw proton beam from the linac to the tritium target/blanket assembly, or a tuning beam stop. The HEBT includes extensive beam diagnostics, collimators, and beam jitter correction, to monitor and control the 170-MW beam prior to expansion. A zero-degree beamline conveys the beam to the beam stop, and an achromatic bend conveys the beam to the tritium production target. Nonlinear beam expanders make use of higher-order multipole magnets and dithering dipoles to expand the beam to a uniform-density, 16-cm wide by 160-cm high rectangular profile on the tritium-production target. The overall optics design will be reviewed, and beam simulations will be presented

  2. GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome.

    Science.gov (United States)

    Deng, Feilong; Chen, Shi-Yi; Wu, Zhou-Lin; Hu, Yongsong; Jia, Xianbo; Lai, Song-Jia

    2017-10-01

    Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization. GFFview is very useful for investigating quality and difference of the de novo assembled transcriptome in RNA-seq studies.

  3. “Less of the Heroine than the Woman”: Parsing Gender in the British Novel

    Directory of Open Access Journals (Sweden)

    Susan Carlile

    2017-06-01

    Full Text Available This essay offers two methods that will help students resist the temptation to judge eighteenth-century novels by twenty-first-century standards. These methods prompt students to parse the question of whether female protagonists in novels—in this case, Daniel Defoe’s Roxana (1724, Samuel Johnson’s Rasselas (1759, and Charlotte Lennox’s Sophia (1762—are portrayed as perfect models or as complex humans. The first method asks them to engage with definitions of the term “heroine,” and the second method uses word clouds to extend their thinking about the complexity of embodying a mid-eighteenth-century female identity.

  4. A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

    Science.gov (United States)

    Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

    2015-01-15

    Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  5. Study of different 3-aminopropyl triethoxysilane (APTES) concentration on TiO2 particles based IDE for cervical cancer detection

    Science.gov (United States)

    Raqeema, S.; Hashim, U.; Azizah, N.; Nadzirah, Sh.; Arshad, M. K. Md; Ruslinda, A. R.; Gopinath, Subash C. B.

    2017-03-01

    HPV that also called Human Papillomaviruses is the major cause of the cervical cancer. HPV 16 and HPV 18 are the two types of HPV are the most HPV-associated cancers and responsible as a high-risk HPV. Cervical cancer taken about 70 percent of all cases due HPV infections. Cervical malignancy for the most part development on a lady's cervix and its was developed slowly as cancer disease. TiO2 particles give better performance and low cost of the biosensor. The used of 3-aminopropyl triethoxysilane (APTES) will be more efficient for DNA nanochip. APTES used as absorption reaction to immobilize organic biomolecules on the inorganic surface. Besides, APTES give better functionalization of the adsorption mechanism on IDE. The surface functionalized for immobilizing the DNA, which is the combination of the DNA probe and the HPV target produce high sensitivity andfast detection of the IDE. The Current-Voltage (IV) characteristic proved the sensitivity of the DNA nanochip increase as the concentration varied from 0% concentration to 24% of APTES concentration.

  6. CNET and APT : a comparison of two methods for measuring mental representations underlying activity-travel choices

    NARCIS (Netherlands)

    Horeni, O.; Arentze, T.A.; Dellaert, B.G.C.; Timmermans, H.J.P.

    2010-01-01

    This paper presents and compares the potential of online versions of two interview techniques (APT and CNET) which have been developed for measuring mental representations underlying activity-travel choices. The comparison is based on the results of a first online survey administered in the

  7. Tree Nut Allergies

    Science.gov (United States)

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

  8. Análisis de los posibles desde la teoría de Parse en una persona con Alzheimer The analysis of the possibles through Parse's theory on a person with Alzheimer

    Directory of Open Access Journals (Sweden)

    Virtudes Rodero-Sánchez

    2006-11-01

    Full Text Available Cuando una persona acude al sistema sanitario con un problema de salud, con mucha frecuencia se le va a pedir que introduzca cambios en sus hábitos y estilo de vida. Esta demanda se suele concretar en un pacto-compromiso que se establece persona-profesional. Hemos observado que este pacto, a pesar de que el profesional se esfuerza en enmarcarlo en objetivos realistas, con demasiada frecuencia sobreviene la frustración, sobre todo en escenarios de cronicidad. La teoría de Parse nos ofrece una manera diferente de abordar el cambio. En la teoría de Parse, El Ser Humano en Devenir, los posibles son la expresión de la fuerza, entendida como una manera única de transformación, que consiste en avanzar con las esperanzas, anhelos y los proyectos de la persona. Planteamos: en primer lugar un análisis de los elementos de lo que Parse llama su tercer principio, la co-trancendencia con los posibles; en segundo lugar el análisis de los posibles desde este marco de referencia a través de una narrativa; y por último la práctica enfermera.When a person comes to the Health Care System with a health problem will often be asked to change some of his habits and lifestyles. This demand becomes a compromise-pact between the person and the professional. We have observed that in this compromise-pact, despite the effort of the professional to hide it behind realist targets, the patient usually becomes frustrated, especially in cases of chronic illnesses. Parse's theory offers us a different way to approach the change. In Parse's theory, The Human Becoming, the possibles are the expression of power, understood as a unique way of transformation, consisting in advancing with the hopes, desires and projects of a person. We suggest, first of all, an analysis of the elements that Parse calls her third principle: co-transcendence with the possibles; secondly, the analysis of the possibles from the basis of this reference framework through a narration and, finally

  9. Flowering Trees

    Indian Academy of Sciences (India)

    medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends. Flowers are large, white, attractive, and fragrant. Corolla is funnel-shaped. Fruit is an ...

  10. Flowering Trees

    Indian Academy of Sciences (India)

    Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February. Fruit is ...

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Cerbera manghasL. (SEA MANGO) of Apocynaceae is a medium-sized evergreen coastal tree with milky latex. The bark is grey-brown, thick and ... Fruit is large. (5–10 cm long), oval containing two flattened seeds and resembles a mango, hence the name Mangas or. Manghas. Leaves and fruits contain ...

  12. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowering Trees. Gliricidia sepium(Jacq.) Kunta ex Walp. (Quickstick) of Fabaceae is a small deciduous tree with. Pinnately compound leaves. Flower are prroduced in large number in early summer on terminal racemes. They are attractive, pinkish-white and typically like bean flowers. Fruit is a few-seeded flat pod.

  13. Flowering Trees

    Indian Academy of Sciences (India)

    Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.

  14. Talking Trees

    Science.gov (United States)

    Tolman, Marvin

    2005-01-01

    Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

  15. Drawing Trees

    DEFF Research Database (Denmark)

    Halkjær From, Andreas; Schlichtkrull, Anders; Villadsen, Jørgen

    2018-01-01

    We formally prove in Isabelle/HOL two properties of an algorithm for laying out trees visually. The first property states that removing layout annotations recovers the original tree. The second property states that nodes are placed at least a unit of distance apart. We have yet to formalize three...

  16. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.

  17. A Walk-based Semantically Enriched Tree Kernel Over Distributed Word Representations

    DEFF Research Database (Denmark)

    Srivastava, Shashank; Hovy, Dirk

    2013-01-01

    We propose a walk-based graph kernel that generalizes the notion of tree-kernels to continuous spaces. Our proposed approach subsumes a general framework for word-similarity, and in particular, provides a flexible way to incorporate distributed representations. Using vector representations......, such an approach captures both distributional semantic similarities among words as well as the structural relations between them (encoded as the structure of the parse tree). We show an efficient formulation to compute this kernel using simple matrix multiplication operations. We present our results on three...

  18. Surface modification of TiO2 nanotubes by grafting with APTS coupling agents

    Science.gov (United States)

    Phan Duong, Hong; Le, Minh Duc; Dao, Hung Cuong; Chen, Chia-Yun

    2017-10-01

    Titanium dioxide nanotubes (TNTs) have been considered the promising nanostructures employed for many practical applications such as biomedical, photonic and optoelectronic devices. Nevertheless, strong aggregation of TNTs within various aqueous media significantly hindered their practical utilizations and the capability of dispersing TNTs in the desired solvents are urgent to be improved. Therefore, in this study, the methodic investigations have been performed on the grafted modification of 3-aminopropyl triethoxysilane (APTS) on the surfaces of synthesized TNTs. A preliminary study was carried out to evaluate the influences of key parameters, including the concentrations of coupling agents, temperatures and the reaction durations, on the grafting efficiency of the aminosilane using Statistical design of experiments (DoE) methodology. TNTs with approximately 10-20 nm in diameter were prepared with the controlled hydrothermal treatment of commercialized P25 particles. The obtained products were revealed by the modern physicochemical systems including x-ray diffraction (XRD), transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) analysis. The additions of silane agent, reaction temperature and time have been adjusted to reveal the influences of the grafting efficiency (from 2.5 to 7.8 wt %) by thermal gravimetric analysis (TGA). Analysis of Fourier transform infrared spectroscopy (FTIR) has confirmed the successful link of Ti-O-Si chemical bonds on the grafted TNTs.

  19. Thermal-hydraulic criteria for the APT tungsten neutron source design

    International Nuclear Information System (INIS)

    Pasamehmetoglu, K.

    1998-03-01

    This report presents the thermal-hydraulic design criteria (THDC) developed for the tungsten neutron source (TNS). The THDC are developed for the normal operations, operational transients, and design-basis accidents. The requirements of the safety analyses are incorporated into the design criteria, consistent with the integrated safety management and the safety-by-design philosophy implemented throughout the APT design process. The phenomenology limiting the thermal-hydraulic design and the confidence level requirements for each limit are discussed. The overall philosophy of the uncertainty analyses and the confidence level requirements also are presented. Different sets of criteria are developed for normal operations, operational transients, anticipated accidents, unlikely accidents, extremely unlikely accidents, and accidents during TNS replacement. In general, the philosophy is to use the strictest criteria for the high-frequency events. The criteria is relaxed as the event frequencies become smaller. The THDC must be considered as a guide for the design philosophy and not as a hard limit. When achievable, design margins greater than those required by the THDC must be used. However, if a specific event sequence cannot meet the THDC, expensive design changes are not necessary if the single event sequence results in sufficient margin to safety criteria and does not challenge the plant availability or investment protection considerations

  20. Micah 7:8-20: An apt conclusion to the book of Micah

    Directory of Open Access Journals (Sweden)

    W J Wessels

    2003-10-01

    Full Text Available It is argued in this article that Micah 7:8-20 forms an apt conclusion to the book of Micah. As was the case with Micah 1, the concluding section also focusses on Yahweh and his dealings with the people of the earth. There is a universal tendency to be detected in this section as well. An important aspect to notice� is� the liturgical nature of chapters six and seven, especially 7:8-20. There is a vagueness, almost a timelessness, imbuing this section. This could be intended allowing later generations of believers to apply these words to� their� own� circumstances. With Micah 7:8-20 as the concluding section of the book, one is left with a sense of well-roundedness, of completeness. The collection of oracles attributed� to Micah in general has a sombre tone. For this very reason Micah� 7:8-20� seems� to� change� the mood. It breathes hope into a negative atmosphere of judgment. It ends with a strong emphasis on the power of Yahweh, the power of forgiveness.

  1. Phylogenetic trees

    OpenAIRE

    Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

    2016-01-01

    We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

  2. Guide to LIBXSIF, a Library for Parsing the Extended Standard Input Format of Accelerated Beamlines(LCC-0060)

    International Nuclear Information System (INIS)

    Tenenbaum, P

    2003-01-01

    We describe LIBXSIF, a standalone library for parsing the Extended Standard Input Format of accelerator beamlines. Included in the description are: documentation of user commands; full description of permitted accelerator elements and their attributes; the construction of beamline lists; the mechanics of adding LIBXSIF to an existing program; and ''under the hood'' details for users who wish to modify the library or are merely morbidly curious

  3. A Pipelining Implementation for Parsing X-ray Diffraction Source Data and Removing the Background Noise

    International Nuclear Information System (INIS)

    Bauer, Michael A; Biem, Alain; McIntyre, Stewart; Xie Yuzhen

    2010-01-01

    Synchrotrons can be used to generate X-rays in order to probe materials at the atomic level. One approach is to use X-ray diffraction (XRD) to do this. The data from an XRD experiment consists of a sequence of digital image files which for a single scan could consist of hundreds or even thousands of digital images. Existing analysis software processes these images individually sequentially and is usually used after the experiment is completed. The results from an XRD detector can be thought of as a sequence of images, generated during the scan by the X-ray beam. If these images could be analyzed in near real-time, the results could be sent to the researcher running the experiment and used to improve the overall experimental process and results. In this paper, we report on a stream processing application to remove background from XRD images using a pipelining implementation. We describe our implementation techniques of using IBM Infosphere Streams for parsing XRD source data and removing the background. We present experimental results showing the super-linear speedup attained over a purely sequential version of the algorithm on a quad-core machine. These results demonstrate the potential of making good use of multi-cores for high-performance stream processing of XRD images.

  4. Parsing pyrogenic polycyclic aromatic hydrocarbons: forensic chemistry, receptor models, and source control policy.

    Science.gov (United States)

    O'Reilly, Kirk T; Pietari, Jaana; Boehm, Paul D

    2014-04-01

    A realistic understanding of contaminant sources is required to set appropriate control policy. Forensic chemical methods can be powerful tools in source characterization and identification, but they require a multiple-lines-of-evidence approach. Atmospheric receptor models, such as the US Environmental Protection Agency (USEPA)'s chemical mass balance (CMB), are increasingly being used to evaluate sources of pyrogenic polycyclic aromatic hydrocarbons (PAHs) in sediments. This paper describes the assumptions underlying receptor models and discusses challenges in complying with these assumptions in practice. Given the variability within, and the similarity among, pyrogenic PAH source types, model outputs are sensitive to specific inputs, and parsing among some source types may not be possible. Although still useful for identifying potential sources, the technical specialist applying these methods must describe both the results and their inherent uncertainties in a way that is understandable to nontechnical policy makers. The authors present an example case study concerning an investigation of a class of parking-lot sealers as a significant source of PAHs in urban sediment. Principal component analysis is used to evaluate published CMB model inputs and outputs. Targeted analyses of 2 areas where bans have been implemented are included. The results do not support the claim that parking-lot sealers are a significant source of PAHs in urban sediments. © 2013 SETAC.

  5. Is Accelerated Partner Therapy (APT) a cost-effective alternative to routine patient referral partner notification in the UK? Preliminary cost-consequence analysis of an exploratory trial.

    Science.gov (United States)

    Roberts, Tracy E; Tsourapas, Angelos; Sutcliffe, Lorna; Cassell, Jackie; Estcourt, Claudia

    2012-02-01

    To undertake a cost-consequence analysis to assess two new models of partner notification (PN), known as Accelerated Partner Therapy (APT Hotline and APT Pharmacy), as compared with routine patient referral PN, for sex partners of people with chlamydia, gonorrhoea and non-gonococcal urethritis. Comparison of costs and outcomes alongside an exploratory trial involving two genitourinary medicine clinics and six community pharmacies. Index patients selected the PN method (APT Hotline, APT Pharmacy or routine PN) for their partners. Clinics and pharmacies recorded cost and resource use data including duration of consultation and uptake of treatment pack. Cost data were collected prospectively for two out of three interventions, and data were synthesised and compared in terms of effectiveness and costs. Routine PN had the lowest average cost per partner treated (approximately £46) compared with either APT Hotline (approximately £54) or APT Pharmacy (approximately £53) strategies. The cost-consequence analysis revealed that APT strategies were more costly but also more effective at treating partners compared to routine PN. The hotline strategy costs more than both the alternative PN strategies. If we accept that strategies which identify and treat partners the fastest are likely to be the most effective in reducing reinfection and onward transmission, then APT Hotline appears an effective PN strategy by treating the highest number of partners in the shortest duration. Whether the additional benefit is worth the additional cost cannot be determined in this preliminary analysis. These data will be useful for informing development of future randomised controlled trials of APT.

  6. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

    The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

  7. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    shaped corolla. Fruit is large, ellipsoidal, green with a hard and smooth shell containing numerous flattened seeds, which are embedded in fleshy pulp. Calabash tree is commonly grown in the tropical gardens of the world as a botanical oddity.

  8. High density gold nanoparticles immobilized on surface via plasma deposited APTES film for decomposing organic compounds in microchannels

    Science.gov (United States)

    Rao, Xi; Guyon, Cédric; Ognier, Stephanie; Da Silva, Bradley; Chu, Chenglin; Tatoulian, Michaël; Hassan, Ali Abou

    2018-05-01

    Immobilization of colloidal particles (e.g. gold nanoparticles (AuNps)) on the inner surface of micro-/nano- channels has received a great interest for catalysis. A novel catalytic ozonation setup using a gold-immobilized microchannel reactor was developed in this work. To anchor AuNps, (3-aminopropyl) triethoxysilane (APTES) with functional amine groups was deposited using plasma enhanced chemical vapor deposition (PECVD) process. The results clearly evidenced that PECVD processing exhibited relatively high efficiency for grafting amine groups and further immobilizing AuNPs. The catalytic activity of gold immobilized microchannel was evaluated by pyruvic acid ozonation. The decomposition rate calculated from High Performance Liquid Chromatography (HPLC) indicated a much better catalytic performance of gold in microchannel than that in batch. The results confirmed immobilizing gold nanoparticles on plasma deposited APTES for preparing catalytic microreactors is promising for the wastewater treatment in the future.

  9. New tests to detect antiphospholipid antibodies: antiprothrombin (aPT) and anti-phosphatidylserine/prothrombin (aPS/PT) antibodies.

    Science.gov (United States)

    Sciascia, Savino; Khamashta, Munther A; Bertolaccini, Maria Laura

    2014-05-01

    Antiprothrombin antibodies have been proposed as potential new biomarkers for thrombosis and/or pregnancy morbidity in the setting of the antiphospholipid syndrome (APS). Antiprothrombin antibodies are commonly detected by ELISA, using prothrombin coated onto irradiated plates (aPT), or prothrombin in complex with phosphatidylserine (aPS/PT), as antigen. Although these antibodies can co-exist in the same patient, aPT and aPS/PT seem to belong to different populations of autoantibodies. Early research explored the role of antibodies to prothrombin as potential antigenic targets for the lupus anticoagulant (LA). To date their clinical significance is being investigated and their potential role in identifying patients at higher risk of developing thrombotic events or pregnancy morbidity is being probed.

  10. Radiation protection system installation for the accelerator production of tritium/low energy demonstration accelerator project (APT/LEDA)

    CERN Document Server

    Wilmarth, J E; Tomei, T L

    2000-01-01

    The APT/LEDA personnel radiation protection system installation was accomplished using a flexible, modular proven system which satisfied regulatory orders, project design criteria, operational modes, and facility requirements. The goal of providing exclusion and safe access of personnel to areas where prompt radiation in the LEDA facility is produced was achieved with the installation of a DOE-approved Personnel Access Control System (PACS). To satisfy the facility configuration design, the PACS, a major component of the overall radiation safety system, conveniently provided five independent areas of personnel access control. Because of its flexibility and adaptability the Los-Alamos Neutron- Science-Center-(LANSCE)-designed Radiation Security System (RSS) was efficiently configured to provide the desired operational modes and satisfy the APT/LEDA project design criteria. The Backbone Beam Enable (BBE) system based on the LANSCE RSS provided the accelerator beam control functions with redundant, hardwired, ta...

  11. Chemotherapy-related amenorrhea after adjuvant paclitaxel-trastuzumab (APT trial).

    Science.gov (United States)

    Ruddy, Kathryn J; Guo, Hao; Barry, William; Dang, Chau T; Yardley, Denise A; Moy, Beverly; Marcom, P Kelly; Albain, Kathy S; Rugo, Hope S; Ellis, Matthew J; Shapira, Iuliana; Wolff, Antonio C; Carey, Lisa A; Overmoyer, Beth A; Hudis, Clifford; Krop, Ian E; Burstein, Harold J; Winer, Eric P; Partridge, Ann H; Tolaney, Sara M

    2015-06-01

    Chemotherapy-related amenorrhea (CRA) is associated with infertility and menopausal symptoms. Learning how frequently paclitaxel and trastuzumab cause amenorrhea is important. Most other adjuvant breast cancer therapies induce CRA in approximately 50 % of all premenopausal recipients [1]. 410 patients enrolled on the APT Trial, a single-arm phase 2 adjuvant study of 12 weeks of paclitaxel and trastuzumab followed by nine months of trastuzumab monotherapy. Eligible patients had ≤3 cm node-negative HER2 + breast cancers. Premenopausal enrollees were asked to complete menstrual surveys every 3-12 months for 72 months. Women who responded to at least one survey at least 15 months after chemotherapy initiation (and who did not undergo hysterectomy and/or bilateral oophorectomy or receive ovarian suppressing medications prior to 15 months) were included in this analysis. A participant was defined as having amenorrhea in follow-up if her self-reported last menstrual period at last follow-up was greater than 12 months prior to the survey. Among the 64 women in the evaluable population (median age at study entry 44 years, range 27-52 years), the median time between chemotherapy initiation and last menstrual survey was 51 months (range 16-79). 18 of 64 women (28 %, 95 % CI 18-41 %) were amenorrheic at that time point. Amenorrhea rates among premenopausal women treated with adjuvant paclitaxel and trastuzumab for early stage breast cancer appear lower than those seen historically with standard alkylator-based breast cancer regimens. Future studies are needed to understand the impact of this regimen on related issues of fertility and menopausal symptoms.

  12. APT Blanket System Loss-of-Flow Accident (LOFA) Analysis Based on Initial Conceptual Design - Case 1: with Beam Shutdown and Active RHR

    International Nuclear Information System (INIS)

    Hamm, L.L.

    1998-01-01

    This report is one of a series of reports that document normal operation and accident simulations for the Accelerator Production of Tritium (APT) blanket heat removal system. These simulations were performed for the Preliminary Safety Analysis Report

  13. Anti-prothrombin (aPT) and anti-phosphatidylserine/prothrombin (aPS/PT) antibodies and the risk of thrombosis in the antiphospholipid syndrome. A systematic review.

    Science.gov (United States)

    Sciascia, Savino; Sanna, Giovanni; Murru, Veronica; Roccatello, Dario; Khamashta, Munther A; Bertolaccini, Maria Laura

    2014-02-01

    Antibodies to prothrombin are detected by directly coating prothrombin on irradiated ELISA plates (aPT) or by using the phosphatidylserine/prothrombin complex as antigen (aPS/PT). Although these antibodies have both been associated with antiphospholipid syndrome (APS) and a correlation between the two assays have been reported, it seems that aPT and aPS/PT belong to different populations of autoantibodies. It was our objective to systematically review the available evidence on aPT and aPS/PT antibodies and the risk of thrombosis in APS. Medline-reports published between 1988 and 2013 investigating aPT and aPS/PT as a risk factor for thrombosis were included. Whenever possible, antibody isotype(s) and site of thrombosis were analysed. This systematic review is based on available data from more than 7,000 patients and controls from 38 studies analysing aPT and 10 aPS/PT. Antibodies to prothrombin (both aPT and aPS/PT) increased the risk of thrombosis (odds ratio [OR] 2.3; 95% confidence interval [CI] 1.72-3.5). aPS/PT seemed to represent a stronger risk factor for thrombosis, both arterial and/or venous than aPT (OR 5.11; 95%CI 4.2-6.3 and OR 1.82; 95%CI 1.44-2.75, respectively). In conclusion, routine measurement of aPS/PT (but not aPT) might be useful in establishing the thrombotic risk of patients with previous thrombosis and/or systemic lupus erythematosus. Their inclusion as laboratory criteria for the APS should be indisputably further explored.

  14. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tree with irregularly-shaped trunk, greyish-white scaly bark and milky latex. Leaves in opposite pairs are simple, oblong and whitish beneath. Flowers that occur in branched inflorescence are white, 2–. 3cm across and fragrant. Calyx is glandular inside. Petals bear numerous linear white scales, the corollary.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Berrya cordifolia (Willd.) Burret (Syn. B. ammonilla Roxb.) – Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading ...

  16. Flowering Trees

    Indian Academy of Sciences (India)

    Canthium parviflorum Lam. of Rubiaceae is a large shrub that often grows into a small tree with conspicuous spines. Leaves are simple, in pairs at each node and are shiny. Inflorescence is an axillary few-flowered cymose fascicle. Flowers are small (less than 1 cm across), 4-merous and greenish-white. Fruit is ellipsoid ...

  17. Flowering Trees

    Indian Academy of Sciences (India)

    sriranga

    Hook.f. ex Brandis (Yellow. Cadamba) of Rubiaceae is a large and handsome deciduous tree. Leaves are simple, large, orbicular, and drawn abruptly at the apex. Flowers are small, yellowish and aggregate into small spherical heads. The corolla is funnel-shaped with five stamens inserted at its mouth. Fruit is a capsule.

  18. Flowering Trees

    Indian Academy of Sciences (India)

    Celtis tetrandra Roxb. of Ulmaceae is a moderately large handsome deciduous tree with green branchlets and grayish-brown bark. Leaves are simple with three to four secondary veins running parallel to the mid vein. Flowers are solitary, male, female and bisexual and inconspicuous. Fruit is berry-like, small and globose ...

  19. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Aglaia elaeagnoidea (A.Juss.) Benth. of Meliaceae is a small-sized evergreen tree of both moist and dry deciduous forests. The leaves are alternate and pinnately compound, terminating in a single leaflet. Leaflets are more or less elliptic with entire margin. Flowers are small on branched inflorescence. Fruit is a globose ...

  20. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowers are borne on stiff bunches terminally on short shoots. They are 2-3 cm across, white, sweet-scented with light-brown hairy sepals and many stamens. Loquat fruits are round or pear-shaped, 3-5 cm long and are edible. A native of China, Loquat tree is grown in parks as an ornamental and also for its fruits.

  1. Flowering Trees

    Indian Academy of Sciences (India)

    mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off in large shreds. Leaves are thick, oblong, leathery and bright red when young. The female flowers are drooping and are larger than male flowers. Fruit is large, red in color and velvety.

  2. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  3. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  4. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  5. ~{owering 'Trees

    Indian Academy of Sciences (India)

    . Stamens are fused into a purple staminal tube that is toothed. Fruit is about 0.5 in. across, nearly globose, generally 5-seeded, green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening.

  6. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  7. Flowering Trees

    Indian Academy of Sciences (India)

    Guaiacum officinale L. (LIGNUM-VITAE) of Zygophyllaceae is a dense-crowned, squat, knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5.

  8. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

    Science.gov (United States)

    Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

    2011-08-05

    The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

  9. AptRank: an adaptive PageRank model for protein function prediction on   bi-relational graphs.

    Science.gov (United States)

    Jiang, Biaobin; Kloster, Kyle; Gleich, David F; Gribskov, Michael

    2017-06-15

    Diffusion-based network models are widely used for protein function prediction using protein network data and have been shown to outperform neighborhood-based and module-based methods. Recent studies have shown that integrating the hierarchical structure of the Gene Ontology (GO) data dramatically improves prediction accuracy. However, previous methods usually either used the GO hierarchy to refine the prediction results of multiple classifiers, or flattened the hierarchy into a function-function similarity kernel. No study has taken the GO hierarchy into account together with the protein network as a two-layer network model. We first construct a Bi-relational graph (Birg) model comprised of both protein-protein association and function-function hierarchical networks. We then propose two diffusion-based methods, BirgRank and AptRank, both of which use PageRank to diffuse information on this two-layer graph model. BirgRank is a direct application of traditional PageRank with fixed decay parameters. In contrast, AptRank utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. We evaluate the ability of both methods to predict protein function on yeast, fly and human protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design four different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly discovered function prediction to comprehensively evaluate predictability of all six methods. We find that both BirgRank and AptRank outperform the previous methods, especially in missing function prediction when using only 10% of the data for training. The MATLAB code is available at https://github.rcac.purdue.edu/mgribsko/aptrank . gribskov@purdue.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  10. KAMUS BAHASA ARAB – INDONESIA ONLINE DENGAN PEMECAHAN SUKU KATA MENGGUNAKAN METODE PARSING

    Directory of Open Access Journals (Sweden)

    Anny Yuniarti

    2004-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Kebutuhan umat Islam akan fasilitas penunjang belajar bahasa Arab di Indonesia masih belum terpenuhi dengan optimal. Kamus bahasa Arab yang beredar di pasaran sulit dipahami karena minimnya pengetahuan tentang ilmu tata bahasa Arab di kalangan umat Islam. Pada penelitian ini dikembangkan sebuah perangkat lunak yang berfungsi menerjemahkan kata berbahasa Arab dengan metode parsing sehingga dapat mencakup kata-kata yang telah mengalami perubahan bentuk dari bentuk dasarnya. Karena kata bahasa Arab memiliki turunan kata yang jumlahnya cukup besar, dan supaya kamus efisien, maka tidak semua turunan kata disimpan dalam basisdata. Oleh sebab itu diperlukan suatu cara untuk mengenali pola kata, dan cara mengetahui bentuk dasar suatu kata. Keseluruhan perangkat lunak ini diimplementasikan berbasis web sehingga memudahkan pengaksesan pengguna. Dan pengguna tidak memerlukan proses instalasi perangkat lunak atau sistem operasi tertentu. Pembuatan perangkat lunak ini didahului dengan perancangan proses dan perancangan interface. Kemudian rancangan tersebut diimplementasikan menjadi sebuah perangkat lunak yang siap untuk dipakai. Perangkat lunak yang sudah jadi tersebut telah diuji coba sesuai dengan spesifikasi kebutuhan

  11. Can we improve partner notification rates through expedited partner therapy in the UK? Findings from an exploratory trial of Accelerated Partner Therapy (APT).

    Science.gov (United States)

    Estcourt, Claudia; Sutcliffe, Lorna; Cassell, Jackie; Mercer, Catherine H; Copas, Andrew; James, Laura; Low, Nicola; Horner, Patrick; Clarke, Michael; Symonds, Merle; Roberts, Tracy; Tsourapas, Angelos; Johnson, Anne M

    2012-02-01

    To develop two new models of expedited partner therapy for the UK, and evaluate them for feasibility, acceptability and preliminary outcome estimates to inform the design of a randomised controlled trial (RCT). Two models of expedited partner therapy (APTHotline and APTPharmacy), known as 'Accelerated Partner Therapy' (APT) were developed. A non-randomised comparative study was conducted of the two APT models and routine partner notification (PN), in which the index patient chose the PN option for his/her partner(s) in two contrasting clinics. The proportion of contactable partners treated when routine PN was chosen was 42/117 (36%) and was significantly higher if either APT option was chosen: APTHotline 80/135 (59%), p=0.003; APTPharmacy 29/44 (66%) p=0.001. However, partner treatment was often achieved through other routes. Although 40-60% of partners in APT groups returned urine samples for sexually transmitted infection (STI) testing, almost none accessed HIV and syphilis testing. APT options appear to facilitate faster treatment of sex partners than routine PN. Preferences and recruitment rates varied between sites, related to staff satisfaction with existing routine PN; approach to consent; and possibly, characteristics of local populations. Both methods of APT were feasible and acceptable to many patients and led to higher rates of partner treatment than routine PN. Preferences and recruitment rates varied greatly between settings, suggesting that organisational and cultural factors may have an important impact on the feasibility of an RCT and on outcomes. Mindful of these factors, it is proposed that APT should now be evaluated in a cluster RCT.

  12. The effect of recognizability on figure-ground processing: does it affect parsing or only figure selection?

    Science.gov (United States)

    Navon, David

    2011-03-01

    Though figure-ground assignment has been shown to be probably affected by recognizability, it appears sensible that object recognition must follow at least the earlier process of figure-ground segregation. To examine whether or not rudimentary object recognition could, counterintuitively, start even before the completion of the stage of parsing in which figure-ground segregation is done, participants were asked to respond, in a go/no-go fashion, whenever any out of 16 alternative connected patterns (that constituted familiar stimuli in the upright orientation) appeared. The white figure of the to-be-attended stimulus-target or foil-could be segregated from the white ambient ground only by means of a frame surrounding it. Such a frame was absent until the onset of target display. Then, to manipulate organizational quality, the greyness of the frame was either gradually increased from zero (in Experiment 1) or changed abruptly to a stationary level whose greyness was varied between trials (in Experiments 2 and 3). Stimulus recognizability was manipulated by orientation angle. In all three experiments the effect of recognizability was found to be considerably larger when organizational quality was minimal due to an extremely faint frame. This result is argued to be incompatible with any version of a serial thesis suggesting that processing aimed at object recognition starts only with a good enough level of organizational quality. The experiments rather provide some support to the claim, termed here "early interaction hypothesis", positing interaction between early recognition processing and preassignment parsing processes.

  13. Optimization and characterization of biomolecule immobilization on silicon substrates using (3-aminopropyl)triethoxysilane (APTES) and glutaraldehyde linker

    International Nuclear Information System (INIS)

    Gunda, Naga Siva Kumar; Singh, Minashree; Norman, Lana; Kaur, Kamaljit; Mitra, Sushanta K.

    2014-01-01

    In the present work, we developed and optimized a technique to produce a thin, stable silane layer on silicon substrate in a controlled environment using (3-aminopropyl)triethoxysilane (APTES). The effect of APTES concentration and silanization time on the formation of silane layer is studied using spectroscopic ellipsometry and Fourier transform infrared spectroscopy (FTIR). Biomolecules of interest are immobilized on optimized silane layer formed silicon substrates using glutaraldehyde linker. Surface analytical techniques such as ellipsometry, FTIR, contact angle measurement system, and atomic force microscopy are employed to characterize the bio-chemically modified silicon surfaces at each step of the biomolecule immobilization process. It is observed that a uniform, homogenous and highly dense layer of biomolecules are immobilized with optimized silane layer on the silicon substrate. The developed immobilization method is successfully implemented on different silicon substrates (flat and pillar). Also, different types of biomolecules such as anti-human IgG (rabbit monoclonal to human IgG), Listeria monocytogenes, myoglobin and dengue capture antibodies were successfully immobilized. Further, standard sandwich immunoassay (antibody–antigen–antibody) is employed on respective capture antibody coated silicon substrates. Fluorescence microscopy is used to detect the respective FITC tagged detection antibodies bound to the surface after immunoassay.

  14. Characteristics of Polysilicon Wire Glucose Sensors with a Surface Modified by Silica Nanoparticles/γ-APTES Nanocomposite

    Directory of Open Access Journals (Sweden)

    Jheng-Jia Jhuang

    2011-03-01

    Full Text Available This report investigates the sensing characteristics of polysilicon wire (PSW glucose biosensors, including thickness characteristics and line-width effects on detection limits, linear range and interference immunity with membranes coated by micropipette/spin-coating and focus-ion-beam (FIB processed capillary atomic-force-microscopy (C-AFM tip scan/coating methods. The PSW surface was modified with a mixture of 3-aminopropyl-triethoxysilane (γ-APTES and polydimethylsiloxane (PDMS-treated hydrophobic fumed silica nanoparticles (NPs. We found that the thickness of the γ-APTES+NPs nonocomposite could be controlled well at about 22 nm with small relative standard deviation (RSD with repeated C-AFM tip scan/coatings. The detection limit increased and linear range decreased with the line width of the PSW through the tip-coating process. Interestingly, the interference immunity ability improves as the line width increases. For a 500 nm-wide PSW, the percentage changes of the channel current density changes (ΔJ caused by acetaminophen (AP can be kept below 3.5% at an ultra-high AP-to-glucose concentration ratio of 600:1. Simulation results showed that the line width dependence of interference immunity was strongly correlated with the channel electrical field of the PSW biosensor.

  15. The RF system for the Accelerator Production of Tritium (APT) Low Energy Demonstration Accelerator (LEDA) at Los Alamos

    International Nuclear Information System (INIS)

    Lynch, M.T.; Rees, D.; Tallerico, P.; Regan, A.

    1996-01-01

    To develop and demonstrate the crucial front end of the APT accelerator and some of the critical components for APT, Los Alamos is building a CW proton accelerator (LEDA) to provide 100 mA at up to 40 MeV. LEDA will be installed where the SDI-sponsored Ground Test Accelerator was located. The first accelerating structure for LEDA is a 7-MeV RFQ operating at 350 MHz, followed by several stages of a coupled-cavity Drift Tube Linac (CCDTL) operating at 700 MHz. The first stage of LEDA will go to 12 MeV. Higher energies, up to 40 MeV, come later in the program. Three 1.2-MW CW RF systems will be used to power the RFQ. This paper describes the RF systems being assembled for LEDA, including the 350 and 700-MHz klystrons, the High Voltage Power Supplies, transmitters, RF transport, window/coupler assemblies, and controls. Some of the limitations imposed by the schedule and the building itself are addressed

  16. Optimization and characterization of biomolecule immobilization on silicon substrates using (3-aminopropyl)triethoxysilane (APTES) and glutaraldehyde linker

    Energy Technology Data Exchange (ETDEWEB)

    Gunda, Naga Siva Kumar [Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8 (Canada); Singh, Minashree [Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada T6G 1C9 (Canada); Norman, Lana [Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada T6G 2V4 (Canada); Kaur, Kamaljit [Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada T6G 1C9 (Canada); Mitra, Sushanta K., E-mail: sushanta.mitra@ualberta.ca [Department of Mechanical Engineering, University of Alberta, Edmonton, Canada T6G 2G8 (Canada)

    2014-06-01

    In the present work, we developed and optimized a technique to produce a thin, stable silane layer on silicon substrate in a controlled environment using (3-aminopropyl)triethoxysilane (APTES). The effect of APTES concentration and silanization time on the formation of silane layer is studied using spectroscopic ellipsometry and Fourier transform infrared spectroscopy (FTIR). Biomolecules of interest are immobilized on optimized silane layer formed silicon substrates using glutaraldehyde linker. Surface analytical techniques such as ellipsometry, FTIR, contact angle measurement system, and atomic force microscopy are employed to characterize the bio-chemically modified silicon surfaces at each step of the biomolecule immobilization process. It is observed that a uniform, homogenous and highly dense layer of biomolecules are immobilized with optimized silane layer on the silicon substrate. The developed immobilization method is successfully implemented on different silicon substrates (flat and pillar). Also, different types of biomolecules such as anti-human IgG (rabbit monoclonal to human IgG), Listeria monocytogenes, myoglobin and dengue capture antibodies were successfully immobilized. Further, standard sandwich immunoassay (antibody–antigen–antibody) is employed on respective capture antibody coated silicon substrates. Fluorescence microscopy is used to detect the respective FITC tagged detection antibodies bound to the surface after immunoassay.

  17. Surface tree languages and parallel derivation trees

    NARCIS (Netherlands)

    Engelfriet, Joost

    1976-01-01

    The surface tree languages obtained by top-down finite state transformation of monadic trees are exactly the frontier-preserving homomorphic images of sets of derivation trees of ETOL systems. The corresponding class of tree transformation languages is therefore equal to the class of ETOL languages.

  18. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

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

  19. Synthesis, characterization and catalytic activity of CoFe{sub 2}O{sub 4}-APTES-Pd magnetic recyclable catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Demirelli, M. [Department of Chemistry, Faculty of Arts and Sciences, Yıldız Teknik University Davutpaşa Campus, Esenler, İstanbul (Turkey); Department of Chemistry, Faculty of Arts and Sciences, Fatih University, B. Cekmece, İstanbul 34500 (Turkey); Karaoğlu, E., E-mail: ebubekirkaraoglu@gmail.com [Department of Chemistry, Faculty of Arts and Sciences, Fatih University, B. Cekmece, İstanbul 34500 (Turkey); Department of Medical Biochemistry, Faculty of Medicine, Sakarya University, Korucuk, Sakarya (Turkey); Baykal, A. [Department of Chemistry, Faculty of Arts and Sciences, Fatih University, B. Cekmece, İstanbul 34500 (Turkey); Sözeri, H.; Uysal, E. [TUBITAK-UME, National Metrology Institute, PO Box 54, 41470 Gebze, Kocaeli (Turkey)

    2014-01-05

    Highlights: • CoFe{sub 2}O{sub 4}-APTES-Pd (0) nanocomposite, as effective catalysts for reduction reactions. • It could be reused several times without significant loss in hydrogenation reaction. • So far, CoFe{sub 2}O{sub 4}-APTES-Pd (0) nanocomposite have not been synthesized. • CoFe{sub 2}O{sub 4}-APTES-Pd (0) nanocomposite was confirmed by XRD, FT-IR. • Pd containing nanoparticles embedded in organic surfactant observed by TEM. -- Abstract: A new magnetically recyclable catalyst, CoFe{sub 2}O{sub 4}-APTES-Pd(0) nanocomposite, as highly effective catalysts for reduction reactions in liquid phase was fabricated and characterized. The reduction of Pd{sup 2+} was accomplished with sodium borohydride (NaBH{sub 4}). The chemical characterization of the product was done with X-ray diffractometry, infrared spectroscopy, transmission electron microscopy, UV–Vis spectroscopy and inductively coupled plasma. It was found that the combination of CoFe{sub 2}O{sub 4} and 3-aminopropyltriethoxysilane (APTES) could give rise to structurally stable catalytic sites. Furthermore, the high magnetization CoFe{sub 2}O{sub 4}-APTES-Pd(0) catalyst can be recovered by magnet and reused for ten runs for hydrogenation reaction of 4-nitro aniline, 1,3 dinitro and cyclohexanone. The catalyst was easily isolated from the reaction mixture by a magnetic bar and reused at least 10 times without significant degradation in the activity which shows the indicative of a potential applications of these catalysts in industry.

  20. Prevalence of antibodies to prothrombin in solid phase (aPT) and to phosphatidylserine-prothrombin complex (aPS/PT) in patients with and without lupus anticoagulant.

    Science.gov (United States)

    Bertolaccini, Maria Laura; Sciascia, Savino; Murru, Veronica; Garcia-Fernandez, Cesar; Sanna, Giovanni; Khamashta, Munther A

    2013-02-01

    Antibodies to prothrombin in solid phase (aPT) and those to phosphatidiyserine-prothrombin complex (aPS/PT) have been suggested to strongly correlate with the presence of lupus anticoagulant (LA). As their clinical diagnostic value and true relationship with the LA remains elusive, we designed this study to evaluate the prevalence and significance of aPT and aPS/PT in a large cohort of patients with and without LA. Samples from 257 patients were included. aPT and aPS/PT were tested by ELISA. LA was tested as per the current criteria from the ISTH Subcommittee on LA-Phospholipid-dependent antibodies. aPS/PT and aPT were found in 51% and 32% of LA-positive (LA+ve) patients and in 22% and 28% of LA-negative (LA-ve) patients, respectively. Thrombosis, particularly venous thrombosis was associated with IgG aPT in the LA+ve group (p=0.0006) and in the LA-ve group (p=0.017). Antibodies to phosphatidylserine-prothrombin, either IgG and IgM were associated with thrombosis in general (p=0.0003) in particularly with venous thrombosis in the LA+ve group (paPS/PT were independent risk factors for thrombosis and pregnancy loss. In conclusion, aPS/PT, but not aPT, are more frequently found in patients with LA. Their association with thrombosis seems to be independent of the presence of LA.

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

    Science.gov (United States)

    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 .

  2. Modular tree automata

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

    Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular...

  3. Simple street tree sampling

    Science.gov (United States)

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

    2015-01-01

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

  4. Parsing in a Dynamical System: An Attractor-Based Account of the Interaction of Lexical and Structural Constraints in Sentence Processing.

    Science.gov (United States)

    Tabor, Whitney; And Others

    1997-01-01

    Proposes a dynamical systems approach to parsing in which syntactic hypotheses are associated with attractors in a metric space. The experiments discussed documented various contingent frequency effects that cut across traditional linguistic grains, each of which was predicted by the dynamical systems model. (47 references) (Author/CK)

  5. City of Pittsburgh Trees

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...

  6. A Python-based Interface for Wide Coverage Lexicalized Tree-adjoining Grammars

    Directory of Open Access Journals (Sweden)

    Wang Ziqi

    2015-04-01

    Full Text Available This paper describes the design and implementation of a Python-based interface for wide coverage Lexicalized Tree-adjoining Grammars. The grammars are part of the XTAG Grammar project at the University of Pennsylvania, which were hand-written and semi-automatically curated to parse real-world corpora. We provide an interface to the wide coverage English and Korean XTAG grammars. Each XTAG grammar is lexicalized, which means at least one word selects a tree fragment (called an elementary tree or etree. Derivations for sentences are built by combining etrees using substitution (replacement of a tree node with an etree at the frontier of another etree and adjunction (replacement of an internal tree node in an etree by another etree. Each etree is associated with a feature structure representing constraints on substitution and adjunction. Feature structures are combined using unification during the combination of etrees. We plan to integrate our toolkit for XTAG grammars into the Python-based Natural Language Toolkit (NLTK: nltk.org. We have provided an API capable of searching the lexicalized etrees for a given word or multiple words, searching for a etree by name or function, display the lexicalized etrees to the user using a graphical view, display the feature structure associated with each tree node in an etree, hide or highlight features based on a regular expression, and browsing the entire tree database for each XTAG grammar.

  7. APTES Functionalized Iron Oxide-Silver Magnetic Hetero-Nanocomposites for Selective Capture and Rapid Removal of Salmonella enteritidis from Aqueous Solution

    Science.gov (United States)

    Trang, Vu Thi; Dinh, Ngo Xuan; Lan, Hoang; Tam, Le Thi; Huy, Tran Quang; Tuan, Pham Anh; Phan, Vu Ngoc; Le, Anh-Tuan

    2018-02-01

    Magnetic nanomaterials, as a promising platform for the fast and sensitive detection of bacterial pathogens, have attracted increasing interest from researchers in recent years. In this work, by utilizing a two-step synthetic technique consisting of co-precipitation and subsequent hydrothermal reaction, followed by functionalization steps with (3-aminopropyl)triethoxysilane (APTES) and the antibody against Salmonella enteritidis, antibody-conjugated Fe3O4-Ag@APTES hetero-nanocomposites were successfully prepared. Due to the specific antibody, the developed Fe3O4-Ag@APTES@SE-Ab conjugates are capable of selectively capturing S. enteritidis at a low concentration of about 101 CFU/mL. Moreover, the prepared magnetic conjugates also revealed that the S. enteritidis could be rapidly removed from water solution in 20 min by using an external magnetic field with a removal efficiency obtained of ˜ 91.36%. These results indicated that the Fe3O4-Ag@APTES@SE-Ab conjugates are promising for the rapid selective capture and removal of bacterial pathogens from aqueous environments, and can be used for improving the detection quality of pathogens in water samples using immunosensor-based diagnostic tests.

  8. Revealed or hidden?: insights into ways of measuring mental representations online: A comparative study of APT and CNET applied to an online agent

    NARCIS (Netherlands)

    Horeni, O.; Arentze, T.A.; Dellaert, B.G.C.; Timmermans, H.J.P.

    2010-01-01

    This paper presents and compares newly developed interview techniques (APT and CNET) which were implemented and tested by an online agent in order to measure mental representations underlying activity-choices. The comparison is supported and completed by the results from a first online survey with

  9. The Characteristics of Fibres within Coppiced and Non-Coppiced Rosewood (Pterocarpus erinaceus Poir. and their Aptness for Wood - and Paper - Based Products

    Directory of Open Access Journals (Sweden)

    Frederick ANTHONIO

    2017-06-01

    Full Text Available Rosewood (Pterocarpus erinaceus is highly priced for furniture, flooring and cabinetry for its rich hue and durability. Its coppiced wood augments the timber for regular supply and sustainable utilization. Fibre morphology from macerated slivers within its coppiced and non-coppiced stems and their utilization potential were assessed. Derived ratios for the fibres were also calculated. The axial positions (butt, middle, crown affected the fibre dimensions. Fibre length was greater for coppiced trees [i.e., 1663±11, 1488±5, 1511±10µm (for sapwood and 1498±10, 1486±9, 1394±4µm (for heartwood] than the non-coppiced [i.e., 1240±7, 1013±5, 1137±5µm (sapwood and 1094±8, 1002±2, 1041±9µm (heartwood]. In all, those for sapwoods were greater than heartwoods’. Significant differences (P˂0.05 existed between fibre lengths from the coppiced (1394±4-1663±11µm and non-coppiced trees (1002±2-1240±7µm. Fibre diameters for coppiced sapwood and heartwood were 23±1, 20±1, 22±0.8µm and 21.5±0.3, 20.7±0.5, 21.3±2µm and noncoppiced recorded 21±0.6, 20.7±0.3, 20.6±0.1µm and 21±0, 21±0.4, 21±0.8µm respectively. Their respective double wall thicknesses were 8.4±0.2, 7.2±0.2, 9.4±1µm and 8.2±0.2, 9±0.3, 9.1±0.4µm for coppiced wood, and 9.1±1, 7.8±0.1, 8.1±0.3µm and 8.5±0.3, 8±0.4, 8±1 for non-coppiced. Thus, radial stem position also influenced fibre morphology. The fibre indices [i.e., Runkel Ratio, Slenderness Ratio and Flexibility Coefficient for coppiced wood (0.6±0.06-0.85±0.06, 68±4-77±6, 56±4-64±2 respectively and non-coppiced (0.64±0.12-0.8±0, 49±1-58±4, 57±3-62±2 respectively] indicate the timber’s aptness for pulp and paper. Besides, the Wood Industry could exploit the fibre characteristics of coppiced wood also for engineering of fibre-based products and structural applications.

  10. Categorizing ideas about trees: a tree of trees.

    Science.gov (United States)

    Fisler, Marie; Lecointre, Guillaume

    2013-01-01

    The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

  11. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

    This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

  12. Keeping trees as assets

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...

  13. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J

    1984-01-01

    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  14. Three-dimensional segmentation and skeletonization to build an airway tree data structure for small animals

    International Nuclear Information System (INIS)

    Chaturvedi, Ashutosh; Lee, Zhenghong

    2005-01-01

    Quantitative analysis of intrathoracic airway tree geometry is important for objective evaluation of bronchial tree structure and function. Currently, there is more human data than small animal data on airway morphometry. In this study, we implemented a semi-automatic approach to quantitatively describe airway tree geometry by using high-resolution computed tomography (CT) images to build a tree data structure for small animals such as rats and mice. Silicon lung casts of the excised lungs from a canine and a mouse were used for micro-CT imaging of the airway trees. The programming language IDL was used to implement a 3D region-growing threshold algorithm for segmenting out the airway lung volume from the CT data. Subsequently, a fully-parallel 3D thinning algorithm was implemented in order to complete the skeletonization of the segmented airways. A tree data structure was then created and saved by parsing through the skeletonized volume using the Python programming language. Pertinent information such as the length of all airway segments was stored in the data structure. This approach was shown to be accurate and efficient for up to six generations for the canine lung cast and ten generations for the mouse lung cast

  15. Quantitative description of proton exchange processes between water and endogenous and exogenous agents for WEX, CEST, and APT experiments.

    Science.gov (United States)

    Zhou, Jinyuan; Wilson, David A; Sun, Phillip Zhe; Klaus, Judith A; Van Zijl, Peter C M

    2004-05-01

    The proton exchange processes between water and solutes containing exchangeable protons have recently become of interest for monitoring pH effects, detecting cellular mobile proteins and peptides, and enhancing the detection sensitivity of various low-concentration endogenous and exogenous species. In this work, the analytic expressions for water exchange (WEX) filter spectroscopy, chemical exchange-dependent saturation transfer (CEST), and amide proton transfer (APT) experiments are derived by the use of Bloch equations with exchange terms. The effects of the initial states for the system, the difference between a steady state and a saturation state, and the relative contributions of the forward and backward exchange processes are discussed. The theory, in combination with numerical calculations, provides a useful tool for designing experimental schemes and assessing magnetization transfer (MT) processes between water protons and solvent-exchangeable protons. As an example, the case of endogenous amide proton exchange in the rat brain at 4.7 T is analyzed in detail. Copyright 2004 Wiley-Liss, Inc.

  16. High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation

    Energy Technology Data Exchange (ETDEWEB)

    Vega, Sebastián L. [Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ (United States); Liu, Er; Arvind, Varun [Department of Biomedical Engineering, Rutgers University, Piscataway, NJ (United States); Bushman, Jared [Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ (United States); School of Pharmacy, University of Wyoming, Laramie, WY (United States); Sung, Hak-Joon [Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ (United States); Department of Biomedical Engineering, Vanderbilt University, Nashville, TN (United States); Becker, Matthew L. [Department of Polymer Science and Engineering, University of Akron, Akron, OH (United States); Lelièvre, Sophie [Department of Basic Medical Sciences, Purdue University, West Lafayette, IN (United States); Kohn, Joachim [Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ (United States); Vidi, Pierre-Alexandre, E-mail: pvidi@wakehealth.edu [Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC (United States); Moghe, Prabhas V., E-mail: moghe@rutgers.edu [Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ (United States); Department of Biomedical Engineering, Rutgers University, Piscataway, NJ (United States)

    2017-02-01

    Stem and progenitor cells that exhibit significant regenerative potential and critical roles in cancer initiation and progression remain difficult to characterize. Cell fates are determined by reciprocal signaling between the cell microenvironment and the nucleus; hence parameters derived from nuclear remodeling are ideal candidates for stem/progenitor cell characterization. Here we applied high-content, single cell analysis of nuclear shape and organization to examine stem and progenitor cells destined to distinct differentiation endpoints, yet undistinguishable by conventional methods. Nuclear descriptors defined through image informatics classified mesenchymal stem cells poised to either adipogenic or osteogenic differentiation, and oligodendrocyte precursors isolated from different regions of the brain and destined to distinct astrocyte subtypes. Nuclear descriptors also revealed early changes in stem cells after chemical oncogenesis, allowing the identification of a class of cancer-mitigating biomaterials. To capture the metrology of nuclear changes, we developed a simple and quantitative “imaging-derived” parsing index, which reflects the dynamic evolution of the high-dimensional space of nuclear organizational features. A comparative analysis of parsing outcomes via either nuclear shape or textural metrics of the nuclear structural protein NuMA indicates the nuclear shape alone is a weak phenotypic predictor. In contrast, variations in the NuMA organization parsed emergent cell phenotypes and discerned emergent stages of stem cell transformation, supporting a prognosticating role for this protein in the outcomes of nuclear functions. - Highlights: • High-content analysis of nuclear shape and organization classify stem and progenitor cells poised for distinct lineages. • Early oncogenic changes in mesenchymal stem cells (MSCs) are also detected with nuclear descriptors. • A new class of cancer-mitigating biomaterials was identified based on image

  17. High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation

    International Nuclear Information System (INIS)

    Vega, Sebastián L.; Liu, Er; Arvind, Varun; Bushman, Jared; Sung, Hak-Joon; Becker, Matthew L.; Lelièvre, Sophie; Kohn, Joachim; Vidi, Pierre-Alexandre; Moghe, Prabhas V.

    2017-01-01

    Stem and progenitor cells that exhibit significant regenerative potential and critical roles in cancer initiation and progression remain difficult to characterize. Cell fates are determined by reciprocal signaling between the cell microenvironment and the nucleus; hence parameters derived from nuclear remodeling are ideal candidates for stem/progenitor cell characterization. Here we applied high-content, single cell analysis of nuclear shape and organization to examine stem and progenitor cells destined to distinct differentiation endpoints, yet undistinguishable by conventional methods. Nuclear descriptors defined through image informatics classified mesenchymal stem cells poised to either adipogenic or osteogenic differentiation, and oligodendrocyte precursors isolated from different regions of the brain and destined to distinct astrocyte subtypes. Nuclear descriptors also revealed early changes in stem cells after chemical oncogenesis, allowing the identification of a class of cancer-mitigating biomaterials. To capture the metrology of nuclear changes, we developed a simple and quantitative “imaging-derived” parsing index, which reflects the dynamic evolution of the high-dimensional space of nuclear organizational features. A comparative analysis of parsing outcomes via either nuclear shape or textural metrics of the nuclear structural protein NuMA indicates the nuclear shape alone is a weak phenotypic predictor. In contrast, variations in the NuMA organization parsed emergent cell phenotypes and discerned emergent stages of stem cell transformation, supporting a prognosticating role for this protein in the outcomes of nuclear functions. - Highlights: • High-content analysis of nuclear shape and organization classify stem and progenitor cells poised for distinct lineages. • Early oncogenic changes in mesenchymal stem cells (MSCs) are also detected with nuclear descriptors. • A new class of cancer-mitigating biomaterials was identified based on image

  18. Fault tree handbook

    International Nuclear Information System (INIS)

    Haasl, D.F.; Roberts, N.H.; Vesely, W.E.; Goldberg, F.F.

    1981-01-01

    This handbook describes a methodology for reliability analysis of complex systems such as those which comprise the engineered safety features of nuclear power generating stations. After an initial overview of the available system analysis approaches, the handbook focuses on a description of the deductive method known as fault tree analysis. The following aspects of fault tree analysis are covered: basic concepts for fault tree analysis; basic elements of a fault tree; fault tree construction; probability, statistics, and Boolean algebra for the fault tree analyst; qualitative and quantitative fault tree evaluation techniques; and computer codes for fault tree evaluation. Also discussed are several example problems illustrating the basic concepts of fault tree construction and evaluation

  19. Conceptual plural information is used to guide early parsing decisions: Evidence from garden-path sentences with reciprocal verbs.

    Science.gov (United States)

    Patson, Nikole D; Ferreira, Fernanda

    2009-05-01

    In three eyetracking studies, we investigated the role of conceptual plurality in initial parsing decisions in temporarily ambiguous sentences with reciprocal verbs (e.g., While the lovers kissed the baby played alone). We varied the subject of the first clause using three types of plural noun phrases: conjoined noun phrases (the bride and the groom), plural definite descriptions (the lovers), and numerically quantified noun phrases (the two lovers). We found no evidence for garden-path effects when the subject was conjoined (Ferreira & McClure, 1997), but traditional garden-path effects were found with the other plural noun phrases. In addition, we tested plural anaphors that had a plural antecedent present in the discourse. We found that when the antecedent was conjoined, garden-path effects were absent compared to cases in which the antecedent was a plural definite description. Our results indicate that the parser is sensitive to the conceptual representation of a plural constituent. In particular, it appears that a Complex Reference Object (Moxey et al., 2004) automatically activates a reciprocal reading of a reciprocal verb.

  20. SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript.

    Science.gov (United States)

    Probst, Daniel; Reymond, Jean-Louis

    2018-01-22

    Here we present SmilesDrawer, a dependency-free JavaScript component capable of both parsing and drawing SMILES-encoded molecular structures client-side, developed to be easily integrated into web projects and to display organic molecules in large numbers and fast succession. SmilesDrawer can draw structurally and stereochemically complex structures such as maitotoxin and C 60 without using templates, yet has an exceptionally small computational footprint and low memory usage without the requirement for loading images or any other form of client-server communication, making it easy to integrate even in secure (intranet, firewalled) or offline applications. These features allow the rendering of thousands of molecular structure drawings on a single web page within seconds on a wide range of hardware supporting modern browsers. The source code as well as the most recent build of SmilesDrawer is available on Github ( http://doc.gdb.tools/smilesDrawer/ ). Both yarn and npm packages are also available.

  1. There's Life in Hazard Trees

    Science.gov (United States)

    Mary Torsello; Toni McLellan

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

  2. High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation.

    Science.gov (United States)

    Vega, Sebastián L; Liu, Er; Arvind, Varun; Bushman, Jared; Sung, Hak-Joon; Becker, Matthew L; Lelièvre, Sophie; Kohn, Joachim; Vidi, Pierre-Alexandre; Moghe, Prabhas V

    2017-02-01

    Stem and progenitor cells that exhibit significant regenerative potential and critical roles in cancer initiation and progression remain difficult to characterize. Cell fates are determined by reciprocal signaling between the cell microenvironment and the nucleus; hence parameters derived from nuclear remodeling are ideal candidates for stem/progenitor cell characterization. Here we applied high-content, single cell analysis of nuclear shape and organization to examine stem and progenitor cells destined to distinct differentiation endpoints, yet undistinguishable by conventional methods. Nuclear descriptors defined through image informatics classified mesenchymal stem cells poised to either adipogenic or osteogenic differentiation, and oligodendrocyte precursors isolated from different regions of the brain and destined to distinct astrocyte subtypes. Nuclear descriptors also revealed early changes in stem cells after chemical oncogenesis, allowing the identification of a class of cancer-mitigating biomaterials. To capture the metrology of nuclear changes, we developed a simple and quantitative "imaging-derived" parsing index, which reflects the dynamic evolution of the high-dimensional space of nuclear organizational features. A comparative analysis of parsing outcomes via either nuclear shape or textural metrics of the nuclear structural protein NuMA indicates the nuclear shape alone is a weak phenotypic predictor. In contrast, variations in the NuMA organization parsed emergent cell phenotypes and discerned emergent stages of stem cell transformation, supporting a prognosticating role for this protein in the outcomes of nuclear functions. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. The interaction of parsing rules and argument – Predicate constructions: implications for the structure of the Grammaticon in FunGramKB

    Directory of Open Access Journals (Sweden)

    María del Carmen Fumero Pérez

    2017-07-01

    Full Text Available The Functional Grammar Knowledge Base (FunGramKB, (Periñán-Pascual and Arcas-Túnez 2010 is a multipurpose lexico-conceptual knowledge base designed to be used in different Natural Language Processing (NLP tasks. It is complemented with the ARTEMIS (Automatically Representing Text Meaning via an Interlingua–based System application, a parsing device linguistically grounded on Role and Reference Grammar (RRG that transduces natural language fragments into their corresponding grammatical and semantic structures. This paper unveils the different phases involved in its parsing routine, paying special attention to the treatment of argumental constructions. As an illustrative case, we will follow all the steps necessary to effectively parse a For-Benefactive structure within ARTEMIS. This methodology will reveal the necessity to distinguish between Kernel constructs and L1-constructions, since the latter involve a modification of the lexical template of the verb. Our definition of L1-constructions leads to the reorganization of the catalogue of FunGramKB L1-constructions, formerly based on Levin’s (1993 alternations. Accordingly, a rearrangement of the internal configuration of the L1-Constructicon within the Grammaticon is proposed.

  4. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

  5. Microradiographic investigations on experimentally provoked structural alterations in hard tooth tissues after sealing with plastic material in places where caries is apt to develop

    International Nuclear Information System (INIS)

    Falten, E.

    1981-01-01

    The aim of the present investigation was, after sealing three areas in extracted human teeth: fissures, dental necksand approximate areas and subsequent exposure to experimentally produced cariogenous noxae, to establish possible alterations in the area of transition between sealed and unsealed dental enamal. This would provide a further decision-taking aid with regard to the question whether also the remaining parts where caries is apt to develop should be sealed. (orig./MG) [de

  6. The Parsing Syllable Envelopes Test for Assessment of Amplitude Modulation Discrimination Skills in Children: Development, Normative Data, and Test-Retest Reliability Studies.

    Science.gov (United States)

    Cameron, Sharon; Chong-White, Nicky; Mealings, Kiri; Beechey, Tim; Dillon, Harvey; Young, Taegan

    2018-02-01

    Intensity peaks and valleys in the acoustic signal are salient cues to syllable structure, which is accepted to be a crucial early step in phonological processing. As such, the ability to detect low-rate (envelope) modulations in signal amplitude is essential to parse an incoming speech signal into smaller phonological units. The Parsing Syllable Envelopes (ParSE) test was developed to quantify the ability of children to recognize syllable boundaries using an amplitude modulation detection paradigm. The envelope of a 750-msec steady-state /a/ vowel is modulated into two or three pseudo-syllables using notches with modulation depths varying between 0% and 100% along an 11-step continuum. In an adaptive three-alternative forced-choice procedure, the participant identified whether one, two, or three pseudo-syllables were heard. Development of the ParSE stimuli and test protocols, and collection of normative and test-retest reliability data. Eleven adults (aged 23 yr 10 mo to 50 yr 9 mo, mean 32 yr 10 mo) and 134 typically developing, primary-school children (aged 6 yr 0 mo to 12 yr 4 mo, mean 9 yr 3 mo). There were 73 males and 72 females. Data were collected using a touchscreen computer. Psychometric functions (PFs) were automatically fit to individual data by the ParSE software. Performance was related to the modulation depth at which syllables can be detected with 88% accuracy (referred to as the upper boundary of the uncertainty region [UBUR]). A shallower PF slope reflected a greater level of uncertainty. Age effects were determined based on raw scores. z Scores were calculated to account for the effect of age on performance. Outliers, and individual data for which the confidence interval of the UBUR exceeded a maximum allowable value, were removed. Nonparametric tests were used as the data were skewed toward negative performance. Across participants, the performance criterion (UBUR) was met with a median modulation depth of 42%. The effect of age on the UBUR was

  7. Adsorption of Pb(II) using silica gel composite from rice husk ash modified 3-aminopropyltriethoxysilane (APTES)-activated carbon from coconut shell

    Science.gov (United States)

    Yusmaniar, Purwanto, Agung; Putri, Elfriyana Awalita; Rosyidah, Dzakiyyatur

    2017-03-01

    Silica gel modified by 3-aminopropyltriethoxysilane (APTES) was synthesized from rice husk ash combined with activated carbon from coconut shell yielded the composite adsorbent. The composite was characterized by Fourier Transform Infra Red spectroscopy (FT-IR), Electron Dispersive X-Ray (EDX), Surface Area Analyzer (SAA) and adsorption test by Atomic Absorption Spectrometry (AAS). This composite adsorbent has been used moderately for the removal of lead ions from metal solutions and compared with silica gel modified APTES and activated carbon. The adsorption experiments of Pb -ions by adsorbents were performed at different pH and contact time with the same metal solutions concentration, volume solution, and adsorbent dosage. The optimum pH for the adsorption was found to be 5.0 and the equilibrium was achieved for Pb with 20 min of contact time. Pb ions adsorption by composite silica gel modified APTES-activated carbon followed by Langmuir isotherm model with qmax value of 46.9483 mg/g that proved an adsorbent mechanism consistent to the mechanism of monolayer formation.

  8. IN VITRO Cr(VI SPECIATION IN SYNTHETIC SALIVA AFTER RELEASING FROM ORTHODONTIC BRACKETS USING SILICA-APTES SEPARATION AND GF AAS DETERMINATION

    Directory of Open Access Journals (Sweden)

    Maciel S. Luz

    Full Text Available A method for Cr(VI speciation in synthetic saliva after releasing from orthodontic brackets, using silica nanoparticles organofunctionalized with (3-aminopropyltriethoxysilane (APTES for Cr(III/Cr(VI separation and GF AAS determination is proposed. Under the optimized conditions, Cr(VI speciation was performed using 150 mg of silica organofunctionalized with 2.0% (v v-1 of APTES at pH 8. It was observed different sensitivity when calibrations of GF AAS were performed using Cr(III or Cr(VI as standard solutions. Consequently, calibrations using stoichiometric mixtures (Cr(III + Cr(VI were used for total Cr determination and calibration using Cr(VI was used only for the determination of this specie. The reliability of the proposed silica-APTES separation procedure and GF AAS determination was checked by addition of both species in synthetic saliva. Recoveries ranging from 97 to 110% were obtained. The repeatability, based on the relative standard deviation (RSD inter days was less than 6%. A corrosion test was carried out on 20 orthodontic brackets from two different models, after immersion in synthetic saliva (pH=6.0 at 37 °C with agitation (125 rpm for 24 h. It was observed that about 40% of the total chromium released from the analyzed orthodontic brackets was Cr(VI.

  9. Trees and highway safety.

    Science.gov (United States)

    2011-03-01

    To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...

  10. Astrometry, Radial Velocity, and Photometry: The HD 128311 System Remixed with Data from HST, HET, and APT

    Science.gov (United States)

    McArthur, Barbara. E.; Benedict, G. Fritz; Henry, Gregory W.; Hatzes, Artie; Cochran, William D.; Harrison, Tom E.; Johns-Krull, Chris; Nelan, Ed

    2014-11-01

    We have used high-cadence radial velocity measurements from the Hobby-Eberly Telescope with published velocities from the Lick 3 m Shane Telescope, combined with astrometric data from the Hubble Space Telescope (HST) Fine Guidance Sensors to refine the orbital parameters of the HD 128311 system, and determine an inclination of 55.°95 ± 14.°55 and true mass of 3.789 +0.924 -0.432 M JUP for HD 128311 c. The combined radial velocity data also reveal a short period signal which could indicate a third planet in the system with an Msin i of 0.133 ± 0.005 M JUP or stellar phenomena. Photometry from the T12 0.8 m automatic photometric telescope at the Fairborn Observatory and HST are used to determine a photometric period close to, but not within the errors of the radial velocity signal. We performed a cross-correlation bisector analysis of the radial velocity data to look for correlations with the photometric period and found none. Dynamical integrations of the proposed system show long-term stability with the new orbital parameters of over 10 million years. Our new orbital elements do not support the claims of HD 128311 b and c being in mean motion resonance. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Based on observations obtained with the Hobby-Eberly Telescope, which is a joint project of the University of Texas at Austin, the Pennsylvania State University, Stanford University, Ludwig-Maximilians-Universität München, and Georg-August-Universität Göttingen, and observations with T12 0.8 m automatic photoelectric telescope (APT) at Fairborn Observatory.

  11. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

    IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

  12. Minnesota's Forest Trees. Revised.

    Science.gov (United States)

    Miles, William R.; Fuller, Bruce L.

    This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

  13. D2-tree

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

    2015-01-01

    We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers...

  14. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

    2013-01-01

    We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting ...

  15. Winter Birch Trees

    Science.gov (United States)

    Sweeney, Debra; Rounds, Judy

    2011-01-01

    Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

  16. Total well dominated trees

    DEFF Research Database (Denmark)

    Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

    cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

  17. TreePics: visualizing trees with pictures

    Directory of Open Access Journals (Sweden)

    Nicolas Puillandre

    2017-09-01

    Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.

  18. Spectra of chemical trees

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1982-01-01

    A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees

  19. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  20. The valuative tree

    CERN Document Server

    Favre, Charles

    2004-01-01

    This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.

  1. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

  2. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  3. Are trees long-lived?

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

    Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

  4. Fragmentation of random trees

    International Nuclear Information System (INIS)

    Kalay, Z; Ben-Naim, E

    2015-01-01

    We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N→∞. We obtain analytically the size density ϕ s of trees of size s. The size density has power-law tail ϕ s ∼s −α with exponent α=1+(1/m). Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees. (paper)

  5. The tree BVOC index

    Science.gov (United States)

    J.R. Simpson; E.G. McPherson

    2011-01-01

    Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...

  6. Tree growth visualization

    Science.gov (United States)

    L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

    2005-01-01

    In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

  7. Flowering T Flowering Trees

    Indian Academy of Sciences (India)

    Adansonia digitata L. ( The Baobab Tree) of Bombacaceae is a tree with swollen trunk that attains a dia. of 10m. Leaves are digitately compound with leaflets up to 18cm. long. Flowers are large, solitary, waxy white, and open at dusk. They open in 30 seconds and are bat pollinated. Stamens are many. Fruit is about 30 cm ...

  8. Fault tree graphics

    International Nuclear Information System (INIS)

    Bass, L.; Wynholds, H.W.; Porterfield, W.R.

    1975-01-01

    Described is an operational system that enables the user, through an intelligent graphics terminal, to construct, modify, analyze, and store fault trees. With this system, complex engineering designs can be analyzed. This paper discusses the system and its capabilities. Included is a brief discussion of fault tree analysis, which represents an aspect of reliability and safety modeling

  9. Tree biology and dendrochemistry

    Science.gov (United States)

    Kevin T. Smith; Walter C. Shortle

    1996-01-01

    Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

  10. Individual tree control

    Science.gov (United States)

    Harvey A. Holt

    1989-01-01

    Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

  11. Trees and Climate Change

    OpenAIRE

    Dettenmaier, Megan; Kuhns, Michael; Unger, Bethany; McAvoy, Darren

    2017-01-01

    This fact sheet describes the complex relationship between forests and climate change based on current research. It explains ways that trees can mitigate some of the risks associated with climate change. It details the impacts that forests are having on the changing climate and discuss specific ways that trees can be used to reduce or counter carbon emissions directly and indirectly.

  12. Structural Equation Model Trees

    Science.gov (United States)

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

    2013-01-01

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

  13. Matching Subsequences in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2009-01-01

    Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...

  14. Environmental tritium in trees

    International Nuclear Information System (INIS)

    Brown, R.M.

    1979-01-01

    The distribution of environmental tritium in the free water and organically bound hydrogen of trees growing in the vicinity of the Chalk River Nuclear Laboratories (CRNL) has been studied. The regional dispersal of HTO in the atmosphere has been observed by surveying the tritium content of leaf moisture. Measurement of the distribution of organically bound tritium in the wood of tree ring sequences has given information on past concentrations of HTO taken up by trees growing in the CRNL Liquid Waste Disposal Area. For samples at background environmental levels, cellulose separation and analysis was done. The pattern of bomb tritium in precipitation of 1955-68 was observed to be preserved in the organically bound tritium of a tree ring sequence. Reactor tritium was discernible in a tree growing at a distance of 10 km from CRNL. These techniques provide convenient means of monitoring dispersal of HTO from nuclear facilities. (author)

  15. Generalising tree traversals and tree transformations to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2017-01-01

    We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....

  16. A recursive algorithm for trees and forests

    OpenAIRE

    Guo, Song; Guo, Victor J. W.

    2017-01-01

    Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\\{1,2,\\ldots,n\\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.

  17. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  18. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  19. The gravity apple tree

    International Nuclear Information System (INIS)

    Aldama, Mariana Espinosa

    2015-01-01

    The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion. (paper)

  20. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

    Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

    2017-02-02

    Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

  1. Tree-growth analyses to estimate tree species' drought tolerance

    NARCIS (Netherlands)

    Eilmann, B.; Rigling, A.

    2012-01-01

    Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree

  2. Big trees, old trees, and growth factor tables

    Science.gov (United States)

    Kevin T. Smith

    2018-01-01

    The potential for a tree to reach a great size and to live a long life frequently captures the public's imagination. Sometimes the desire to know the age of an impressively large tree is simple curiosity. For others, the date-of-tree establishment can make a big diff erence for management, particularly for trees at historic sites or those mentioned in property...

  3. A bijection between phylogenetic trees and plane oriented recursive trees

    OpenAIRE

    Prodinger, Helmut

    2017-01-01

    Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the respective representations a 2-partitions and trapezoidal words.

  4. A Suffix Tree Or Not a Suffix Tree?

    DEFF Research Database (Denmark)

    Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

    2015-01-01

    In this paper we study the structure of suffix trees. Given an unlabeled tree r on n nodes and suffix links of its internal nodes, we ask the question “Is r a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as r? We place no restrictions on S, in part...

  5. NLCD 2001 - Tree Canopy

    Data.gov (United States)

    Minnesota Department of Natural Resources — The National Land Cover Database 2001 tree canopy layer for Minnesota (mapping zones 39-42, 50-51) was produced through a cooperative project conducted by the...

  6. Trees for future forests

    DEFF Research Database (Denmark)

    Lobo, Albin

    Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... organisms. The aim of the present thesis is therefore to explore genetic resilience and phenotypic plasticity mechanisms that allows trees to adapt and evolve with changing climates. The thesis focus on the abiotic factors associated with climate change, especially raised temperatures and lack...... age of these tree species and the uncertainty around the pace and effect of climate, it remains an open question if the native populations can respond fast enough. Phenotypic plasticity through epigenetic regulation of spring phenology is found to be present in a tree species which might act...

  7. Value tree analysis

    International Nuclear Information System (INIS)

    Keeney, R.; Renn, O.; Winterfeldt, D. von; Kotte, U.

    1985-01-01

    What are the targets and criteria on which national energy policy should be based. What priorities should be set, and how can different social interests be matched. To answer these questions, a new instrument of decision theory is presented which has been applied with good results to controversial political issues in the USA. The new technique is known under the name of value tree analysis. Members of important West German organisations (BDI, VDI, RWE, the Catholic and Protestant Church, Deutscher Naturschutzring, and ecological research institutions) were asked about the goals of their organisations. These goals were then ordered systematically and arranged in a hierarchical tree structure. The value trees of different groups can be combined into a catalogue of social criteria of acceptability and policy assessment. The authors describe the philosophy and methodology of value tree analysis and give an outline of its application in the development of a socially acceptable energy policy. (orig.) [de

  8. Multiscale singularity trees

    DEFF Research Database (Denmark)

    Somchaipeng, Kerawit; Sporring, Jon; Johansen, Peter

    2007-01-01

    We propose MultiScale Singularity Trees (MSSTs) as a structure to represent images, and we propose an algorithm for image comparison based on comparing MSSTs. The algorithm is tested on 3 public image databases and compared to 2 state-of-theart methods. We conclude that the computational complexity...... of our algorithm only allows for the comparison of small trees, and that the results of our method are comparable with state-of-the-art using much fewer parameters for image representation....

  9. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

    We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....

  10. Tree felling 2014

    CERN Multimedia

    2014-01-01

    With a view to creating new landscapes and making its population of trees safer and healthier, this winter CERN will complete the tree-felling campaign started in 2010.   Tree felling will take place between 15 and 22 November on the Swiss part of the Meyrin site. This work is being carried out above all for safety reasons. The trees to be cut down are at risk of falling as they are too old and too tall to withstand the wind. In addition, the roots of poplar trees are very powerful and spread widely, potentially damaging underground networks, pavements and roadways. Compensatory tree planting campaigns will take place in the future, subject to the availability of funding, with the aim of creating coherent landscapes while also respecting the functional constraints of the site. These matters are being considered in close collaboration with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP). GS-SE Group

  11. Benefit-based tree valuation

    Science.gov (United States)

    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...

  12. Attack Trees with Sequential Conjunction

    NARCIS (Netherlands)

    Jhawar, Ravi; Kordy, Barbara; Mauw, Sjouke; Radomirović, Sasa; Trujillo-Rasua, Rolando

    2015-01-01

    We provide the first formal foundation of SAND attack trees which are a popular extension of the well-known attack trees. The SAND at- tack tree formalism increases the expressivity of attack trees by intro- ducing the sequential conjunctive operator SAND. This operator enables the modeling of

  13. Topical report on a preconceptual design for the Spallation-Induced Lithium Conversion (SILC) target for the accelerator production of tritium (APT)

    International Nuclear Information System (INIS)

    Van Tuyle, G.J.; Cokinos, D.M.; Czajkowski, C.; Franz, E.M.; Kroeger, P.; Todosow, M.; Youngblood, R.; Zucker, M.

    1993-01-01

    The preconceptual design of the APT Li-Al target system, also referred to as the Spallation-Induced Lithium Conversion (SILC), target system, is summarized in this report. The system has been designed to produce a ''3/8 Goal'' quantity of tritium using the 200-mA, 1.0 GeV proton beam emerging from the LANL-designed LINAC. The SILC target system consists of a beam expander, a heavy-water-cooled lead spallation neutron source assembly surrounded by light-water-cooled Li-Al blankets, a target window, heat removal systems, and related safety systems. The preconceptual design of each of these major components is described. Descriptions are also provided for the target fabrication, tritium extraction, and waste-steam processes. Performance characteristics are presented and discussed

  14. First Characterization of the Ultra-Shielded Chamber in the Low-noise Underground Laboratory (LSBB) of Rustrel Pays d'Apt

    CERN Document Server

    Waysand, G; Bongiraud, J P; Collar, J I; Dolabdjian, C; Le Thiec, P; Thiec, Ph. Le

    2000-01-01

    In compliance with international agreements on nuclear weapons limitation, the French ground-based nuclear arsenal has been decommissioned in its totality. One of its former underground missile control centers, located in Rustrel, 60 km east of Avignon (Provence) has been converted into the ``Laboratoire Souterrain à Bas Bruit de Rustrel-Pays d'Apt'' (LSBB). The deepest experimental hall (500 m of calcite rock overburden) includes a 100 m$^{2}$ area of sturdy flooring suspended by and resting on shock absorbers, entirely enclosed in a 28 m-long, 8 m-diameter, 1 cm-thick steel Faraday cage. This results in an unparalleled combination of shielding against cosmic rays, acoustic, seismic and electromagnetic noise, which can be exploited for rare event searches using ultra low-temperature and superconducting detectors. The first characterization measurements in this unique civilian site are reported. http://www.gps.jussieu.fr/RUSTREL/rustrel.html

  15. Topical report on a preconceptual design for the Spallation-Induced Lithium Conversion (SILC) target for the accelerator production of tritium (APT)

    Energy Technology Data Exchange (ETDEWEB)

    Van Tuyle, G.J.; Cokinos, D.M.; Czajkowski, C.; Franz, E.M.; Kroeger, P.; Todosow, M.; Youngblood, R.; Zucker, M.

    1993-09-30

    The preconceptual design of the APT Li-Al target system, also referred to as the Spallation-Induced Lithium Conversion (SILC), target system, is summarized in this report. The system has been designed to produce a ``3/8 Goal`` quantity of tritium using the 200-mA, 1.0 GeV proton beam emerging from the LANL-designed LINAC. The SILC target system consists of a beam expander, a heavy-water-cooled lead spallation neutron source assembly surrounded by light-water-cooled Li-Al blankets, a target window, heat removal systems, and related safety systems. The preconceptual design of each of these major components is described. Descriptions are also provided for the target fabrication, tritium extraction, and waste-steam processes. Performance characteristics are presented and discussed.

  16. Vaporization of mercury from molten lead droplets doped with mercury: Pb/Hg source term experiment for the APT/SILC target

    International Nuclear Information System (INIS)

    Tutu, N.K.; Greene, G.A.

    1994-09-01

    Experiments were performed to measure the fraction of mercury inventory released when droplets of molten lead, doped with a known concentration of mercury, fall through a controlled environment. The temperature of molten droplets ranged from 335 C to 346 C, and the concentration of mercury in the droplets ranged from 0.2 mass % to 1.0 mass %. The environment consisted of an air stream, at a temperature nominally equal to the melt temperature, and moving vertically upwards at a velocity of 10 cm/s. Direct observations and chemical analysis showed that no mercury was released from the molten droplets. Based upon the experimental results, it is concluded that no mercury vapor is likely to be released from the potentially molten source rod material in the APT-SILC Neutron Source Array to the confinement atmosphere during a postulated Large Break Loss Of Coolant Accident scenario leading to the melting of a fraction of the source rods

  17. Functionalization of Fe3O4 NPs by Silanization: Use of Amine (APTES and Thiol (MPTMS Silanes and Their Physical Characterization

    Directory of Open Access Journals (Sweden)

    Silvia Villa

    2016-10-01

    Full Text Available In this paper the results concerning the synthesis of magnetite (Fe3O4 nanoparticles (NPs, their functionalization using silane derivatives, such as (3-Aminopropyltriethoxysilane (APTES and (3-mercaptopropyltrimethoxysilane (MPTMS, and their exhaustive morphological and physical characterization by field emission scanning electron microscopy (FE-SEM with energy dispersion X-ray spectrometer (EDX analysis, AC magnetic susceptibility, UV-VIS and IR spectroscopy, and thermogravimetric (TGA analyses are reported. Two different paths were adopted to achieve the desired functionalization: (1 the direct reaction between the functionalized organo-silane molecule and the surface of the magnetite nanoparticle; and (2 the use of an intermediate silica coating. Finally, the occurrence of both the functionalization with amino and thiol groups has been demonstrated by the reaction with ninhydrin and the capture of Au NPs, respectively.

  18. Tree manipulation experiment

    Science.gov (United States)

    Nishina, K.; Takenaka, C.; Ishizuka, S.; Hashimoto, S.; Yagai, Y.

    2012-12-01

    Some forest operations such as thinning and harvesting management could cause changes in N cycling and N2O emission from soils, since thinning and harvesting managements are accompanied with changes in aboveground environments such as an increase of slash falling and solar radiation on the forest floor. However, a considerable uncertainty exists in effects of thinning and harvesting on N2O fluxes regarding changes in belowground environments by cutting trees. To focus on the effect of changes in belowground environments on the N2O emissions from soils, we conducted a tree manipulation experiment in Japanese cedar (Cryptomeria japonica) stand without soil compaction and slash falling near the chambers and measured N2O flux at 50 cm and 150 cm distances from the tree trunk (stump) before and after cutting. We targeted 5 trees for the manipulation and established the measurement chambers to the 4 directions around each targeted tree relative to upper slope (upper, left, right, lower positions). We evaluated the effect of logging on the emission by using hierarchical Bayesian model. HB model can evaluate the variability in observed data and their uncertainties in the estimation with various probability distributions. Moreover, the HB model can easily accommodate the non-linear relationship among the N2O emissions and the environmental factors, and explicitly take non-independent data (nested structure of data) for the estimation into account by using random effects in the model. Our results showed tree cutting stimulated N2O emission from soils, and also that the increase of N2O flux depended on the distance from the trunk (stump): the increase of N2O flux at 50 cm from the trunk (stump) was greater than that of 150 cm from the trunk. The posterior simulation of the HB model indicated that the stimulation of N2O emission by tree cut- ting could reach up to 200 cm in our experimental plot. By tree cutting, the estimated N2O emission at 0-40 cm from the trunk doubled

  19. Steiner trees in industry

    CERN Document Server

    Du, Ding-Zhu

    2001-01-01

    This book is a collection of articles studying various Steiner tree prob­ lems with applications in industries, such as the design of electronic cir­ cuits, computer networking, telecommunication, and perfect phylogeny. The Steiner tree problem was initiated in the Euclidean plane. Given a set of points in the Euclidean plane, the shortest network interconnect­ ing the points in the set is called the Steiner minimum tree. The Steiner minimum tree may contain some vertices which are not the given points. Those vertices are called Steiner points while the given points are called terminals. The shortest network for three terminals was first studied by Fermat (1601-1665). Fermat proposed the problem of finding a point to minimize the total distance from it to three terminals in the Euclidean plane. The direct generalization is to find a point to minimize the total distance from it to n terminals, which is still called the Fermat problem today. The Steiner minimum tree problem is an indirect generalization. Sch...

  20. Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human-viral Infection Patterns.

    Science.gov (United States)

    Smoly, Ilan; Carmel, Amir; Shemer-Avni, Yonat; Yeger-Lotem, Esti; Ziv-Ukelson, Michal

    2016-03-01

    Network querying is a powerful approach to mine molecular interaction networks. Most state-of-the-art network querying tools either confine the search to a prespecified topology in the form of some template subnetwork, or do not specify any topological constraints at all. Another approach is grammar-based queries, which are more flexible and expressive as they allow for expressing the topology of the sought pattern according to some grammar-based logic. Previous grammar-based network querying tools were confined to the identification of paths. In this article, we extend the patterns identified by grammar-based query approaches from paths to trees. For this, we adopt a higher order query descriptor in the form of a regular tree grammar (RTG). We introduce a novel problem and propose an algorithm to search a given graph for the k highest scoring subgraphs matching a tree accepted by an RTG. Our algorithm is based on the combination of dynamic programming with color coding, and includes an extension of previous k-best parsing optimization approaches to avoid isomorphic trees in the output. We implement the new algorithm and exemplify its application to mining viral infection patterns within molecular interaction networks. Our code is available online.

  1. Visualization of Uncertain Contour Trees

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

    Contour trees can represent the topology of large volume data sets in a relatively compact, discrete data structure. However, the resulting trees often contain many thousands of nodes; thus, many graph drawing techniques fail to produce satisfactory results. Therefore, several visualization methods...... were proposed recently for the visualization of contour trees. Unfortunately, none of these techniques is able to handle uncertain contour trees although any uncertainty of the volume data inevitably results in partially uncertain contour trees. In this work, we visualize uncertain contour trees...... by combining the contour trees of two morphologically filtered versions of a volume data set, which represent the range of uncertainty. These two contour trees are combined and visualized within a single image such that a range of potential contour trees is represented by the resulting visualization. Thus...

  2. Generic Ising trees

    DEFF Research Database (Denmark)

    Durhuus, Bergfinnur Jøgvan; Napolitano, George Maria

    2012-01-01

    The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove that they......The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove...... that they exhibit no spontaneous magnetization. Furthermore, the values of the Hausdorff and spectral dimensions of the underlying trees are calculated and found to be, respectively,¯dh =2 and¯ds = 4/3....

  3. ColorTree: a batch customization tool for phylogenic trees.

    Science.gov (United States)

    Chen, Wei-Hua; Lercher, Martin J

    2009-07-31

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

  4. A parallel buffer tree

    DEFF Research Database (Denmark)

    Sitchinava, Nodar; Zeh, Norbert

    2012-01-01

    We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number of...... in the optimal OhOf(psortN + K/PB) parallel I/O complexity, where K is the size of the output reported in the process and psortN is the parallel I/O complexity of sorting N elements using P processors....

  5. Exposure experiments of trees to sulfur dioxide gas. Part I

    Energy Technology Data Exchange (ETDEWEB)

    Otani, A.

    1974-12-01

    The effects of gaseous sulfur dioxide on trees were studied. Twenty species of plant seedlings (70 cm in height) including Cedrus deodara, Metasequoia glyptostroboides, Ginkgo biloba, Celmus parvifolia var. albo-marginata, Pinus thumbergii, P. densiflora, Cryptomeria japonica, and Quercus myrsinaefolia, were exposed in a room to gaseous sulfur dioxide at 0.8 ppm for 7.5 hr/day (from 9 am to 4:30 pm) for 24 days at a temperature of 20-35 deg C and RH of 55-75%. Visible damage to plants was lighter in C.j. and Chamae cyparis obtusa, more severe in P.t., G.b., and C.d. The damage appeared earlier in G.b., Cinnamomum camphona, and Ilex rotunda, and the change of early symptoms was smaller in P.t., C.j., and C.o. The leaves of the 4-5th positions from the sprout were apt to be damaged. Although the sulfur content of exposed leaves increased markedly, that in other parts did not increase. Because of the high concentration of the gas and the short period of exposure, the absorption of sulfur into leaves should have differed from the situation in fields where longer exposure to lower concentrations of the gas would be expected. 6 references.

  6. Embedding complete ternary tree in hypercubes using AVL trees

    NARCIS (Netherlands)

    S.A. Choudum; I. Raman (Indhumathi)

    2008-01-01

    htmlabstractA complete ternary tree is a tree in which every non-leaf vertex has exactly three children. We prove that a complete ternary tree of height h, TTh, is embeddable in a hypercube of dimension . This result coincides with the result of [2]. However, in this paper, the embedding utilizes

  7. Portraits of Tree Families

    NARCIS (Netherlands)

    Balgooy, van M.M.J.

    1998-01-01

    With the publication of the second volume of the series ‘Malesian Seed Plants’, entitled ‘Portraits of Tree Families’, I would like to refer to the Introduction of the first volume, ‘Spot-characters’ for a historical background and an explanation of the aims of this series. The present book treats

  8. P{owering 'Trees

    Indian Academy of Sciences (India)

    Melia dubia Cav. of Meliaceae is a large deciduous tree. Leaves are compound with toothed leaflets. Flowers are small, greenish-yellow in much-branched inflorescences. Fruits are green, ellipsoidal with a single seed covered by hard portion ( as in a mango fruit) and surrounded by fleshy pulp outside. The bark is bitter ...

  9. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    transducers can be concisely represented in Haskell, and demonstrate the benefits of utilising such an approach with a number of examples. In particular, tree transducers afford a modular programming style as they can be easily composed and manipulated. Our Haskell representation generalises the original...

  10. Chapter 5 - Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2014-01-01

    Tree mortality is a natural process in all forest ecosystems. Extremely high mortality, however, can also be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  11. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  12. Base tree property

    Czech Academy of Sciences Publication Activity Database

    Balcar, B.; Doucha, Michal; Hrušák, M.

    2015-01-01

    Roč. 32, č. 1 (2015), s. 69-81 ISSN 0167-8094 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : forcing * Boolean algebras * base tree Subject RIV: BA - General Mathematics Impact factor: 0.614, year: 2015 http://link.springer.com/article/10.1007/s11083-013-9316-2

  13. Multiquarks and Steiner trees

    International Nuclear Information System (INIS)

    Richard, Jean-Marc

    2010-01-01

    A brief review review is presented of models tentatively leading to stable multiquarks. A new attempt is presented, based on a Steiner-tree model of confinement, which is inspired by by QCD. It leads to more attraction than the empirical colour-additive model used in earlier multiquark calculations, and predict several multiquark states in configurations with different flavours.

  14. Tree Transduction Tools for Cdec

    Directory of Open Access Journals (Sweden)

    Austin Matthews

    2014-09-01

    Full Text Available We describe a collection of open source tools for learning tree-to-string and tree-to-tree transducers and the extensions to the cdec decoder that enable translation with these. Our modular, easy-to-extend tools extract rules from trees or forests aligned to strings and trees subject to different structural constraints. A fast, multithreaded implementation of the Cohn and Blunsom (2009 model for extracting compact tree-to-string rules is also included. The implementation of the tree composition algorithm used by cdec is described, and translation quality and decoding time results are presented. Our experimental results add to the body of evidence suggesting that tree transducers are a compelling option for translation, particularly when decoding speed and translation model size are important.

  15. Selecting Landscape Plants: Shade Trees

    OpenAIRE

    Relf, Diane; Appleton, Bonnie Lee, 1948-2012; Close, David

    2015-01-01

    Because of the permanency of trees and their importance in the landscape, care must be taken to select the best species for each situation. This publication goes over how to choose landscape trees that are shade tolerant.

  16. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

  17. Introduction to fault tree analysis

    International Nuclear Information System (INIS)

    Barlow, R.E.; Lambert, H.E.

    1975-01-01

    An elementary, engineering oriented introduction to fault tree analysis is presented. The basic concepts, techniques and applications of fault tree analysis, FTA, are described. The two major steps of FTA are identified as (1) the construction of the fault tree and (2) its evaluation. The evaluation of the fault tree can be qualitative or quantitative depending upon the scope, extensiveness and use of the analysis. The advantages, limitations and usefulness of FTA are discussed

  18. The Re-Think Tree.

    Science.gov (United States)

    Gear, Jim

    1993-01-01

    The Re-Think Tree is a simple framework to help individuals assess and improve their behaviors related to environmental issues. The branches of the tree in order of priority are refuse, reduce, re-use, and recycle. Roots of the tree include such things as public opinion, education, and watchdog groups. (KS)

  19. The Hopi Fruit Tree Book.

    Science.gov (United States)

    Nyhuis, Jane

    Referring as often as possible to traditional Hopi practices and to materials readily available on the reservation, the illustrated booklet provides information on the care and maintenance of young fruit trees. An introduction to fruit trees explains the special characteristics of new trees, e.g., grafting, planting pits, and watering. The…

  20. Rectilinear Full Steiner Tree Generation

    DEFF Research Database (Denmark)

    Zachariasen, Martin

    1999-01-01

    The fastest exact algorithm (in practice) for the rectilinear Steiner tree problem in the plane uses a two-phase scheme: First, a small but sufficient set of full Steiner trees (FSTs) is generated and then a Steiner minimum tree is constructed from this set by using simple backtrack search, dynamic...

  1. Inferences from growing trees backwards

    Science.gov (United States)

    David W. Green; Kent A. McDonald

    1997-01-01

    The objective of this paper is to illustrate how longitudinal stress wave techniques can be useful in tracking the future quality of a growing tree. Monitoring the quality of selected trees in a plantation forest could provide early input to decisions on the effectiveness of management practices, or future utilization options, for trees in a plantation. There will...

  2. Genetic transformation of forest trees

    African Journals Online (AJOL)

    Admin

    In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

  3. TREE SELECTING AND TREE RING MEASURING IN DENDROCHRONOLOGICAL INVESTIGATIONS

    Directory of Open Access Journals (Sweden)

    Sefa Akbulut

    2004-04-01

    Full Text Available Dendrochronology is a method of dating which makes use of the annual nature of tree growth. Dendrochronology may be divided into a number of subfields, each of which covers one or more aspects of the use of tree ring data: dendroclimatology, dendrogeomorphology, dendrohydrology, dendroecology, dendroarchaelogy, and dendrogylaciology. Basic of all form the analysis of the tree rings. The wood or tree rings can aid to dating past events about climatology, ecology, geology, hydrology. Dendrochronological studies are conducted either on increment cores or on discs. It may be seen abnormalities on tree rings during the measurement like that false rings, missing rings, reaction wood. Like that situation, increment cores must be extracted from four different sides of each tree and be studied as more as on tree.

  4. Tree Colors: Color Schemes for Tree-Structured Data.

    Science.gov (United States)

    Tennekes, Martijn; de Jonge, Edwin

    2014-12-01

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

  5. BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees.

    Science.gov (United States)

    Bond, Stephen R; Keat, Karl E; Barreira, Sofia N; Baxevanis, Andreas D

    2017-06-01

    The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction. Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data. The project has been engineered to easily accommodate the addition of new tools, is written in the popular programming language Python, and is hosted on the Python Package Index and GitHub to maximize accessibility. Documentation for each BuddySuite tool, including usage examples, is available at http://tiny.cc/buddysuite_wiki. All software is open source and freely available through http://research.nhgri.nih.gov/software/BuddySuite. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

  6. Detecting Difference between Process Models Based on the Refined Process Structure Tree

    Directory of Open Access Journals (Sweden)

    Jing Fan

    2017-01-01

    Full Text Available The development of mobile workflow management systems (mWfMS leads to large number of business process models. In the meantime, the location restriction embedded in mWfMS may result in different process models for a single business process. In order to help users quickly locate the difference and rebuild the process model, detecting the difference between different process models is needed. Existing detection methods either provide a dissimilarity value to represent the difference or use predefined difference template to generate the result, which cannot reflect the entire composition of the difference. Hence, in this paper, we present a new approach to solve this problem. Firstly, we parse the process models to their corresponding refined process structure trees (PSTs, that is, decomposing a process model into a hierarchy of subprocess models. Then we design a method to convert the PST to its corresponding task based process structure tree (TPST. As a consequence, the problem of detecting difference between two process models is transformed to detect difference between their corresponding TPSTs. Finally, we obtain the difference between two TPSTs based on the divide and conquer strategy, where the difference is described by an edit script and we make the cost of the edit script close to minimum. The extensive experimental evaluation shows that our method can meet the real requirements in terms of precision and efficiency.

  7. Rate of tree carbon accumulation increases continuously with tree size.

    Science.gov (United States)

    Stephenson, N L; Das, A J; Condit, R; Russo, S E; Baker, P J; Beckman, N G; Coomes, D A; Lines, E R; Morris, W K; Rüger, N; Alvarez, E; Blundo, C; Bunyavejchewin, S; Chuyong, G; Davies, S J; Duque, A; Ewango, C N; Flores, O; Franklin, J F; Grau, H R; Hao, Z; Harmon, M E; Hubbell, S P; Kenfack, D; Lin, Y; Makana, J-R; Malizia, A; Malizia, L R; Pabst, R J; Pongpattananurak, N; Su, S-H; Sun, I-F; Tan, S; Thomas, D; van Mantgem, P J; Wang, X; Wiser, S K; Zavala, M A

    2014-03-06

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

  8. Study on usability of Fusarium oxysporum Schlecht.f.sp. tulipae Apt. metabolites for screening for basal rot resistance in tulip

    Directory of Open Access Journals (Sweden)

    Małgorzata Podwyszyńska

    2013-12-01

    Full Text Available The usefulness of fungus culture filtrates and fusaric acid as selecting agents for Fusarium resistance breeding in tulip was examined on in vitro cultures of shoots and embryonic calli of seven tulip genotypes differing in resistance to Fusarium oxysporum Schlecht. f. sp. tulipae Apt. (F.o.t. and four virulent F.o.t. isolates. Fusaric acid influenced the shoot growth of all cultivars tested in a similar way, irrespectively of their greenhouse resistance to basal rot. Also, the sensitivity of calli of the cultivars studied to fusaric acid did not correspond with their resistance to F.o.t. evaluated in the greenhouse screening. The phytotoxity of F.o.t. culture filtrates did not depend on their fusaric acid contents. There was a negative correlation between cultivar's resistance to F.o.t in greenhouse tests and the sensitivity of their shoots to fungus culture filtrates in in vitro tests. This indicates that defence mechanism against F.o.t. in tulip tissue may have a nature of hypersensitive response. Considering the results of our study, it may be concluded that the use of fusaric acid or fungus culture filtrates for the in vitro selection of somaclones resistant to F.o.t. in tulip is not feasible.

  9. Parsing multiple processes of high temperature impacts on corn/soybean yield using a newly developed CLM-APSIM modeling framework

    Science.gov (United States)

    Peng, B.; Guan, K.; Chen, M.

    2016-12-01

    Future agricultural production faces a grand challenge of higher temperature under climate change. There are multiple physiological or metabolic processes of how high temperature affects crop yield. Specifically, we consider the following major processes: (1) direct temperature effects on photosynthesis and respiration; (2) speed-up growth rate and the shortening of growing season; (3) heat stress during reproductive stage (flowering and grain-filling); (4) high-temperature induced increase of atmospheric water demands. In this work, we use a newly developed modeling framework (CLM-APSIM) to simulate the corn and soybean growth and explicitly parse the above four processes. By combining the strength of CLM in modeling surface biophysical (e.g., hydrology and energy balance) and biogeochemical (e.g., photosynthesis and carbon-nitrogen interactions), as well as that of APSIM in modeling crop phenology and reproductive stress, the newly developed CLM-APSIM modeling framework enables us to diagnose the impacts of high temperature stress through different processes at various crop phenology stages. Ground measurements from the advanced SoyFACE facility at University of Illinois is used here to calibrate, validate, and improve the CLM-APSIM modeling framework at the site level. We finally use the CLM-APSIM modeling framework to project crop yield for the whole US Corn Belt under different climate scenarios.

  10. Fault tree analysis

    International Nuclear Information System (INIS)

    1981-09-01

    Suggestion are made concerning the method of the fault tree analysis, the use of certain symbols in the examination of system failures. This purpose of the fault free analysis is to find logical connections of component or subsystem failures leading to undesirable occurrances. The results of these examinations are part of the system assessment concerning operation and safety. The objectives of the analysis are: systematical identification of all possible failure combinations (causes) leading to a specific undesirable occurrance, finding of reliability parameters such as frequency of failure combinations, frequency of the undesirable occurrance or non-availability of the system when required. The fault tree analysis provides a near and reconstructable documentation of the examination. (orig./HP) [de

  11. Tree-level formalism

    International Nuclear Information System (INIS)

    Brandhuber, Andreas; Spence, Bill; Travaglini, Gabriele

    2011-01-01

    We review two novel techniques used to calculate tree-level scattering amplitudes efficiently: MHV diagrams, and on-shell recursion relations. For the MHV diagrams, we consider applications to tree-level amplitudes and focus in particular on the N=4 supersymmetric formulation. We also briefly describe the derivation of loop amplitudes using MHV diagrams. For the recursion relations, after presenting their general proof, we discuss several applications to massless theories with and without supersymmetry, to theories with massive particles, and to graviton amplitudes in general relativity. This article is an invited review for a special issue of Journal of Physics A: Mathematical and Theoretical devoted to 'Scattering amplitudes in gauge theories'. (review)

  12. Tree Rings: Timekeepers of the Past.

    Science.gov (United States)

    Phipps, R. L.; McGowan, J.

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

  13. Wood for the trees

    Directory of Open Access Journals (Sweden)

    Rob Garbutt

    2013-10-01

    Full Text Available Our paper focuses on the materiality, cultural history and cultural relations of selected artworks in the exhibition Wood for the trees (Lismore Regional Gallery, New South Wales, Australia, 10 June – 17 July 2011. The title of the exhibition, intentionally misreading the aphorism “Can’t see the wood for the trees”, by reading the wood for the resource rather than the collective wood[s], implies conservation, preservation, and the need for sustaining the originating resource. These ideas have particular resonance on the NSW far north coast, a region once rich in rainforest. While the Indigenous population had sustainable practices of forest and land management, the colonists deployed felling and harvesting in order to convert the value of the local, abundant rainforest trees into high-value timber. By the late twentieth century, however, a new wave of settlers launched a protest movements against the proposed logging of remnant rainforest at Terania Creek and elsewhere in the region. Wood for the trees, curated by Gallery Director Brett Adlington, plays on this dynamic relationship between wood, trees and people. We discuss the way selected artworks give expression to the themes or concepts of productive labour, nature and culture, conservation and sustainability, and memory. The artworks include Watjinbuy Marrawilil’s (1980 Carved ancestral figure ceremonial pole, Elizabeth Stops’ (2009/10 Explorations into colonisation, Hossein Valamanesh’s (2008 Memory stick, and AñA Wojak’s (2008 Unread book (in a forgotten language. Our art writing on the works, a practice informed by Bal (2002, Muecke (2008 and Papastergiadis (2004, becomes a conversation between the works and the themes or concepts. As a form of material excess of the most productive kind (Grosz, 2008, p. 7, art seeds a response to that which is in the air waiting to be said of the past, present and future.

  14. Recursive Trees for Practical ORAM

    Directory of Open Access Journals (Sweden)

    Moataz Tarik

    2015-06-01

    Full Text Available We present a new, general data structure that reduces the communication cost of recent tree-based ORAMs. Contrary to ORAM trees with constant height and path lengths, our new construction r-ORAM allows for trees with varying shorter path length. Accessing an element in the ORAM tree results in different communication costs depending on the location of the element. The main idea behind r-ORAM is a recursive ORAM tree structure, where nodes in the tree are roots of other trees. While this approach results in a worst-case access cost (tree height at most as any recent tree-based ORAM, we show that the average cost saving is around 35% for recent binary tree ORAMs. Besides reducing communication cost, r-ORAM also reduces storage overhead on the server by 4% to 20% depending on the ORAM’s client memory type. To prove r-ORAM’s soundness, we conduct a detailed overflow analysis. r-ORAM’s recursive approach is general in that it can be applied to all recent tree ORAMs, both constant and poly-log client memory ORAMs. Finally, we implement and benchmark r-ORAM in a practical setting to back up our theoretical claims.

  15. Mathematical foundations of event trees

    International Nuclear Information System (INIS)

    Papazoglou, Ioannis A.

    1998-01-01

    A mathematical foundation from first principles of event trees is presented. The main objective of this formulation is to offer a formal basis for developing automated computer assisted construction techniques for event trees. The mathematical theory of event trees is based on the correspondence between the paths of the tree and the elements of the outcome space of a joint event. The concept of a basic cylinder set is introduced to describe joint event outcomes conditional on specific outcomes of basic events or unconditional on the outcome of basic events. The concept of outcome space partition is used to describe the minimum amount of information intended to be preserved by the event tree representation. These concepts form the basis for an algorithm for systematic search for and generation of the most compact (reduced) form of an event tree consistent with the minimum amount of information the tree should preserve. This mathematical foundation allows for the development of techniques for automated generation of event trees corresponding to joint events which are formally described through other types of graphical models. Such a technique has been developed for complex systems described by functional blocks and it is reported elsewhere. On the quantification issue of event trees, a formal definition of a probability space corresponding to the event tree outcomes is provided. Finally, a short discussion is offered on the relationship of the presented mathematical theory with the more general use of event trees in reliability analysis of dynamic systems

  16. Making CSB + -Trees Processor Conscious

    DEFF Research Database (Denmark)

    Samuel, Michael; Pedersen, Anders Uhl; Bonnet, Philippe

    2005-01-01

    of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose......Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... a systematic method for adapting CSB+-tree to new platforms. This work is a first step towards integrating CSB+-tree in MySQL’s heap storage manager....

  17. Submodular unsplittable flow on trees

    DEFF Research Database (Denmark)

    Adamaszek, Anna Maria; Chalermsook, Parinya; Ene, Alina

    2016-01-01

    We study the Unsplittable Flow problem (UFP) on trees with a submodular objective function. The input to this problem is a tree with edge capacities and a collection of tasks, each characterized by a source node, a sink node, and a demand. A subset of the tasks is feasible if the tasks can...... simultaneously send their demands from the source to the sink without violating the edge capacities. The goal is to select a feasible subset of the tasks that maximizes a submodular objective function. Our main result is an O(k log n)-approximation algorithm for Submodular UFP on trees where k denotes...... the pathwidth of the given tree. Since every tree has pathwidth O(log n), we obtain an O(log2 n) approximation for arbitrary trees. This is the first non-trivial approximation guarantee for the problem and it matches the best approximation known for UFP on trees with a linear objective function. Our main...

  18. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  19. Rate of tree carbon accumulation increases continuously with tree size

    Science.gov (United States)

    Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

    2014-01-01

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

  20. On Determining if Tree-based Networks Contain Fixed Trees.

    Science.gov (United States)

    Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

    2016-05-01

    We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

  1. Trees in the city: valuing street trees in Portland, Oregon

    Science.gov (United States)

    G.H. Donovan; D.T. Butry

    2010-01-01

    We use a hedonic price model to simultaneously estimate the effects of street trees on the sales price and the time-on-market (TOM) of houses in Portland. Oregon. On average, street trees add $8,870 to sales price and reduce TOM by 1.7 days. In addition, we found that the benefits of street trees spill over to neighboring houses. Because the provision and maintenance...

  2. Systolic trees and systolic language recognition by tree automata

    Energy Technology Data Exchange (ETDEWEB)

    Steinby, M

    1983-01-01

    K. Culik II, J. Gruska, A. Salomaa and D. Wood have studied the language recognition capabilities of certain types of systolically operating networks of processors (see research reports Cs-81-32, Cs-81-36 and Cs-82-01, Univ. of Waterloo, Ontario, Canada). In this paper, their model for systolic VLSI trees is formalised in terms of standard tree automaton theory, and the way in which some known facts about recognisable forests and tree transductions can be applied in VLSI tree theory is demonstrated. 13 references.

  3. Tree felling: a necessary evil

    CERN Multimedia

    CERN Bulletin

    2013-01-01

    CERN started a campaign of tree felling in 2010 for safety reasons, and it will continue this year in various parts of the Meyrin site. As in previous years, the trees cut down in 2013 will be recycled and some will be replaced.   Diseased tree that had to be cut down on the Meyrin site. In association with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP), CERN commissioned the Geneva school of landscaping, engineering and architecture (Haute école du paysage, d’ingénierie et d’architecture, HEPIA) to compile an inventory of the trees on the Meyrin site. In total, 1285 trees (excluding poplars) were recorded. 75.5% of these trees were declared to be in a good state of health (i.e. 971 trees), 21.5% in a moderate state of health (276 trees) and 3% in a poor state of health (38 trees). As for the poplars, the 236 specimens recorded on the Meyrin site were judged to be too old, to...

  4. Human decision error (HUMDEE) trees

    International Nuclear Information System (INIS)

    Ostrom, L.T.

    1993-01-01

    Graphical presentations of human actions in incident and accident sequences have been used for many years. However, for the most part, human decision making has been underrepresented in these trees. This paper presents a method of incorporating the human decision process into graphical presentations of incident/accident sequences. This presentation is in the form of logic trees. These trees are called Human Decision Error Trees or HUMDEE for short. The primary benefit of HUMDEE trees is that they graphically illustrate what else the individuals involved in the event could have done to prevent either the initiation or continuation of the event. HUMDEE trees also present the alternate paths available at the operator decision points in the incident/accident sequence. This is different from the Technique for Human Error Rate Prediction (THERP) event trees. There are many uses of these trees. They can be used for incident/accident investigations to show what other courses of actions were available and for training operators. The trees also have a consequence component so that not only the decision can be explored, also the consequence of that decision

  5. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

    It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

  6. Occurrence of leguminous trees

    Energy Technology Data Exchange (ETDEWEB)

    Kirkbride, J.H.; Arkcoll, D.B.A.; Turnbull, J.W.; Magalhaes, L.M.S.; Fernandes, N.P.

    1984-01-01

    Five papers from the symposium are presented. Kirkbride, J.H. Jr.; Legumes of the cerrado. pp 23-46 (Refs. 55) A review is given. Some 548 legume species in 59 genera are listed that have been reported from cerrado vegetation. Felker, P.; Legume trees in semi-arid and arid areas. pp 47-59 (Refs. 41) A review is given of worldwide research activities. Arkcoll, D.B.; A comparison of some fast growing species suitable for woodlots in the wet tropics. pp 61-68 (Refs. 9) Studies are described near Manaus on intensive silviculture (for fuelwood production) of Eucalyptus deglupta, Cedrelinga catanaeformis (catenaeformis), Jacaranda copaia, and Inga edulis. Turnbull, J.W.; Six phyllodinous Acacia species for planting in the humid tropical lowlands. pp 69-73 (Refs. 14) Distribution, ecology, growth, and utilization are described for A. auriculiformis, A. mangium, A. aulacocarpa, A. crassicarpa, A. cincinnata, and A. polystachya. Magalhaes, L.M.S., Fernandes, N.P.; Experimental stands of leguminous trees in the Manaus region. pp 75-79 (Refs. 8) Performance up to age 20 yr of Cedrelinga catenaeformis, Dalbergia nigra, Dinizia excelsa, Dipteryx odorata, Dipteryx sp., Diplotropis sp., Eperua bijuga, Pithecellobium racemosum, Vouacapoua pallidior, and Hymenaea sp. is described.

  7. The Steiner tree problem

    CERN Document Server

    Hwang, FK; Winter, P

    1992-01-01

    The Steiner problem asks for a shortest network which spans a given set of points. Minimum spanning networks have been well-studied when all connections are required to be between the given points. The novelty of the Steiner tree problem is that new auxiliary points can be introduced between the original points so that a spanning network of all the points will be shorter than otherwise possible. These new points are called Steiner points - locating them has proved problematic and research has diverged along many different avenues. This volume is devoted to the assimilation of the rich field of intriguing analyses and the consolidation of the fragments. A section has been given to each of the three major areas of interest which have emerged. The first concerns the Euclidean Steiner Problem, historically the original Steiner tree problem proposed by Jarník and Kössler in 1934. The second deals with the Steiner Problem in Networks, which was propounded independently by Hakimi and Levin and has enjoyed the most...

  8. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  9. Distributed Merge Trees

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

    Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions. As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization. We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.

  10. Visualizing Individual Tree Differences in Tree-Ring Studies

    Directory of Open Access Journals (Sweden)

    Mario Trouillier

    2018-04-01

    Full Text Available Averaging tree-ring measurements from multiple individuals is one of the most common procedures in dendrochronology. It serves to filter out noise from individual differences between trees, such as competition, height, and micro-site effects, which ideally results in a site chronology sensitive to regional scale factors such as climate. However, the climate sensitivity of individual trees can be modulated by factors like competition, height, and nitrogen deposition, calling attention to whether average chronologies adequately assess climatic growth-control. In this study, we demonstrate four simple but effective methods to visually assess differences between individual trees. Using individual tree climate-correlations we: (1 employed jitter plots with superimposed metadata to assess potential causes for these differences; (2 plotted the frequency distributions of climate correlations over time as heat maps; (3 mapped the spatial distribution of climate sensitivity over time to assess spatio-temporal dynamics; and (4 used t-distributed Stochastic Neighborhood Embedding (t-SNE to assess which trees were generally more similar in terms of their tree-ring pattern and their correlation with climate variables. This suite of exploratory methods can indicate if individuals in tree-ring datasets respond differently to climate variability, and therefore, should not solely be explored with climate correlations of the mean population chronology.

  11. Tree Size Comparison of Some Important Street Trees Growing at ...

    African Journals Online (AJOL)

    PROF HORSFALL

    More research is needed on these trees for healthy environment of city. The present ..... use and CO2 emissions from power plants. Environ. Poll. .... Anna. Bot., 65:567-574. Kozlowski, T.T., 1971. Growth and Development of. Trees. Vol. 1.

  12. Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

    Science.gov (United States)

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

    2013-11-01

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

  13. DIF Trees: Using Classification Trees to Detect Differential Item Functioning

    Science.gov (United States)

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

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

  14. Picking a tree: habitat use by the tree agama, Acanthocercus ...

    African Journals Online (AJOL)

    We studied tree agama (Acanthocercus a. atricollis) habitat use in the Magaliesberg mountain range in northern South Africa using sightings of marked individuals, and in a few cases, radio-telemetry. Acanthocercus a. atricollis preferentially selected thorn trees (46%; Acacia karroo), followed by common sugarbush (10%; ...

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

    Science.gov (United States)

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

    2004-01-01

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

  16. Better trees through systematic breeding

    Science.gov (United States)

    Robert Z. Callaham

    1957-01-01

    Today I would like to tell you briefly about the efforts of forest geneticists to improve the quality of forest trees. What do we mean by quality? Here, the consumer has the first word. The trees we produce are primarily for timber production, and the timber growing and wood-using industries give us our guidelines. Nevertheless, many of the characteristics sought by...

  17. Tree physiology and bark beetles

    Science.gov (United States)

    Michael G. Ryan; Gerard Sapes; Anna Sala; Sharon Hood

    2015-01-01

    Irruptive bark beetles usually co-occur with their co-evolved tree hosts at very low (endemic) population densities. However, recent droughts and higher temperatures have promoted widespread tree mortality with consequences for forest carbon, fire and ecosystem services (Kurz et al., 2008; Raffa et al., 2008; Jenkins et al., 2012). In this issue of New Phytologist,...

  18. Tree Hydraulics: How Sap Rises

    Science.gov (United States)

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown--a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by…

  19. Boosted decision trees and applications

    International Nuclear Information System (INIS)

    Coadou, Y.

    2013-01-01

    Decision trees are a machine learning technique more and more commonly used in high energy physics, while it has been widely used in the social sciences. After introducing the concepts of decision trees, this article focuses on its application in particle physics. (authors)

  20. Who pays for tree improvement?

    Science.gov (United States)

    Tom D. Byram; E. M. Raley

    2011-01-01

    Tree improvement has been one of the most successful collaborative research efforts in history, eliciting participation from a wide variety of players. This effort has included state forestry agencies, research universities, integrated forest industries, and the USDA Forest Service. Tree improvement was organized through cooperatives whose objectives were to distribute...

  1. Mean-field lattice trees

    NARCIS (Netherlands)

    Borgs, C.; Chayes, J.T.; Hofstad, van der R.W.; Slade, G.

    1999-01-01

    We introduce a mean-field model of lattice trees based on embeddings into d of abstract trees having a critical Poisson offspring distribution. This model provides a combinatorial interpretation for the self-consistent mean-field model introduced previously by Derbez and Slade [9], and provides an

  2. Modelling tree biomasses in Finland

    Energy Technology Data Exchange (ETDEWEB)

    Repola, J.

    2013-06-01

    Biomass equations for above- and below-ground tree components of Scots pine (Pinus sylvestris L), Norway spruce (Picea abies [L.] Karst) and birch (Betula pendula Roth and Betula pubescens Ehrh.) were compiled using empirical material from a total of 102 stands. These stands (44 Scots pine, 34 Norway spruce and 24 birch stands) were located mainly on mineral soil sites representing a large part of Finland. The biomass models were based on data measured from 1648 sample trees, comprising 908 pine, 613 spruce and 127 birch trees. Biomass equations were derived for the total above-ground biomass and for the individual tree components: stem wood, stem bark, living and dead branches, needles, stump, and roots, as dependent variables. Three multivariate models with different numbers of independent variables for above-ground biomass and one for below-ground biomass were constructed. Variables that are normally measured in forest inventories were used as independent variables. The simplest model formulations, multivariate models (1) were mainly based on tree diameter and height as independent variables. In more elaborated multivariate models, (2) and (3), additional commonly measured tree variables such as age, crown length, bark thickness and radial growth rate were added. Tree biomass modelling includes consecutive phases, which cause unreliability in the prediction of biomass. First, biomasses of sample trees should be determined reliably to decrease the statistical errors caused by sub-sampling. In this study, methods to improve the accuracy of stem biomass estimates of the sample trees were developed. In addition, the reliability of the method applied to estimate sample-tree crown biomass was tested, and no systematic error was detected. Second, the whole information content of data should be utilized in order to achieve reliable parameter estimates and applicable and flexible model structure. In the modelling approach, the basic assumption was that the biomasses of

  3. Decision trees in epidemiological research

    Directory of Open Access Journals (Sweden)

    Ashwini Venkatasubramaniam

    2017-09-01

    Full Text Available Abstract Background In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. Main text We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART technique and the newer Conditional Inference tree (CTree technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Conclusions Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

  4. Decision trees in epidemiological research.

    Science.gov (United States)

    Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

    2017-01-01

    In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

  5. Totally optimal decision trees for Boolean functions

    KAUST Repository

    Chikalov, Igor; Hussain, Shahid; Moshkov, Mikhail

    2016-01-01

    We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters

  6. MAD parsing and conversion code

    International Nuclear Information System (INIS)

    Mokhov, Dmitri N.

    2000-01-01

    The authors describe design and implementation issues while developing an embeddable MAD language parser. Two working applications of the parser are also described, namely, MAD-> C++ converter and C++ factory. The report contains some relevant details about the parser and examples of converted code. It also describes some of the problems that were encountered and the solutions found for them

  7. Parsing Universal Dependencies without training

    NARCIS (Netherlands)

    Martínez Alonso, Héctor; Agić, Željko; Plank, Barbara; Søgaard, Anders

    2017-01-01

    We propose UDP, the first training-free parser for Universal Dependencies (UD). Our algorithm is based on PageRank and a small set of head attachment rules. It features two-step decoding to guarantee that function words are attached as leaf nodes. The parser requires no training, and it is

  8. Partial dependency parsing for Irish

    OpenAIRE

    Uí Dhonnchadha, Elaine; van Genabith, Josef

    2010-01-01

    In this paper we present a partial dependency parser for Irish, in which Constraint Grammar (CG) rules are used to annotate dependency relations and grammatical functions in unrestricted Irish text. Chunking is performed using a regular-expression grammar which operates on the dependency tagged sentences. As this is the first implementation of a parser for unrestricted Irish text (to our knowledge), there were no guidelines or precedents available. Therefore deciding what constitutes a syntac...

  9. Parsing statistical machine translation output

    NARCIS (Netherlands)

    Carter, S.; Monz, C.; Vetulani, Z.

    2009-01-01

    Despite increasing research into the use of syntax during statistical machine translation, the incorporation of syntax into language models has seen limited success. We present a study of the discriminative abilities of generative syntax-based language models, over and above standard n-gram models,

  10. Are There Infinite Irrigation Trees?

    Science.gov (United States)

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

    2006-08-01

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

  11. Maximum Gene-Support Tree

    Directory of Open Access Journals (Sweden)

    Yunfeng Shan

    2008-01-01

    Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

  12. Linking and Cutting Spanning Trees

    Directory of Open Access Journals (Sweden)

    Luís M. S. Russo

    2018-04-01

    Full Text Available We consider the problem of uniformly generating a spanning tree for an undirected connected graph. This process is useful for computing statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs, we prove that this approach significantly outperforms existing algorithms. For general graphs, experimental results show that the chain converges quickly. This yields an efficient algorithm due to the use of proper fast data structures. To obtain the mixing time of the chain we describe a coupling, which we analyze for cycle graphs and simulate for other graphs.

  13. Tree Ordination as Invented Tradition

    Directory of Open Access Journals (Sweden)

    Avery Morrow

    2012-01-01

    Full Text Available The symbolic ordination of trees as monks in Thailand is widely perceived in Western scholarship to be proof of the power of Buddhism to spur ecological thought. However, a closer analysis of tree ordination demonstrates that it is not primarily about Buddhist teaching, but rather is an invented tradition based on the sanctity of Thai Buddhist symbols as well as those of spirit worship and the monarchy. Tree ordinations performed by non-Buddhist minorities in Thailand do not demonstrate a religious commitment but rather a political one.

  14. Tree Coding of Bilevel Images

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    Presently, sequential tree coders are the best general purpose bilevel image coders and the best coders of halftoned images. The current ISO standard, Joint Bilevel Image Experts Group (JBIG), is a good example. A sequential tree coder encodes the data by feeding estimates of conditional...... is one order of magnitude slower than JBIG, obtains excellent and highly robust compression performance. A multipass free tree coding scheme produces superior compression results for all test images. A multipass free template coding scheme produces significantly better results than JBIG for difficult...... images such as halftones. By utilizing randomized subsampling in the template selection, the speed becomes acceptable for practical image coding...

  15. Multiple-purpose trees for pastoral farming in New Zealand: with emphasis on tree legumes. [Lucerne Tree: Medick Tree

    Energy Technology Data Exchange (ETDEWEB)

    Davies, D J.G.; Macfarlane, R P

    1979-01-01

    The potential for soil conservation and agroforestry of several native and exotic legumes is discussed. Flowering period, chemical composition of leaves/pods, hardiness to frost and drought, timber value, forage potential for livestock and bees, ornamental value and other products are tabulated with information on up to 38 species. Two low-growing species that have proved useful for slope stabilization as well as forage are tree lucerne (Cytisus palmensis) and tree medick (Medicago arborea), the latter being shrubby and more suitable for cold districts. Gleditsia triacanthos is recommended as a shade and fodder tree for farm pasture.

  16. Generalising tree traversals to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2015-01-01

    We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal and then apply it to compact graph representations of trees instead. The resulting graph traversals avoid...... is not sound. Therefore, we complement our implementation of the recursion scheme with a number of correspondence theorems that ensure soundness for various classes of traversals. We illustrate the practical applicability of the implementation as well as the complementing theory with a number of examples....

  17. Tree-growth analyses to estimate tree species' drought tolerance.

    Science.gov (United States)

    Eilmann, Britta; Rigling, Andreas

    2012-02-01

    Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.

  18. TreeCluster: Massively scalable transmission clustering using phylogenetic trees

    OpenAIRE

    Moshiri, Alexander

    2018-01-01

    Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...

  19. Moose?tree interactions: rebrowsing is common across tree species

    OpenAIRE

    Mathisen, Karen Marie; Milner, Jos M.; Skarpe, Christina

    2017-01-01

    Background Plant strategies to resist herbivory include tolerance and avoidance. Tolerance strategies, such as rapid regrowth which increases the palatability of new shoots, can lead to positive feedback loops between plants and herbivores. An example of such a positive feedback occurs when moose (Alces alces) browse trees in boreal forests. We described the degree of change in tree morphology that accumulated over time in response to repeated browsing by moose, using an index of accumulated ...

  20. Resummed tree heptagon

    Science.gov (United States)

    Belitsky, A. V.

    2018-04-01

    The form factor program for the regularized space-time S-matrix in planar maximally supersymmetric gauge theory, known as the pentagon operator product expansion, is formulated in terms of flux-tube excitations propagating on a dual two-dimensional world-sheet, whose dynamics is known exactly as a function of 't Hooft coupling. Both MHV and non-MHV amplitudes are described in a uniform, systematic fashion within this framework, with the difference between the two encoded in coupling-dependent helicity form factors expressed via Zhukowski variables. The nontrivial SU(4) tensor structure of flux-tube transitions is coupling independent and is known for any number of charged excitations from solutions of a system of Watson and Mirror equations. This description allows one to resum the infinite series of form factors and recover the space-time S-matrix exactly in kinematical variables at a given order of perturbation series. Recently, this was done for the hexagon. Presently, we successfully perform resummation for the seven-leg tree NMHV amplitude. To this end, we construct the flux-tube integrands of the fifteen independent Grassmann component of the heptagon with an infinite number of small fermion-antifermion pairs accounted for in NMHV two-channel conformal blocks.

  1. Random ancestor trees

    International Nuclear Information System (INIS)

    Ben-Naim, E; Krapivsky, P L

    2010-01-01

    We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

  2. Trees as metal scavengers

    International Nuclear Information System (INIS)

    Hallman, N.

    2000-01-01

    Full text: Tree roots extract metal ions form wet soils in two different ways. At the soil/root hair interface soluble ions in contact with the cellulose wall move through it and enter the cell through the plasmalemma; the semi permeable membrane that encloses every living cell. Some ions, especially those that are part of cellular metabolic processes eg. Na, K, Fe, Mg, S move into the cytoplasm, are bound into organic complexes and travel from cell to cell within the cytoplasm. This requires energy, and the amount of any of these metabolically active ions taken in tends to be regulated by the plant. The movement of the ions from cell to cell is slow, selective, and regulated by requirements of synthesis of for example Mg in the chlorophyll molecule. This means that more Mg is transported to cells of leaves than of cells of roots. This movement of ions is simplistic, or within the cytoplasm. Other ions are swept along in the transpiration stream and enter the complex plumbing system that brings water to the leaves for metabolism and cooling. Water in this apoplastic pathway travels within the pipes (xylem) of the wood and in the cellulose of the walls. It travels along essentially non-living parts of the plant. Ions such as As, Pb, Ni, Cr accumulate in sites such as leaves and bark. Analysis of plant parts can indicate the presence of heavy metals and can give an indication of ore bodies within the root zone

  3. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

    Directory of Open Access Journals (Sweden)

    Corinne Rancurel

    2017-09-01

    Full Text Available Horizontal gene transfer (HGT is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application available at http://alienness.sophia.inra.fr. Alienness parses BLAST results against public libraries to rapidly identify candidate HGT in any genome of interest. Alienness takes as input the result of a BLAST of a whole proteome of interest against any National Center for Biotechnology Information (NCBI protein library. The user defines recipient (e.g., Metazoa and donor (e.g., bacteria, fungi branches of interest in the NCBI taxonomy. Based on the best BLAST E-values of candidate donor and recipient taxa, Alienness calculates an Alien Index (AI for each query protein. An AI > 0 indicates a better hit to candidate donor than recipient taxa and a possible HGT. Higher AI represent higher gap of E-values between candidate donor and recipient and a more likely HGT. We confirmed the accuracy of Alienness on phylogenetically confirmed HGT of non-metazoan origin in plant-parasitic nematodes. Alienness scans whole proteomes to rapidly identify possible HGT in any species of interest and thus fosters exploration of HGT more easily and largely across the tree of life.

  4. The Tree of Industrial Life

    DEFF Research Database (Denmark)

    Andersen, Esben Sloth

    2002-01-01

    The purpose of this paper is to bring forth an interaction between evolutionary economics and industrial systematics. The suggested solution is to reconstruct the "family tree" of the industries. Such a tree is based on similarities, but it may also reflect the evolutionary history in industries....... For this purpose the paper shows how matrices of input-output coefficients can be transformed into binary characteristics matrices and to distance matrices, and it also discusses the possible evolutionary meaning of this translation. Then these derived matrices are used as inputs to algorithms for the heuristic...... finding of optimal industrial trees. The results are presented as taxonomic trees that can easily be compared with the hierarchical structure of existing systems of industrial classification....

  5. Fremont Tree-Well Filter

    Science.gov (United States)

    Information about the SFBWQP Fremont Tree-Well Filter Spine project, part of an EPA competitive grant program to improve SF Bay water quality focused on restoring impaired waters and enhancing aquatic resources.

  6. Algorithms for Decision Tree Construction

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    The study of algorithms for decision tree construction was initiated in 1960s. The first algorithms are based on the separation heuristic [13, 31] that at each step tries dividing the set of objects as evenly as possible. Later Garey and Graham [28] showed that such algorithm may construct decision trees whose average depth is arbitrarily far from the minimum. Hyafil and Rivest in [35] proved NP-hardness of DT problem that is constructing a tree with the minimum average depth for a diagnostic problem over 2-valued information system and uniform probability distribution. Cox et al. in [22] showed that for a two-class problem over information system, even finding the root node attribute for an optimal tree is an NP-hard problem. © Springer-Verlag Berlin Heidelberg 2011.

  7. Decision tree modeling using R.

    Science.gov (United States)

    Zhang, Zhongheng

    2016-08-01

    In machine learning field, decision tree learner is powerful and easy to interpret. It employs recursive binary partitioning algorithm that splits the sample in partitioning variable with the strongest association with the response variable. The process continues until some stopping criteria are met. In the example I focus on conditional inference tree, which incorporates tree-structured regression models into conditional inference procedures. While growing a single tree is subject to small changes in the training data, random forests procedure is introduced to address this problem. The sources of diversity for random forests come from the random sampling and restricted set of input variables to be selected. Finally, I introduce R functions to perform model based recursive partitioning. This method incorporates recursive partitioning into conventional parametric model building.

  8. Visualizing Contour Trees within Histograms

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

    Many of the topological features of the isosurfaces of a scalar volume field can be compactly represented by its contour tree. Unfortunately, the contour trees of most real-world volume data sets are too complex to be visualized by dot-and-line diagrams. Therefore, we propose a new visualization...... that is suitable for large contour trees and efficiently conveys the topological structure of the most important isosurface components. This visualization is integrated into a histogram of the volume data; thus, it offers strictly more information than a traditional histogram. We present algorithms...... to automatically compute the graph layout and to calculate appropriate approximations of the contour tree and the surface area of the relevant isosurface components. The benefits of this new visualization are demonstrated with the help of several publicly available volume data sets....

  9. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

    2016-01-01

    We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille...... variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta...

  10. Generic physical protection logic trees

    International Nuclear Information System (INIS)

    Paulus, W.K.

    1981-10-01

    Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle

  11. Border trees of complex networks

    International Nuclear Information System (INIS)

    Villas Boas, Paulino R; Rodrigues, Francisco A; Travieso, Gonzalo; Fontoura Costa, Luciano da

    2008-01-01

    The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small-world properties of real networks were fundamental to stimulate more realistic models and to understand important dynamical processes related to network growth. However, the properties of the network borders (nodes with degree equal to 1), one of its most fragile parts, remained little investigated and understood. The border nodes may be involved in the evolution of structures such as geographical networks. Here we analyze the border trees of complex networks, which are defined as the subgraphs without cycles connected to the remainder of the network (containing cycles) and terminating into border nodes. In addition to describing an algorithm for identification of such tree subgraphs, we also consider how their topological properties can be quantified in terms of their depth and number of leaves. We investigate the properties of border trees for several theoretical models as well as real-world networks. Among the obtained results, we found that more than half of the nodes of some real-world networks belong to the border trees. A power-law with cut-off was observed for the distribution of the depth and number of leaves of the border trees. An analysis of the local role of the nodes in the border trees was also performed

  12. Generic physical protection logic trees

    Energy Technology Data Exchange (ETDEWEB)

    Paulus, W.K.

    1981-10-01

    Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle.

  13. Objective consensus from decision trees

    International Nuclear Information System (INIS)

    Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Pra, Alan Dal; Hundsberger, Thomas; Plasswilm, Ludwig

    2014-01-01

    Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties

  14. Objective consensus from decision trees.

    Science.gov (United States)

    Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Dal Pra, Alan; Hundsberger, Thomas; Plasswilm, Ludwig

    2014-12-05

    Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties.

  15. Longest common extensions in trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2016-01-01

    to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

  16. Longest Common Extensions in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

    2015-01-01

    to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

  17. Factors that influence Christmas tree sales

    Science.gov (United States)

    Thomas H. Pendleton; Lawrence D. Garrett

    1970-01-01

    An analysis of the metropolitan Christmas tree market in Winston-Salem, N. C., shows that to sell more trees, Christmas tree retailers should locate their lots on heavily traveled streets in business areas, have adequate parking facilities, advertise, and have attractive displays of trees. Retailers who follow these practices can expect to receive higher prices for...

  18. Critical wind speed at which trees break

    Science.gov (United States)

    Virot, E.; Ponomarenko, A.; Dehandschoewercker, É.; Quéré, D.; Clanet, C.

    2016-02-01

    Data from storms suggest that the critical wind speed at which trees break is constant (≃42 m /s ), regardless of tree characteristics. We question the physical origin of this observation both experimentally and theoretically. By combining Hooke's law, Griffith's criterion, and tree allometry, we show that the critical wind speed indeed hardly depends on the height, diameter, and elastic properties of trees.

  19. Field guide to red tree vole nests

    Science.gov (United States)

    Damon B. Lesmeister; James K. Swingle

    2017-01-01

    Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (≥80 years old) that are structurally complex, but are often...

  20. Mitered fractal trees: constructions and properties

    NARCIS (Netherlands)

    Verhoeff, T.; Verhoeff, K.; Bosch, R.; McKenna, D.; Sarhangi, R.

    2012-01-01

    Tree-like structures, that is, branching structures without cycles, are attractive for artful expression. Especially interesting are fractal trees, where each subtree is a scaled and possibly otherwise transformed version of the entire tree. Such trees can be rendered in 3D by using beams with a

  1. Critical wind speed at which trees break.

    Science.gov (United States)

    Virot, E; Ponomarenko, A; Dehandschoewercker, É; Quéré, D; Clanet, C

    2016-02-01

    Data from storms suggest that the critical wind speed at which trees break is constant (≃42m/s), regardless of tree characteristics. We question the physical origin of this observation both experimentally and theoretically. By combining Hooke's law, Griffith's criterion, and tree allometry, we show that the critical wind speed indeed hardly depends on the height, diameter, and elastic properties of trees.

  2. Microwave sensing of tree trunks

    Science.gov (United States)

    Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

    2015-04-01

    The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

  3. Colourings of (k-r,k-trees

    Directory of Open Access Journals (Sweden)

    M. Borowiecki

    2017-01-01

    Full Text Available Trees are generalized to a special kind of higher dimensional complexes known as \\((j,k\\-trees ([L. W. Beineke, R. E. Pippert, On the structure of \\((m,n\\-trees, Proc. 8th S-E Conf. Combinatorics, Graph Theory and Computing, 1977, 75-80], and which are a natural extension of \\(k\\-trees for \\(j=k-1\\. The aim of this paper is to study\\((k-r,k\\-trees ([H. P. Patil, Studies on \\(k\\-trees and some related topics, PhD Thesis, University of Warsaw, Poland, 1984], which are a generalization of \\(k\\-trees (or usual trees when \\(k=1\\. We obtain the chromatic polynomial of \\((k-r,k\\-trees and show that any two \\((k-r,k\\-trees of the same order are chromatically equivalent. However, if \\(r\

  4. A bicriterion Steiner tree problem on graph

    Directory of Open Access Journals (Sweden)

    Vujošević Mirko B.

    2003-01-01

    Full Text Available This paper presents a formulation of bicriterion Steiner tree problem which is stated as a task of finding a Steiner tree with maximal capacity and minimal length. It is considered as a lexicographic multicriteria problem. This means that the bottleneck Steiner tree problem is solved first. After that, the next optimization problem is stated as a classical minimums Steiner tree problem under the constraint on capacity of the tree. The paper also presents some computational experiments with the multicriteria problem.

  5. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

    Science.gov (United States)

    Leaché, Adam D; Banbury, Barbara L; Felsenstein, Joseph; de Oca, Adrián Nieto-Montes; Stamatakis, Alexandros

    2015-11-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the

  6. Utilization of nitrogen fixing trees

    Energy Technology Data Exchange (ETDEWEB)

    Brewbaker, J.L.; Beldt, R. van den; MacDicken, K.; Budowski, G.; Kass, D.C.L.; Russo, R.O.; Escalante, G.; Herrera, R.; Aranguren, J.; Arkcoll, D.B.; Doebereinger, J. (cord.)

    1983-01-01

    Six papers from the symposium are noted. Brewbaker, J.L., Beldt, R. van den, MacDicken, K. Fuelwood uses and properties of nitrogen-fixing trees, pp 193-204, (Refs. 15). Includes a list of 35 nitrogen-fixing trees of high fuelwood value. Budowski, G.; Kass, D.C.L.; Russo, R.O. Leguminous trees for shade, pp 205-222, (Refs. 68). Escalante, G., Herrera, R., Aranguren, J.; Nitrogen fixation in shade trees (Erythrina poeppigiana) in cocoa plantations in northern Venezuela, pp 223-230, (Refs. 13). Arkcoll, D.B.; Some leguminous trees providing useful fruits in the North of Brazil, pp 235-239, (Refs. 13). This paper deals with Parkia platycephala, Pentaclethra macroloba, Swartzia sp., Cassia leiandra, Hymenaea courbaril, dipteryz odorata, Inga edulis, I. macrophylla, and I. cinnamonea. Baggio, A.J.; Possibilities of the use of Gliricidia sepium in agroforestry systems in Brazil, pp 241-243; (Refs. 15). Seiffert, N.F.; Biological nitrogen and protein production of Leucaena cultivars grown to supplement the nutrition of ruminants, pp 245-249, (Refs. 14). Leucaena leucocephala cv. Peru, L. campina grande (L. leucocephala), and L. cunningham (L. leucocephalae) were promising for use as browse by beef cattle in central Brazil.

  7. Isoprene emission from Indian trees

    Science.gov (United States)

    Varshney, C. K.; Singh, Abhai Pratap

    2003-12-01

    Isoprene is the most dominant non-methane volatile organic compound (NMVOC) emitted by plants. NMVOCs play an important role in regulating the composition of atmospheric trace gases including global concentration of tropospheric ozone. Our present knowledge about NMVOCs emission is mainly from studies on temperate tree species. So far information on biogenic NMVOCs emission from tropical tree species is limited. In this study, isoprene emission rates from 40 tropical Indian tree species belonging to 33 genera and 17 families were measured for the first time using a dynamic flow through enclosure chamber technique. The isoprene emission rate from plants (30°C and PAR 1000 μmolm-2s-1) ranged from undetectable to 81.5 μg g-1 h-1 and values were found to be comparable with other studies on tropical tree species. Tree species screened for isoprene emission in the present study may be grouped into the four categories, proposed by [2001], namely, 18 species were negligible or BDL isoprene emitting (Morus alba Linn., which were earlier reported as BDL or non isoprene emitters in US [, 1998; , 2001] were found to be appreciably high isoprene emitters (0.61-21.60 μg g-1 h-1) in the present study.

  8. Automated Generation of Attack Trees

    DEFF Research Database (Denmark)

    Vigo, Roberto; Nielson, Flemming; Nielson, Hanne Riis

    2014-01-01

    Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error-prone and impractica......Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error......-prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...... are automatically inferred from a process algebraic specification in a syntax-directed fashion, encompassing a great many application domains and avoiding incurring systematically an exponential explosion. Moreover, we show how the standard propositional denotation of an attack tree can be used to phrase...

  9. Drawing Contour Trees in the Plane.

    Science.gov (United States)

    Heine, C; Schneider, D; Carr, Hamish; Scheuermann, G

    2011-11-01

    The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Applying known techniques to convey this information proves hard and sometimes even impossible. We present several adaptions of popular graph drawing approaches to the problem of contour tree drawing and evaluate them. We identify five esthetic criteria for drawing contour trees and present a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria. Our implementation is fast and effective for contour tree sizes usually used in interactive systems (around 100 branches) and also produces readable pictures for larger trees, as is shown for an 800 branch example.

  10. Totally optimal decision trees for Boolean functions

    KAUST Repository

    Chikalov, Igor

    2016-07-28

    We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters characterizing both time (in the worst- and average-case) and space complexity of decision trees, i.e., depth, total path length (average depth), and number of nodes. We have created tools based on extensions of dynamic programming to study totally optimal trees. These tools are applicable to both exact and approximate decision trees, and allow us to make multi-stage optimization of decision trees relative to different parameters and to count the number of optimal trees. Based on the experimental results we have formulated the following hypotheses (and subsequently proved): for almost all Boolean functions there exist totally optimal decision trees (i) relative to the depth and number of nodes, and (ii) relative to the depth and average depth.

  11. Integrated fault tree development environment

    International Nuclear Information System (INIS)

    Dixon, B.W.

    1986-01-01

    Probabilistic Risk Assessment (PRA) techniques are utilized in the nuclear industry to perform safety analyses of complex defense-in-depth systems. A major effort in PRA development is fault tree construction. The Integrated Fault Tree Environment (IFTREE) is an interactive, graphics-based tool for fault tree design. IFTREE provides integrated building, editing, and analysis features on a personal workstation. The design philosophy of IFTREE is presented, and the interface is described. IFTREE utilizes a unique rule-based solution algorithm founded in artificial intelligence (AI) techniques. The impact of the AI approach on the program design is stressed. IFTREE has been developed to handle the design and maintenance of full-size living PRAs and is currently in use

  12. Interpreting the universal phylogenetic tree

    Science.gov (United States)

    Woese, C. R.

    2000-01-01

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

  13. Columnar apple tree named 'Moonlight'

    OpenAIRE

    Tupý, J. (Jaroslav); Louda, O. (Otto); Zima, J. (Jan)

    2010-01-01

    A new and distinct Malus domestica (Borkh.) apple tree variety is provided which exhibits a columnar tree type, weakly vigorous compact growth, predominant bearing on spurs and V.sub.f-resistance against scab. The new variety yields late maturing, medium-sized, globose-conical to conical fruits having good storage quality. The fruit color is yellow-green to yellow with a partial red to orange blush. The fruits have a yellow-colored firm flesh that is crisp and juicy with a good sweet/sour bal...

  14. Interpreting CNNs via Decision Trees

    OpenAIRE

    Zhang, Quanshi; Yang, Yu; Wu, Ying Nian; Zhu, Song-Chun

    2018-01-01

    This paper presents a method to learn a decision tree to quantitatively explain the logic of each prediction of a pre-trained convolutional neural networks (CNNs). Our method boosts the following two aspects of network interpretability. 1) In the CNN, each filter in a high conv-layer must represent a specific object part, instead of describing mixed patterns without clear meanings. 2) People can explain each specific prediction made by the CNN at the semantic level using a decision tree, i.e....

  15. Usefulness of problem tree, objective tree and logical framework ...

    African Journals Online (AJOL)

    The discussion has led to the conclusion that higher learning institutions are not adequately preparing graduates to face the increasing labor market demands in terms of skills and competitiveness. Having outlined the roots of the problem through the problem tree, the researchers proposed potential strategies to handle the ...

  16. DLRS: gene tree evolution in light of a species tree.

    Science.gov (United States)

    Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

    2012-11-15

    PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

  17. Water Transport in Trees--An Artificial Laboratory Tree

    Science.gov (United States)

    Susman, K.; Razpet, N.; Cepic, M.

    2011-01-01

    Water transport in tall trees is an everyday phenomenon, seldom noticed and not completely understood even by scientists. As a topic of current research in plant physiology it has several advantages for presentation within school physics lectures: it is interdisciplinary and clearly shows the connection between physics and biology; the…

  18. Integrating cyber attacks within fault trees

    International Nuclear Information System (INIS)

    Nai Fovino, Igor; Masera, Marcelo; De Cian, Alessio

    2009-01-01

    In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.

  19. Edge-Disjoint Fibonacci Trees in Hypercube

    Directory of Open Access Journals (Sweden)

    Indhumathi Raman

    2014-01-01

    Full Text Available The Fibonacci tree is a rooted binary tree whose number of vertices admit a recursive definition similar to the Fibonacci numbers. In this paper, we prove that a hypercube of dimension h admits two edge-disjoint Fibonacci trees of height h, two edge-disjoint Fibonacci trees of height h-2, two edge-disjoint Fibonacci trees of height h-4 and so on, as subgraphs. The result shows that an algorithm with Fibonacci trees as underlying data structure can be implemented concurrently on a hypercube network with no communication latency.

  20. On Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    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.

  1. Human action analysis with randomized trees

    CERN Document Server

    Yu, Gang; Liu, Zicheng

    2014-01-01

    This book will provide a comprehensive overview on human action analysis with randomized trees. It will cover both the supervised random trees and the unsupervised random trees. When there are sufficient amount of labeled data available, supervised random trees provides a fast method for space-time interest point matching. When labeled data is minimal as in the case of example-based action search, unsupervised random trees is used to leverage the unlabelled data. We describe how the randomized trees can be used for action classification, action detection, action search, and action prediction.

  2. Integrating cyber attacks within fault trees

    Energy Technology Data Exchange (ETDEWEB)

    Nai Fovino, Igor [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy)], E-mail: igor.nai@jrc.it; Masera, Marcelo [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy); De Cian, Alessio [Department of Electrical Engineering, University di Genova, Genoa (Italy)

    2009-09-15

    In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.

  3. Recursive algorithms for phylogenetic tree counting.

    Science.gov (United States)

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

    2013-10-28

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

  4. A Metric on Phylogenetic Tree Shapes.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2011-06-01

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

  7. GumTree: Data reduction

    Energy Technology Data Exchange (ETDEWEB)

    Rayner, Hugh [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)]. E-mail: hrz@ansto.gov.au; Hathaway, Paul [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Hauser, Nick [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Fei, Yang [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Franceschini, Ferdi [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Lam, Tony [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    2006-11-15

    Access to software tools for interactive data reduction, visualisation and analysis during a neutron scattering experiment enables instrument users to make informed decisions regarding the direction and success of their experiment. ANSTO aims to enhance the experiment experience of its facility's users by integrating these data reduction tools with the instrument control interface for immediate feedback. GumTree is a software framework and application designed to support an Integrated Scientific Experimental Environment, for concurrent access to instrument control, data acquisition, visualisation and analysis software. The Data Reduction and Analysis (DRA) module is a component of the GumTree framework that allows users to perform data reduction, correction and basic analysis within GumTree while an experiment is running. It is highly integrated with GumTree, able to pull experiment data and metadata directly from the instrument control and data acquisition components. The DRA itself uses components common to all instruments at the facility, providing a consistent interface. It features familiar ISAW-based 1D and 2D plotting, an OpenGL-based 3D plotter and peak fitting performed by fityk. This paper covers the benefits of integration, the flexibility of the DRA module, ease of use for the interface and audit trail generation.

  8. Tree value conversion standards revisited

    Science.gov (United States)

    Paul S. DeBald; Martin E. Dale; Martin E. Dale

    1991-01-01

    Updated tree value conversion standards (TVCS) are presented for 12 important hardwood species of the oak-hickory forest. These updated standards-developed for each species by butt-log grade, merchantable height, and diameter at breast height-reflect the changes in lumber prices and in conversion costs which have occurred since 1976 when the original TVCS were...

  9. Induction of Ordinal Decision Trees

    NARCIS (Netherlands)

    J.C. Bioch (Cor); V. Popova (Viara)

    2003-01-01

    textabstractThis paper focuses on the problem of monotone decision trees from the point of view of the multicriteria decision aid methodology (MCDA). By taking into account the preferences of the decision maker, an attempt is made to bring closer similar research within machine learning and MCDA.

  10. Are there tides within trees?

    Science.gov (United States)

    Fisahn, Joachim

    2018-01-24

    Tree stem diameters and electrical stem potentials exhibit rhythmic variations with periodicities of 24-25 h. Under free-running conditions of constant light or darkness these rhythms were suggested to be mediated by the lunisolar gravitational force. To further unravel the regulation of tree stem diameter dilatations, many of the published time courses of diameter variations were re-evaluated in conjunction with the contemporaneous time courses of the lunisolar tidal acceleration. This was accomplished by application of the Etide program, which estimates, with high temporal resolution, local gravitational changes as a consequence of the diurnal variations of the lunisolar gravitational force due to the orbits and relative positions of Earth, Moon and Sun. In all instances investigated, it was evident that a synchronism exists between the times of the turning points of both the lunisolar tide and stem diameter variations when the direction of extension changes. This finding of synchrony documents that the lunisolar tide is a regulator of the tree stem diameter dilatations. Under the described experimental conditions, rhythms in tree stem diameter dilations and electrical stem potentials are controlled by the lunisolar gravitational acceleration. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Tree improvement and environmental forestry

    Science.gov (United States)

    Warren T. Doolittle

    1971-01-01

    I was invited to talk to you about some of the things tree improvement can do to help our forest environment. Now I do not claim to have a corner on the market for ideas that geneticists can use in our environment, and I know that a number of scholarly papers have been presented previously on this subject.

  12. Eucalyptus as a landscape tree

    Science.gov (United States)

    W. Douglas Hamilton

    1983-01-01

    Ninety-two species of Eucalyptus were evaluated at the University of California re- search station in San Jose. The purpose: to find acceptable new street and park trees. Growth rates and horticultural characteristics were noted. Forty-three species were studied in locations statewide to evaluate site adaptation and landscape usefulness; flooded, cold, dry, saline....

  13. A Distributed Spanning Tree Algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Sven Hauge

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two-way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well...

  14. Trees of Our National Forests.

    Science.gov (United States)

    Forest Service (USDA), Washington, DC.

    Presented is a description of the creation of the National Forests system, how trees grow, managing the National Forests, types of management systems, and managing for multiple use, including wildlife, water, recreation and other uses. Included are: (1) photographs; (2) line drawings of typical leaves, cones, flowers, and seeds; and (3)…

  15. The Trees that surround us

    Science.gov (United States)

    Costa, M. E. G.; Rodrigues, M. A. S.

    2012-04-01

    In our school the activities linked with sciences are developed in a partnership with other school subjects. Interdisciplinary projects are always valued from beginning to end of a project. It is common for teachers of different areas to work together in a Science project. Research of English written articles is very important not only for the development of our students' scientific literacy but also as a way of widening knowledge and a view on different perspectives of life instead of being limited to research of any articles in Portuguese language. In this study we are going to collect data about the predominant tree species in the region, especially the invasive trees from the acacia species, the native tree species and the commercial species. We are going to study the reasons for the appearance of each species and draw a chart of soil occupation in the council. This chart will also allow the study of the distribution and use of land for each tree species. This research work is the first stage for a contribution to warn the town council of the dangers of the invasive species to the future economy of the council.

  16. Wellhead and tree standards updated

    International Nuclear Information System (INIS)

    Dach, A.J. Jr.; Haeberle, T.

    1996-01-01

    Revisions in the API 6A, 17th Edition, have resolved a number of long-term problems and expanded its scope and coverage of wellhead and christmas tree equipment. The 17th Edition, Feb. 1, 1996, represents the state-of-the-art in international requirements for wellhead and christmas tree equipment. The design, materials, and quality control aspects of API 6A have all been improved with an emphasis on making the document more acceptable around the world. However, there are unresolved issues that raise many questions about the future direction of efforts aimed at international standardization of wellhead and christmas tree equipment. Unfortunately, these unresolved issues confuse both manufacturers and companies purchasing this equipment. This ultimately increases wellhead and christmas tree costs, so it is to everyone's advantage to resolve these issues. This article describes the significant revisions that are included in API 6A, 17th Edition. Also discussed are the regulatory, standardization, and customer acceptance issues that cloud the future of API 6A, 17th Edition

  17. The Tree of Life Project

    Science.gov (United States)

    Milbrath, Sherry

    2009-01-01

    Middle-school students are just beginning to recognize their place in the world. That is why this author believes it is important to incorporate their world into their art. In this article, the author discusses the "Tree of Life" project, which she developed for her students in order to make them aware of various environmental issues, and how to…

  18. GumTree: Data reduction

    International Nuclear Information System (INIS)

    Rayner, Hugh; Hathaway, Paul; Hauser, Nick; Fei, Yang; Franceschini, Ferdi; Lam, Tony

    2006-01-01

    Access to software tools for interactive data reduction, visualisation and analysis during a neutron scattering experiment enables instrument users to make informed decisions regarding the direction and success of their experiment. ANSTO aims to enhance the experiment experience of its facility's users by integrating these data reduction tools with the instrument control interface for immediate feedback. GumTree is a software framework and application designed to support an Integrated Scientific Experimental Environment, for concurrent access to instrument control, data acquisition, visualisation and analysis software. The Data Reduction and Analysis (DRA) module is a component of the GumTree framework that allows users to perform data reduction, correction and basic analysis within GumTree while an experiment is running. It is highly integrated with GumTree, able to pull experiment data and metadata directly from the instrument control and data acquisition components. The DRA itself uses components common to all instruments at the facility, providing a consistent interface. It features familiar ISAW-based 1D and 2D plotting, an OpenGL-based 3D plotter and peak fitting performed by fityk. This paper covers the benefits of integration, the flexibility of the DRA module, ease of use for the interface and audit trail generation

  19. Algorithms for Decision Tree Construction

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    The study of algorithms for decision tree construction was initiated in 1960s. The first algorithms are based on the separation heuristic [13, 31] that at each step tries dividing the set of objects as evenly as possible. Later Garey and Graham [28

  20. Can Children Read Evolutionary Trees?

    Science.gov (United States)

    Ainsworth, Shaaron; Saffer, Jessica

    2013-01-01

    Representations of the "tree of life" such as cladograms show the history of lineages and their relationships. They are increasingly found in formal and informal learning settings. Unfortunately, there is evidence that these representations can be challenging to interpret correctly. This study explored the question of whether children…

  1. Top tips from tree tops

    Science.gov (United States)

    Ornes, Stephen

    2018-04-01

    The ability of trees to cool by transporting water from their roots to the leaves has been known for centuries. But as Stephen Ornes discovers, the principles of transpiration are also inspiring innovative techniques to cool vehicles travelling at hypersonic speeds, where unwanted heat is a problem too

  2. A distributed spanning tree algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Svend Hauge

    1988-01-01

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well as comm...

  3. International Tree Ring Data Bank (ITRDB)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives. Data include raw treering measurements (most are...

  4. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sö ren; Jarząbek, Michał; Hadrich, Torsten; Michels, Dominik L.; Palubicki, Wojciech

    2017-01-01

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical

  5. EDITORIAL Development Linkages between Tree Breeding ...

    African Journals Online (AJOL)

    EDITORIAL Development Linkages between Tree Breeding Programmes and National/Regional Tree Seed Centres in Africa. ... Discovery and Innovation. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives.

  6. Systolic automata for VLSI on balanced trees

    Energy Technology Data Exchange (ETDEWEB)

    Culik, K Ii; Gruska, J; Salomaa, A

    1983-01-01

    Systolic tree automata with a binary (or, more generally, balanced) underlying tree are investigated. The main emphasis is on input conditions, decidability, and characterization of acceptable languages. 4 references.

  7. Representing Boolean Functions by Decision Trees

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms

  8. Computing Refined Buneman Trees in Cubic Time

    DEFF Research Database (Denmark)

    Brodal, G.S.; Fagerberg, R.; Östlin, A.

    2003-01-01

    Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence...... in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each...... proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our...

  9. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    ary search tree model (where stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results.

  10. Tree rings and radiocarbon calibration

    International Nuclear Information System (INIS)

    Barbetti, M.

    1999-01-01

    Only a few kinds of trees in Australia and Southeast Asia are known to have growth rings that are both distinct and annual. Those that do are therefore extremely important to climatic and isotope studies. In western Tasmania, extensive work with Huon pine (Lagarostrobos franklinii) has shown that many living trees are more than 1,000 years old, and that their ring widths are sensitive to temperature, rainfall and cloud cover (Buckley et al. 1997). At the Stanley River there is a forest of living (and recently felled) trees which we have sampled and measured. There are also thousands of subfossil Huon pine logs, buried at depths less than 5 metres in an area of floodplain extending over a distance of more than a kilometre with a width of tens of metres. Some of these logs have been buried for 50,000 years or more, but most of them belong to the period between 15,000 years and the present. In previous expeditions in the 1980s and 1990s, we excavated and sampled about 350 logs (Barbetti et al. 1995; Nanson et al. 1995). By measuring the ring-width patterns, and matching them between logs and living trees, we have constructed a tree-ring dated chronology from 571 BC to AD 1992. We have also built a 4254-ring floating chronology (placed by radiocarbon at ca. 3580 to 7830 years ago), and an earlier 1268-ring chronology (ca. 7,580 to 8,850 years ago). There are many individuals, or pairs of logs which match and together span several centuries, at 9,000 years ago and beyond

  11. A Durable Flash Memory Search Tree

    OpenAIRE

    Clay III, James; Wortman, Kevin

    2012-01-01

    We consider the task of optimizing the B-tree data structure, used extensively in operating systems and databases, for sustainable usage on multi-level flash memory. Empirical evidence shows that this new flash memory tree, or FM Tree, extends the operational lifespan of each block of flash memory by a factor of roughly 27 to 70 times, while still supporting logarithmic-time search tree operations.

  12. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

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

    2009-04-29

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

  13. Locating a tree in a phylogenetic network

    OpenAIRE

    van Iersel, Leo; Semple, Charles; Steel, Mike

    2010-01-01

    Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider t...

  14. The transposition distance for phylogenetic trees

    OpenAIRE

    Rossello, Francesc; Valiente, Gabriel

    2006-01-01

    The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this paper, we generalize the transposition distance from fully resolved to arbi...

  15. Animals and trees: food for thought

    Energy Technology Data Exchange (ETDEWEB)

    Openshaw, K.

    1979-01-01

    In many areas of Africa, combining tree-growing with animal rearing is advantageous, as the trees provide shade, animal fodder and timber for fuel and building, while grazing animals reduce the fire hazard from ground vegetation and improve soil fertility through droppings. Acacia albida, Prosopis cineraria, P. chilensis, leucaena leucocephala and Ailanthus excelsa are discussed as promising fodder trees, and an appendix is included with notes on 21 other trees for fodder or the production of medicines.

  16. The national tree-list layer

    Science.gov (United States)

    Stacy A. Drury; Jason M. Herynk

    2011-01-01

    The National Tree-List Layer (NTLL) project used LANDFIRE map products to produce the first national tree-list map layer that represents tree populations at stand and regional levels. The NTLL was produced in a short time frame to address the needs of Fire and Aviation Management for a map layer that could be used as input for simulating fire-caused tree mortality...

  17. On Tree-Constrained Matchings and Generalizations

    NARCIS (Netherlands)

    S. Canzar (Stefan); K. Elbassioni; G.W. Klau (Gunnar); J. Mestre

    2011-01-01

    htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that

  18. Measuring and analyzing urban tree cover

    Science.gov (United States)

    David J. Nowak; Rowan A. Rowntree; E. Gregory McPherson; Susan M. Sisinni; Esther R. Kirkmann; Jack C. Stevens

    1996-01-01

    Measurement of city tree cover can aid in urban vegetation planning, management, and research by revealing characteristics of vegetation across a city. Urban tree cover in the United States ranges from 0.4% in Lancaster, California, to 55% in Baton Rouge, Louisiana. Two important factors that affect the amount of urban tree cover are the natural environment and land...

  19. Understanding the challenges of municipal tree planting

    Science.gov (United States)

    E.G. McPherson; R. Young

    2010-01-01

    Nine of the twelve largest cities in the U.S. have mayoral tree planting initiatives (TPIs), with pledges to plant nearly 20 million trees. Although executive-level support for trees has never been this widespread, many wonder if this support will endure as administrations change and budgets tighten. In an effort to share lessons learned from successes and setbacks, a...

  20. THE CONTRIBUTION OF AGROFORESTRY TREE PRODUCTS TO ...

    African Journals Online (AJOL)

    philiph

    contribution of agro-forestry tree products to the livelihood of rural farmers was high and accounted for ... systems in which trees are grown with ... livelihood of farmers in rural areas and .... pulp, the seed are boiled in water and dried .... treatment of fracture/dislocation of bones. Some agroforestry trees that provides the rural ...

  1. Sampling the quality of hardwood trees

    Science.gov (United States)

    Adrian M. Gilbert

    1959-01-01

    Anyone acquainted with the conversion of hardwood trees into wood products knows that timber has a wide range in quality. Some trees will yield better products than others. So, in addition to rate of growth and size, tree values are affected by the quality of products yielded.

  2. Locating a tree in a phylogenetic network

    NARCIS (Netherlands)

    Iersel, van L.J.J.; Semple, C.; Steel, M.A.

    2010-01-01

    Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster

  3. Finding small equivalent decision trees is hard

    NARCIS (Netherlands)

    Zantema, H.; Bodlaender, H.L.

    2000-01-01

    Two decision trees are called decision equivalent if they represent the same function, i.e., they yield the same result for every possible input. We prove that given a decision tree and a number, to decide if there is a decision equivalent decision tree of size at most that number is NPcomplete. As

  4. Which trees should be removed in thinning?

    Directory of Open Access Journals (Sweden)

    Timo Pukkala

    2015-12-01

    Full Text Available Background: In economically optimal management, trees that are removed in a thinning treatment should be selected on the basis of their value, relative value increment and the effect of removal on the growth of remaining trees. Large valuable trees with decreased value increment should be removed, especially when they overtop smaller trees. Methods: This study optimized the tree selection rule in the thinning treatments of continuous cover management when the aim is to maximize the profitability of forest management. The weights of three criteria (stem value, relative value increment and effect of removal on the competition of remaining trees were optimized together with thinning intervals. Results and conclusions: The results confirmed the hypothesis that optimal thinning involves removing predominantly large trees. Increasing stumpage value, decreasing relative value increment, and increasing competitive influence increased the likelihood that removal is optimal decision. However, if the spatial distribution of trees is irregular, it is optimal to leave large trees in sparse places and remove somewhat smaller trees from dense places. However, the benefit of optimal thinning, as compared to diameter limit cutting is not usually large in pure one-species stands. On the contrary, removing the smallest trees from the stand may lead to significant (30–40 % reductions in the net present value of harvest incomes. Keywords: Continuous cover forestry, Tree selection, High thinning, Optimal management, Spatial distribution, Spatial growth model

  5. Aspects of insertion in random trees

    NARCIS (Netherlands)

    Bagchi, Arunabha; Reingold, E.M.

    1982-01-01

    A method formulated by Yao and used by Brown has yielded bounds on the fraction of nodes with specified properties in trees bult by a sequence of random internal nodes in a random tree built by binary search and insertion, and show that in such a tree about bounds better than those now known. We

  6. Coalescent methods for estimating phylogenetic trees.

    Science.gov (United States)

    Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

    2009-10-01

    We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

  7. Evaluating realized genetic gains from tree improvement.

    Science.gov (United States)

    J.B. St. Clair

    1993-01-01

    Tree improvement has become an essential part of the management of forest lands for wood production, and predicting yields and realized gains from forests planted with genetically-improved trees will become increasingly important. This paper discusses concepts of tree improvement and genetic gain important to growth and yield modeling, and reviews previous studies of...

  8. A practical alternative to single tree selection?

    Science.gov (United States)

    Gary W. Miller; H. Clay Smith

    1993-01-01

    When landowners want to develop and maintain an uneven-aged tree structure in eastern hardwood stands, single-tree selection often is suggested as the only advisable, long-term partial regeneration harvest method. Single-tree selection is preferred because it provides a means for improving quality and controlling stocking of the residual stand necessary for sustained...

  9. Do you believe in palm trees?

    Science.gov (United States)

    Kevin T. Smith

    2013-01-01

    Palms are real, but are they really trees? The answer depends on definitions. As usually tall, peremrial plants with roots, stems, and leaves, palms seem to qualify. Palms should also qualify because arborists care for them, and arborists care for trees, right? My introduction to botany class defined trees as plants that produce wood. Unraveling the question of whether...

  10. Carbon dynamics in trees: feast or famine?

    Science.gov (United States)

    Anna Sala; David R. Woodruff; Fredrick C. Meinzer

    2012-01-01

    Research on the degree to which carbon (C) availability limits growth in trees, as well as recent trends in climate change and concurrent increases in drought related tree mortality, have led to a renewed focus on the physiological mechanisms associated with tree growth responses to current and future climate. This has led to some dispute over the role of stored...

  11. Shedding light on tree growth : ring analysis of juvenile tropical trees

    NARCIS (Netherlands)

    Soliz Gamboa, C.C.

    2010-01-01

    In the understory of tropical forests light is believed to be the main limiting growth factor for the newly established trees. Trees growing in shade of the understory may experience periods of slow radial growth. It is expected that gaps created by tree or branch fall will provoke tree growth

  12. Per tree estimates with n-tree distance sampling: an application to increment core data

    Science.gov (United States)

    Thomas B. Lynch; Robert F. Wittwer

    2002-01-01

    Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...

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

    DEFF Research Database (Denmark)

    Feragen, Aasa; Owen, Megan; Petersen, Jens

    2013-01-01

    parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than...

  14. Monitoring Million Trees LA: Tree performance during the early years and future benefits

    Science.gov (United States)

    E. Gregory McPherson

    2014-01-01

    Million Trees LA (MTLA) is one of several large-scale mayoral tree planting initiatives striving to create more livable cities through urban forestry. This study combined field sampling of tree survival and growth with numerical modeling of future benefits to assess performance of MTLA plantings. From 2006 to 2010 MTLA planted a diverse mix of 91,786 trees....

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

    Science.gov (United States)

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

    2008-07-01

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

  16. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

    OpenAIRE

    Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

    2009-01-01

    Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor in...

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

    Science.gov (United States)

    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

  18. Navigation and Tree Mapping in Orchards

    DEFF Research Database (Denmark)

    Jæger-Hansen, Claes Lund; Griepentrog, Hans W.; Andersen, Jens Christian

    In this paper an algorithm for estimating tree positions is presented. The sensors used for the algorithm is GNSS and LIDAR, and data is collected in an orchard with grapefruit trees while driving along the rows. The positions of the trees are estimated using ellipse fitting on point clouds....... The average accuracy for the center point estimation is 0.2 m in the along track direction and 0.35 m in the across track direction. The goal of the tree mapping algorithm is create a database of individual trees, and be the basis for creation of a graph map that can be used for mission planning...

  19. Computer aided construction of fault tree

    International Nuclear Information System (INIS)

    Kovacs, Z.

    1982-01-01

    Computer code CAT for the automatic construction of the fault tree is briefly described. Code CAT makes possible simple modelling of components using decision tables, it accelerates the fault tree construction process, constructs fault trees of different complexity, and is capable of harmonized co-operation with programs PREPandKITT 1,2 for fault tree analysis. The efficiency of program CAT and thus the accuracy and completeness of fault trees constructed significantly depends on the compilation and sophistication of decision tables. Currently, program CAT is used in co-operation with programs PREPandKITT 1,2 in reliability analyses of nuclear power plant systems. (B.S.)

  20. Air pollution and tree growth

    Energy Technology Data Exchange (ETDEWEB)

    Scurfield, G

    1960-01-01

    The problem of air pollution is reviewed with emphasis on its origin and its effects on trees and shrubs. These effects are described from two points of view: the effects of general air pollution, and also the effects of specific pollutants. The considerable mixing, dilution and interaction that pollutants undergo in the air often renders it exceedingly difficult to assign pollution damage to any specific chemical or physical entity. Moreover, it is often impossible to assign responsibility for damage to any particular source. The constituents of general air pollution may be subdivided into those potentially incapable, and those potentially capable, of entering the plant either through the leaf stomata or indirectly by way of the soil. Specific pollutants cause damage directly, as well as indirectly from the chemical reactions that occur in the polluted atmosphere. Sulfur dioxide is discussed in detail in relation to tree and shrub damage, with numerous examples of plant injuries.