WorldWideScience

Sample records for hierarchy additional annotation

  1. Additional symmetries of supersymmetric KP hierarchies

    International Nuclear Information System (INIS)

    Stanciu, S.

    1994-01-01

    We investigate the additional symmetries of several supersymmetric KP hierarchies: the SKP hierarchy of Manin and Radul, the SKP 2 hierarchy, and the Jacobian SKP hierarchy. In all three cases we find that the algebra of symmetries is isomorphic to the algebra of superdifferential operators, or equivalently SW 1+∞ . These results seem to suggest that despite their realization depending on the dynamics, the additional symmetries are kinematical in nature. (orig.)

  2. Additional symmetries of supersymmetric KP hierarchies

    International Nuclear Information System (INIS)

    Stanciu, S.

    1993-09-01

    We investigate the additional symmetries of several supersymmetric KP hierarchies: The SKP hierarchy of Manin and Radul, the SKP 2 hierarchy, and the Jacobian SKP hierarchy. The main technical tool is the supersymmetric generalisation of a map originally due to Radul between the Lie algebra of superdifferential operators and the Lie algebra of vector fields on the space of supersymmetric Lax operators. In the case of the Manin-Radul SKP hierarchy we identify additional symmetries which form an algebra isomorphic to a subalgebra of superdifferential operators; whereas in the case of the Jacobian SKP, the (additional) symmetries are identified with the algebra itself. (orig.)

  3. Sato's Baecklund transformations, additional symmetries and ASvM formula for the discrete KP hierarchy

    International Nuclear Information System (INIS)

    Liu Shaowei; Cheng Yi

    2010-01-01

    Two kinds of symmetries, Sato's Baecklund transformations and additional symmetries, for the discrete KP (dKP) hierarchy are introduced, and the ASvM formula which demonstrates the equivalence of these two kinds of symmetries is obtained. In this process the Fay identity and the difference Fay identity of the dKP hierarchy are introduced and the ASvM formula in the form of tau function is calculated.

  4. Remarks on the additional symmetries and W-constraints in the generalized KdV hierarchy

    International Nuclear Information System (INIS)

    Panda, S.; Roy, S.

    1992-07-01

    Additional symmetries of the p-reduced KP hierarchy are generated by the Lax operator L and another operator M, satisfying res(M n L m+n/p ) = 0 for 1 ≤n≤p - 1 and m ≥ -1 with the condition that γL/γt kp = 0,k = 1,2,.... We show explicitly that the generators of these additional symmetries satisfy a closed and consistent W-algebra only when we impose the extra condition that γM/γt tk = 0. (author). 32 refs

  5. Expressed Peptide Tags: An additional layer of data for genome annotation

    Energy Technology Data Exchange (ETDEWEB)

    Savidor, Alon [ORNL; Donahoo, Ryan S [ORNL; Hurtado-Gonzales, Oscar [University of Tennessee, Knoxville (UTK); Verberkmoes, Nathan C [ORNL; Shah, Manesh B [ORNL; Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL

    2006-01-01

    While genome sequencing is becoming ever more routine, genome annotation remains a challenging process. Identification of the coding sequences within the genomic milieu presents a tremendous challenge, especially for eukaryotes with their complex gene architectures. Here we present a method to assist the annotation process through the use of proteomic data and bioinformatics. Mass spectra of digested protein preparations of the organism of interest were acquired and searched against a protein database created by a six frame translation of the genome. The identified peptides were mapped back to the genome, compared to the current annotation, and then categorized as supporting or extending the current genome annotation. We named the classified peptides Expressed Peptide Tags (EPTs). The well annotated bacterium Rhodopseudomonas palustris was used as a control for the method and showed high degree of correlation between EPT mapping and the current annotation, with 86% of the EPTs confirming existing gene calls and less than 1% of the EPTs expanding on the current annotation. The eukaryotic plant pathogens Phytophthora ramorum and Phytophthora sojae, whose genomes have been recently sequenced and are much less well annotated, were also subjected to this method. A series of algorithmic steps were taken to increase the confidence of EPT identification for these organisms, including generation of smaller sub-databases to be searched against, and definition of EPT criteria that accommodates the more complex eukaryotic gene architecture. As expected, the analysis of the Phytophthora species showed less correlation between EPT mapping and their current annotation. While ~77% of Phytophthora EPTs supported the current annotation, a portion of them (7.2% and 12.6% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms.

  6. Functional annotation of hierarchical modularity.

    Directory of Open Access Journals (Sweden)

    Kanchana Padmanabhan

    Full Text Available In biological networks of molecular interactions in a cell, network motifs that are biologically relevant are also functionally coherent, or form functional modules. These functionally coherent modules combine in a hierarchical manner into larger, less cohesive subsystems, thus revealing one of the essential design principles of system-level cellular organization and function-hierarchical modularity. Arguably, hierarchical modularity has not been explicitly taken into consideration by most, if not all, functional annotation systems. As a result, the existing methods would often fail to assign a statistically significant functional coherence score to biologically relevant molecular machines. We developed a methodology for hierarchical functional annotation. Given the hierarchical taxonomy of functional concepts (e.g., Gene Ontology and the association of individual genes or proteins with these concepts (e.g., GO terms, our method will assign a Hierarchical Modularity Score (HMS to each node in the hierarchy of functional modules; the HMS score and its p-value measure functional coherence of each module in the hierarchy. While existing methods annotate each module with a set of "enriched" functional terms in a bag of genes, our complementary method provides the hierarchical functional annotation of the modules and their hierarchically organized components. A hierarchical organization of functional modules often comes as a bi-product of cluster analysis of gene expression data or protein interaction data. Otherwise, our method will automatically build such a hierarchy by directly incorporating the functional taxonomy information into the hierarchy search process and by allowing multi-functional genes to be part of more than one component in the hierarchy. In addition, its underlying HMS scoring metric ensures that functional specificity of the terms across different levels of the hierarchical taxonomy is properly treated. We have evaluated our

  7. Pharmaceutical supply chain risk assessment in Iran using analytic hierarchy process (AHP) and simple additive weighting (SAW) methods.

    Science.gov (United States)

    Jaberidoost, Mona; Olfat, Laya; Hosseini, Alireza; Kebriaeezadeh, Abbas; Abdollahi, Mohammad; Alaeddini, Mahdi; Dinarvand, Rassoul

    2015-01-01

    Pharmaceutical supply chain is a significant component of the health system in supplying medicines, particularly in countries where main drugs are provided by local pharmaceutical companies. No previous studies exist assessing risks and disruptions in pharmaceutical companies while assessing the pharmaceutical supply chain. Any risks affecting the pharmaceutical companies could disrupt supply medicines and health system efficiency. The goal of this study was the risk assessment in pharmaceutical industry in Iran considering process's priority, hazard and probability of risks. The study was carried out in 4 phases; risk identification through literature review, risk identification in Iranian pharmaceutical companies through interview with experts, risk analysis through a questionnaire and consultation with experts using group analytic hierarchy process (AHP) method and rating scale (RS) and risk evaluation of simple additive weighting (SAW) method. In total, 86 main risks were identified in the pharmaceutical supply chain with perspective of pharmaceutical companies classified in 11 classes. The majority of risks described in this study were related to the financial and economic category. Also financial management was found to be the most important factor for consideration. Although pharmaceutical industry and supply chain were affected by current political conditions in Iran during the study time, but half of total risks in the pharmaceutical supply chain were found to be internal risks which could be fixed by companies, internally. Likewise, political status and related risks forced companies to focus more on financial and supply management resulting in less attention to quality management.

  8. Extracting Tag Hierarchies

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the “flat” organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search

  9. Extracting tag hierarchies.

    Directory of Open Access Journals (Sweden)

    Gergely Tibély

    Full Text Available Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of

  10. Extracting tag hierarchies.

    Science.gov (United States)

    Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

    2013-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the "flat" organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search. Moreover

  11. Additions to the annotated list of marine alien biota in the Mediterranean with special emphasis on Foraminifera and Parasites

    Directory of Open Access Journals (Sweden)

    A. ZENETOS

    2008-05-01

    Full Text Available The present work is an update of the annotated list (ZENETOS et al., 2006 based on literature up to April 2008. Emphasis is given to ecofunctional/taxonomic groups poorly addressed in the annotated list, such as the foraminiferan and parasites, while macrophytes are critically reviewed following the CIESM Atlas (VERLAQUE et al., in press. Moreover, in this update the bio-geographic area addressed includes the Sea of Marmara. The update yields a further 175 alien species in the Mediterranean bringing the total to 903. As evidenced by recent findings, more and more previously known ‘casual’ aliens, are becoming established. Approximately 100 more species have become well established in the region, raising the number of established species to 496 versus 385 until 2005. In the period from January 2006 to April 2008 more than 80 published papers have resulted in the recording of 94 new aliens, which is interpreted as a new introduction every 9 days, a rate beyond the worst scenario.

  12. Diverse Image Annotation

    KAUST Repository

    Wu, Baoyuan

    2017-11-09

    In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

  13. Diverse Image Annotation

    KAUST Repository

    Wu, Baoyuan; Jia, Fan; Liu, Wei; Ghanem, Bernard

    2017-01-01

    In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.

  14. Improved hybridization of Fuzzy Analytic Hierarchy Process (FAHP) algorithm with Fuzzy Multiple Attribute Decision Making - Simple Additive Weighting (FMADM-SAW)

    Science.gov (United States)

    Zaiwani, B. E.; Zarlis, M.; Efendi, S.

    2018-03-01

    In this research, the improvement of hybridization algorithm of Fuzzy Analytic Hierarchy Process (FAHP) with Fuzzy Technique for Order Preference by Similarity to Ideal Solution (FTOPSIS) in selecting the best bank chief inspector based on several qualitative and quantitative criteria with various priorities. To improve the performance of the above research, FAHP algorithm hybridization with Fuzzy Multiple Attribute Decision Making - Simple Additive Weighting (FMADM-SAW) algorithm was adopted, which applied FAHP algorithm to the weighting process and SAW for the ranking process to determine the promotion of employee at a government institution. The result of improvement of the average value of Efficiency Rate (ER) is 85.24%, which means that this research has succeeded in improving the previous research that is equal to 77.82%. Keywords: Ranking and Selection, Fuzzy AHP, Fuzzy TOPSIS, FMADM-SAW.

  15. Extension of noncommutative soliton hierarchies

    International Nuclear Information System (INIS)

    Dimakis, Aristophanes; Mueller-Hoissen, Folkert

    2004-01-01

    A linear system, which generates a Moyal-deformed two-dimensional soliton equation as an integrability condition, can be extended to a three-dimensional linear system, treating the deformation parameter as an additional coordinate. The supplementary integrability conditions result in a first-order differential equation with respect to the deformation parameter, the flow of which commutes with the flow of the deformed soliton equation. In this way, a deformed soliton hierarchy can be extended to a bigger hierarchy by including the corresponding deformation equations. We prove the extended hierarchy properties for the deformed AKNS hierarchy, and specialize to the cases of deformed NLS, KdV and mKdV hierarchies. Corresponding results are also obtained for the deformed KP hierarchy. A deformation equation determines a kind of Seiberg-Witten map from classical solutions to solutions of the respective 'noncommutative' deformed equation

  16. Participatory hierarchies

    DEFF Research Database (Denmark)

    Kristiansen, Marianne; Bloch-Poulsen, Jørgen

    2016-01-01

    projects works in the interface between communication and organisation. Third, the methodological purpose is to show that handling of these participatory hierarchies ought to become a goal in OAR projects to be included along with producing practical and theoretical results. The article argues...

  17. Annotation-based feature extraction from sets of SBML models.

    Science.gov (United States)

    Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron

    2015-01-01

    Model repositories such as BioModels Database provide computational models of biological systems for the scientific community. These models contain rich semantic annotations that link model entities to concepts in well-established bio-ontologies such as Gene Ontology. Consequently, thematically similar models are likely to share similar annotations. Based on this assumption, we argue that semantic annotations are a suitable tool to characterize sets of models. These characteristics improve model classification, allow to identify additional features for model retrieval tasks, and enable the comparison of sets of models. In this paper we discuss four methods for annotation-based feature extraction from model sets. We tested all methods on sets of models in SBML format which were composed from BioModels Database. To characterize each of these sets, we analyzed and extracted concepts from three frequently used ontologies, namely Gene Ontology, ChEBI and SBO. We find that three out of the methods are suitable to determine characteristic features for arbitrary sets of models: The selected features vary depending on the underlying model set, and they are also specific to the chosen model set. We show that the identified features map on concepts that are higher up in the hierarchy of the ontologies than the concepts used for model annotations. Our analysis also reveals that the information content of concepts in ontologies and their usage for model annotation do not correlate. Annotation-based feature extraction enables the comparison of model sets, as opposed to existing methods for model-to-keyword comparison, or model-to-model comparison.

  18. A note on the dispersionless BKP hierarchy

    International Nuclear Information System (INIS)

    Chen, Y.-T.; Tu, M.-H.

    2006-01-01

    We study the integrable hierarchy underlying topological Landau-Ginzburg models of D-type proposed by Takasaki. Since this integrable hierarchy contains the dBKP hierarchy as a sub-hierarchy, we refer it to the extended dBKP (EdBKP) hierarchy. We give a dressing formulation to the EdBKP hierarchy and investigate additional symmetries associated with the solution space of the hierarchy. We obtain hodograph solutions of its finite-dimensional reductions via Riemann-Hilbert problem (twistor construction) and derive Baecklund transformations of the (2 + 1)-dimensional dBKP equation from additional flows. Finally, the modified partner of the dBKP hierarchy is also established through a Miura transformation

  19. New integrable lattice hierarchies

    International Nuclear Information System (INIS)

    Pickering, Andrew; Zhu Zuonong

    2006-01-01

    In this Letter we give a new integrable four-field lattice hierarchy, associated to a new discrete spectral problem. We obtain our hierarchy as the compatibility condition of this spectral problem and an associated equation, constructed herein, for the time-evolution of eigenfunctions. We consider reductions of our hierarchy, which also of course admit discrete zero curvature representations, in detail. We find that our hierarchy includes many well-known integrable hierarchies as special cases, including the Toda lattice hierarchy, the modified Toda lattice hierarchy, the relativistic Toda lattice hierarchy, and the Volterra lattice hierarchy. We also obtain here a new integrable two-field lattice hierarchy, to which we give the name of Suris lattice hierarchy, since the first equation of this hierarchy has previously been given by Suris. The Hamiltonian structure of the Suris lattice hierarchy is obtained by means of a trace identity formula

  20. Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

    Science.gov (United States)

    Zhao, Yingwen; Fu, Guangyuan; Wang, Jun; Guo, Maozu; Yu, Guoxian

    2018-02-23

    Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. Addition by subtraction in coupled-cluster theory: a reconsideration of the CC and CI interface and the nCC hierarchy.

    Science.gov (United States)

    Bartlett, Rodney J; Musiał, Monika

    2006-11-28

    The nCC hierarchy of coupled-cluster approximations, where n guarantees exactness for n electrons and all products of n electrons are derived and applied to several illustrative problems. The condition of exactness for n=2 defines nCCSD=2CC, with nCCSDT=3CC and nCCSDTQ=4CC being exact for three and four electrons. To achieve this, the minimum number of diagrams is evaluated, which is less than in the corresponding CC model. For all practical purposes, nCC is also the proper definition of a size-extensive CI. 2CC is also an orbitally invariant coupled electron pair approximation. The numerical results of nCC are close to those for the full CC variant, and in some cases are closer to the full CI reference result. As 2CC is exact for separated electron pairs, it is the natural zeroth-order approximation for the correlation problem in molecules with other effects introduced as these units start to interact. The nCC hierarchy of approximations has all the attractive features of CC including its size extensivity, orbital invariance, and orbital insensitivity, but in a conceptually appealing form suited to bond breaking, while being computationally less demanding. Excited states from the equation of motion (EOM-2CC) are also reported, which show results frequently approaching those of EOM-CCSDT.

  2. Visualising large hierarchies with Flextree

    Science.gov (United States)

    Song, Hongzhi; Curran, Edwin P.; Sterritt, Roy

    2003-05-01

    One of the main tasks in Information Visualisation research is creating visual tools to facilitate human understanding of large and complex information spaces. Hierarchies, being a good mechanism in organising such information, are ubiquitous. Although much research effort has been spent on finding useful representations for hierarchies, visualising large hierarchies is still a difficult topic. One of the difficulties is how to show both tructure and node content information in one view. Another is how to achieve multiple foci in a focus+context visualisation. This paper describes a novel hierarchy visualisation technique called FlexTree to address these problems. It contains some important features that have not been exploited so far. In this visualisation, a profile or contour unique to the hierarchy being visualised can be gained in a histogram-like layout. A normalised view of a common attribute of all nodes can be acquired, and selection of this attribute is controllable by the user. Multiple foci are consistently accessible within a global context through interaction. Furthermore it can handle a large hierarchy that contains several thousand nodes in a PC environment. In addition results from an informal evaluation are also presented.

  3. Evaluating, Comparing, and Interpreting Protein Domain Hierarchies

    Science.gov (United States)

    2014-01-01

    Abstract Arranging protein domain sequences hierarchically into evolutionarily divergent subgroups is important for investigating evolutionary history, for speeding up web-based similarity searches, for identifying sequence determinants of protein function, and for genome annotation. However, whether or not a particular hierarchy is optimal is often unclear, and independently constructed hierarchies for the same domain can often differ significantly. This article describes methods for statistically evaluating specific aspects of a hierarchy, for probing the criteria underlying its construction and for direct comparisons between hierarchies. Information theoretical notions are used to quantify the contributions of specific hierarchical features to the underlying statistical model. Such features include subhierarchies, sequence subgroups, individual sequences, and subgroup-associated signature patterns. Underlying properties are graphically displayed in plots of each specific feature's contributions, in heat maps of pattern residue conservation, in “contrast alignments,” and through cross-mapping of subgroups between hierarchies. Together, these approaches provide a deeper understanding of protein domain functional divergence, reveal uncertainties caused by inconsistent patterns of sequence conservation, and help resolve conflicts between competing hierarchies. PMID:24559108

  4. Annotated bibliography

    International Nuclear Information System (INIS)

    1997-08-01

    Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

  5. On the ILW hierarchy

    International Nuclear Information System (INIS)

    Tutiya, Y.; Satsuma, J.

    2003-01-01

    In this Letter, we present a new hierarchy which includes the intermediate long wave (ILW) equation at the lowest order. This hierarchy is thought to be a novel reduction of the 1st modified KP type hierarchy. The framework of our investigation is Sato theory

  6. BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments.

    Science.gov (United States)

    López-Fernández, H; Reboiro-Jato, M; Glez-Peña, D; Aparicio, F; Gachet, D; Buenaga, M; Fdez-Riverola, F

    2013-07-01

    Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the software platform includes (i) a rich client enabling users to annotate multiple documents in a user friendly environment, (ii) an extensible and embeddable annotation meta-server allowing for the annotation of documents with local or remote vocabularies and (iii) a simple client/server protocol which facilitates the use of our meta-server from any other third-party application. In addition, BioAnnote implements a powerful scripting engine able to perform advanced batch annotations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  7. The Evolutionary Origins of Hierarchy.

    Science.gov (United States)

    Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

    2016-06-01

    Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  8. The Evolutionary Origins of Hierarchy

    Science.gov (United States)

    Huizinga, Joost; Clune, Jeff

    2016-01-01

    Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force–the cost of connections–promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

  9. The Evolutionary Origins of Hierarchy.

    Directory of Open Access Journals (Sweden)

    Henok Mengistu

    2016-06-01

    Full Text Available Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments. Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

  10. The multicomponent 2D Toda hierarchy: dispersionless limit

    International Nuclear Information System (INIS)

    Mañas, Manuel; Alonso, Luis Martínez

    2009-01-01

    The factorization problem of the multi-component 2D Toda hierarchy is used to analyze the dispersionless limit of this hierarchy. A dispersive version of the Whitham hierarchy defined in terms of scalar Lax and Orlov–Schulman operators is introduced and the corresponding additional symmetries and string equations are discussed. Then, it is shown how KP and Toda pictures of the dispersionless Whitham hierarchy emerge in the dispersionless limit. Moreover, the additional symmetries and string equations for the dispersive Whitham hierarchy are studied in this limit

  11. Higher-Order Hierarchies

    DEFF Research Database (Denmark)

    Ernst, Erik

    2003-01-01

    This paper introduces the notion of higher-order inheritance hierarchies. They are useful because they provide well-known benefits of object-orientation at the level of entire hierarchies-benefits which are not available with current approaches. Three facets must be adressed: First, it must be po...

  12. The Analytical Hierarchy Process

    DEFF Research Database (Denmark)

    Barfod, Michael Bruhn

    2007-01-01

    The technical note gathers the theory behind the Analytical Hierarchy Process (AHP) and present its advantages and disadvantages in practical use.......The technical note gathers the theory behind the Analytical Hierarchy Process (AHP) and present its advantages and disadvantages in practical use....

  13. Why hierarchies thrive.

    Science.gov (United States)

    Leavitt, Harold J

    2003-03-01

    Hardly anyone has a good word to say about hierarchies. Academics, consultants, and management gurus regularly forecast their imminent replacement because hierarchies--even when populated by considerate and intelligent people--can be cruel and stupid. They routinely transform motivated and loyal employees into disaffected Dilberts. It's no wonder that we continue to search for more humane and productive alternatives to them. Yet the intensity with which we struggle against hierarchies only serves to highlight their durability. Hierarchy, it seems, may be intrinsic not only to the natural world but also to our own natures. In this article, organizational behavior expert Harold J. Leavitt presents neither a defense of human hierarchies nor another attack on them. Instead, he offers a reality check, a reminder that hierarchy remains the basic structure of most, if not all, large, ongoing human organizations. That's because although they are often depicted as being out of date, hierarchies have proved to be extraordinarily adaptive. Over the past 50 years, for example, they have co-opted the three major managerial movements--human relations, analytic management, and communities of practice. Hierarchies also persist because they deliver real practical and psychological value, and they fulfill our deep need for order and security. Despite the good they may do, hierarchies are inevitably authoritarian. That authoritarianism shows up in all kinds of ways and influences everything in organizations, particularly communication. In multilevel organizations, for instance, messages get distorted as they travel up and down the ladder of command. Self-protection and self-interest weigh in, and relevant information is lost as messages make stops along the route. Sensitive leaders take steps to make speaking the truth as painless as possible. But it never is in organizations, because authoritarianism is an immutable element of hierarchy.

  14. Neural basis of social status hierarchy across species.

    Science.gov (United States)

    Chiao, Joan Y

    2010-12-01

    Social status hierarchy is a ubiquitous principle of social organization across the animal kingdom. Recent findings in social neuroscience reveal distinct neural networks associated with the recognition and experience of social hierarchy in humans, as well as modulation of these networks by personality and culture. Additionally, allelic variation in the serotonin transporter gene is associated with prevalence of social hierarchy across species and cultures, suggesting the importance of the study of genetic factors underlying social hierarchy. Future studies are needed to determine how genetic and environmental factors shape neural systems involved in the production and maintenance of social hierarchy across ontogeny and phylogeny. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. Pipeline to upgrade the genome annotations

    Directory of Open Access Journals (Sweden)

    Lijin K. Gopi

    2017-12-01

    Full Text Available Current era of functional genomics is enriched with good quality draft genomes and annotations for many thousands of species and varieties with the support of the advancements in the next generation sequencing technologies (NGS. Around 25,250 genomes, of the organisms from various kingdoms, are submitted in the NCBI genome resource till date. Each of these genomes was annotated using various tools and knowledge-bases that were available during the period of the annotation. It is obvious that these annotations will be improved if the same genome is annotated using improved tools and knowledge-bases. Here we present a new genome annotation pipeline, strengthened with various tools and knowledge-bases that are capable of producing better quality annotations from the consensus of the predictions from different tools. This resource also perform various additional annotations, apart from the usual gene predictions and functional annotations, which involve SSRs, novel repeats, paralogs, proteins with transmembrane helices, signal peptides etc. This new annotation resource is trained to evaluate and integrate all the predictions together to resolve the overlaps and ambiguities of the boundaries. One of the important highlights of this resource is the capability of predicting the phylogenetic relations of the repeats using the evolutionary trace analysis and orthologous gene clusters. We also present a case study, of the pipeline, in which we upgrade the genome annotation of Nelumbo nucifera (sacred lotus. It is demonstrated that this resource is capable of producing an improved annotation for a better understanding of the biology of various organisms.

  16. Integral hierarchies and percolation

    International Nuclear Information System (INIS)

    Klein, W.; Stell, G.

    1985-01-01

    For a variation of the Potts model which has been shown to describe continuum percolation, we derive a hierarchy of integral equations of Kirkwood-Salsburg type. The distribution functions which are the solutions of this hierarchy can be simply related to the connectedness functions in continuum percolation. From this hierarchy a second set of equations is derived from which the connectedness functions can be obtained directly. This approach is extremely useful when investigating properties of systems far from the percolation transition. These hierarchies are solved exactly in the mean-field (Kac-Baker) limit and possible implications for cluster growth are discussed. The relation between the Potts model for continuum percolation and the Widom-Rowlinson model is also noted

  17. The gauge hierarchy problem

    International Nuclear Information System (INIS)

    Natale, A.A.; Shellard, R.C.

    1981-01-01

    The problem of gauge hierarchy in Grand Unified Theories using a toy model with O(N) symmetry is discussed. It is shown that there is no escape to the unnatural adjustment of coupling constants, made only after the computation of several orders in perturbation theory is performed. The propositions of some authors on ways to overcome the gauge hierarchy problem are commented. (Author) [pt

  18. Soliton solutions by Darboux transformation and some reductions for a new Hamiltonian lattice hierarchy

    International Nuclear Information System (INIS)

    Tian Shoufu; Zhang Hongqing

    2010-01-01

    In this paper, we start from the discrete spectral problem and construct a lattice hierarchy by properly choosing an auxiliary spectral problem V-tilde n (m) , which can reduce to the Volterra hierarchy, the Ablowitz-Ladik hierarchy, positive and negative lattice hierarchies and a new hierarchy. The new hierarchy is integrable in involutory Lax's sense and possesses multi-Hamiltonian structure. In addition, the Darboux transformation of the lattice hierarchy is obtained when the freely adjustable function εn (1) =0 and m=1. Then some soliton solutions are obtained by using Darboux transformation. This method is also suitable for other more general spectral problems in mathematics and physics.

  19. Integrable Hierarchies and Dispersionless Limit

    OpenAIRE

    Takasaki, Kanehisa; Takebe, Takashi

    1994-01-01

    Analogues of the KP and the Toda lattice hierarchy called dispersionless KP and Toda hierarchy are studied. Dressing operations in the dispersionless hierarchies are introduced as a canonical transformation, quantization of which is dressing operators of the ordinary KP and Toda hierarchy. An alternative construction of general solutions of the ordinary KP and Toda hierarchy is given as twistor construction which is quatization of the similar construction of solutions of dispersionless hierar...

  20. Solving the wrong hierarchy problem

    International Nuclear Information System (INIS)

    Blinov, Nikita; Hook, Anson

    2016-01-01

    Many theories require augmenting the Standard Model with additional scalar fields with large order one couplings. We present a new solution to the hierarchy problem for these scalar fields. We explore parity- and Z_2-symmetric theories where the Standard Model Higgs potential has two vacua. The parity or Z_2 copy of the Higgs lives in the minimum far from the origin while our Higgs occupies the minimum near the origin of the potential. This approach results in a theory with multiple light scalar fields but with only a single hierarchy problem, since the bare mass is tied to the Higgs mass by a discrete symmetry. The new scalar does not have a new hierarchy problem associated with it because its expectation value and mass are generated by dimensional transmutation of the scalar quartic coupling. The location of the second Higgs minimum is not a free parameter, but is rather a function of the matter content of the theory. As a result, these theories are extremely predictive. We develop this idea in the context of a solution to the strong CP problem. Lastly, we show this mechanism postdicts the top Yukawa to be within 1σ of the currently measured value and predicts scalar color octets with masses in the range 9-200 TeV

  1. In praise of hierarchy.

    Science.gov (United States)

    Jaques, E

    1990-01-01

    Hierarchy has not had its day. After 3,000 years as the preferred structure for large organizations, managerial hierarchy is still the most natural and effective organizational form that a big company can employ. Now, as in the past, the key to organizational success is individual accountability, and hierarchy preserves unambiguous accountability for getting work done. Unfortunately, hierarchy is widely misunderstood and abused. Pay grades are confused with real layers of responsibility, for example, and incompetent bosses abound. As a result, many experts now urge us to adopt group-oriented or "flat" structures. But groups are never held accountable as groups for what they do or fail to do, and groups don't have careers. The proper use of hierarchy derives from the nature of work. As organizational tasks range from simple to very complex, there are sharp jumps in the level of difficulty and responsibility. Surprisingly, people in hundreds of companies in dozens of countries agree on where these jumps take place. They are tied to an objective measure-the time span of the longest task or program assigned to each managerial role-and they occur at 3 months, 1 year, 2 years, 5 years, 10 years, and 20 years. As the time span increases, so does the level of experience, knowledge, and mental stamina required to do the work. This increasing level of mental capacity lets companies put people in jobs they can do, it allows managers to add value to the work of their subordinates, it creates hierarchical layers acceptable to everyone in the organization, and it allows employees to be evaluated by people they accept as organizational superiors. Best of all, understanding hierarchy allows organizations to set up hierarchies with no more than seven layers-often fewer-and to know what the structure is good for and how it ought to perform.

  2. Ubiquitous Annotation Systems

    DEFF Research Database (Denmark)

    Hansen, Frank Allan

    2006-01-01

    Ubiquitous annotation systems allow users to annotate physical places, objects, and persons with digital information. Especially in the field of location based information systems much work has been done to implement adaptive and context-aware systems, but few efforts have focused on the general...... requirements for linking information to objects in both physical and digital space. This paper surveys annotation techniques from open hypermedia systems, Web based annotation systems, and mobile and augmented reality systems to illustrate different approaches to four central challenges ubiquitous annotation...... systems have to deal with: anchoring, structuring, presentation, and authoring. Through a number of examples each challenge is discussed and HyCon, a context-aware hypermedia framework developed at the University of Aarhus, Denmark, is used to illustrate an integrated approach to ubiquitous annotations...

  3. Rethinking the waste hierarchy

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, C; Vigsoe, D [eds.

    2005-03-01

    There is an increasing need to couple environmental and economic considerations within waste management. Consumers and companies alike generate ever more waste. The waste-policy challenges of the future lie in decoupling growth in waste generation from growth in consumption, and in setting priorities for the waste management. This report discusses the criteria for deciding priorities for waste management methods, and questions the current principles of EU waste policies. The basis for the discussion is the so-called waste hierarchy which has dominated the waste policy in the EU since the mid-1970s. The waste hierarchy ranks possible methods of waste management. According to the waste hierarchy, the very best solution is to reduce the amount of waste. After that, reuse is preferred to recycling which, in turn, is preferred to incineration. Disposal at a landfill is the least favourable solution. (BA)

  4. Delegation Within Hierarchies

    DEFF Research Database (Denmark)

    Dobrajska, Magdalena; Billinger, Stephan; Karim, Samina

    2015-01-01

    We investigate trade-offs associated with delegating authority over multiple interrelated decisions in a complex task structure. The empirical setting is a business process of a global Fortune 50 firm. The firm decentralized its organization and redefined decision authority across organizational......-relevant knowledge, the matching of required knowledge and managers’ expertise, and information processing intensity affect (a) the occurrence of delegation and, (b) if delegation occurs, how far down the organizational hierarchy authority is delegated. We discuss how these findings complement existing theories...... on delegation by providing insights into when and how interrelated decisions are delegated across multiple levels of an organizational hierarchy....

  5. Comments on gauge hierarchies

    International Nuclear Information System (INIS)

    Natale, A.A.

    The problem of gauge hierarchy in a O(N) model is discussed. It is shown the existence of an upper bound for the hierarchy of order α- 1 / 2 , as proposed by Gildener. This same constraint appears when the breaking is made by the radiative corrections in a scheme elaborated by Weinberg. It is found that fine tunning or redefinition of coupling constants to improve hieracrchy, as proposed in several papers, cannot be done before the calculation of higher order contributions to the effective potential. (Author) [pt

  6. Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics.

    Science.gov (United States)

    Chepelev, Leonid L; Riazanov, Alexandre; Kouznetsov, Alexandre; Low, Hong Sang; Dumontier, Michel; Baker, Christopher J O

    2011-07-26

    The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality. As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of

  7. Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2011-07-01

    Full Text Available Abstract Background The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality. Results As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of

  8. Concept annotation in the CRAFT corpus.

    Science.gov (United States)

    Bada, Michael; Eckert, Miriam; Evans, Donald; Garcia, Kristin; Shipley, Krista; Sitnikov, Dmitry; Baumgartner, William A; Cohen, K Bretonnel; Verspoor, Karin; Blake, Judith A; Hunter, Lawrence E

    2012-07-09

    Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

  9. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  10. Materials with structural hierarchy

    Science.gov (United States)

    Lakes, Roderic

    1993-01-01

    The role of structural hierarchy in determining bulk material properties is examined. Dense hierarchical materials are discussed, including composites and polycrystals, polymers, and biological materials. Hierarchical cellular materials are considered, including cellular solids and the prediction of strength and stiffness in hierarchical cellular materials.

  11. Toda hierarchies and their applications

    Science.gov (United States)

    Takasaki, Kanehisa

    2018-05-01

    The 2D Toda hierarchy occupies a central position in the family of integrable hierarchies of the Toda type. The 1D Toda hierarchy and the Ablowitz–Ladik (aka relativistic Toda) hierarchy can be derived from the 2D Toda hierarchy as reductions. These integrable hierarchies have been applied to various problems of mathematics and mathematical physics since 1990s. A recent example is a series of studies on models of statistical mechanics called the melting crystal model. This research has revealed that the aforementioned two reductions of the 2D Toda hierarchy underlie two different melting crystal models. Technical clues are a fermionic realization of the quantum torus algebra, special algebraic relations therein called shift symmetries, and a matrix factorization problem. The two melting crystal models thus exhibit remarkable similarity with the Hermitian and unitary matrix models for which the two reductions of the 2D Toda hierarchy play the role of fundamental integrable structures.

  12. Multiple Hierarchies and Organizational Control

    Science.gov (United States)

    Evans, Peter B.

    1975-01-01

    Uses a control-loss model to explore the effects of multiple channels in formal organizations, and presents an argument for the superior control properties of dual hierarchies. Two variant forms of multiple hierarchies are considered. (Author)

  13. Functional representations of integrable hierarchies

    International Nuclear Information System (INIS)

    Dimakis, Aristophanes; Mueller-Hoissen, Folkert

    2006-01-01

    We consider a general framework for integrable hierarchies in Lax form and derive certain universal equations from which 'functional representations' of particular hierarchies (such as KP, discrete KP, mKP, AKNS), i.e. formulations in terms of functional equations, are systematically and quite easily obtained. The formalism genuinely applies to hierarchies where the dependent variables live in a noncommutative (typically matrix) algebra. The obtained functional representations can be understood as 'noncommutative' analogues of 'Fay identities' for the KP hierarchy

  14. Hierarchy-associated semantic-rule inference framework for classifying indoor scenes

    Science.gov (United States)

    Yu, Dan; Liu, Peng; Ye, Zhipeng; Tang, Xianglong; Zhao, Wei

    2016-03-01

    Typically, the initial task of classifying indoor scenes is challenging, because the spatial layout and decoration of a scene can vary considerably. Recent efforts at classifying object relationships commonly depend on the results of scene annotation and predefined rules, making classification inflexible. Furthermore, annotation results are easily affected by external factors. Inspired by human cognition, a scene-classification framework was proposed using the empirically based annotation (EBA) and a match-over rule-based (MRB) inference system. The semantic hierarchy of images is exploited by EBA to construct rules empirically for MRB classification. The problem of scene classification is divided into low-level annotation and high-level inference from a macro perspective. Low-level annotation involves detecting the semantic hierarchy and annotating the scene with a deformable-parts model and a bag-of-visual-words model. In high-level inference, hierarchical rules are extracted to train the decision tree for classification. The categories of testing samples are generated from the parts to the whole. Compared with traditional classification strategies, the proposed semantic hierarchy and corresponding rules reduce the effect of a variable background and improve the classification performance. The proposed framework was evaluated on a popular indoor scene dataset, and the experimental results demonstrate its effectiveness.

  15. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

    Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  16. Semantic annotation of consumer health questions.

    Science.gov (United States)

    Kilicoglu, Halil; Ben Abacha, Asma; Mrabet, Yassine; Shooshan, Sonya E; Rodriguez, Laritza; Masterton, Kate; Demner-Fushman, Dina

    2018-02-06

    Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations. The resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most

  17. CellSs: Scheduling Techniques to Better Exploit Memory Hierarchy

    Directory of Open Access Journals (Sweden)

    Pieter Bellens

    2009-01-01

    Full Text Available Cell Superscalar's (CellSs main goal is to provide a simple, flexible and easy programming approach for the Cell Broadband Engine (Cell/B.E. that automatically exploits the inherent concurrency of the applications at a task level. The CellSs environment is based on a source-to-source compiler that translates annotated C or Fortran code and a runtime library tailored for the Cell/B.E. that takes care of the concurrent execution of the application. The first efforts for task scheduling in CellSs derived from very simple heuristics. This paper presents new scheduling techniques that have been developed for CellSs for the purpose of improving an application's performance. Additionally, the design of a new scheduling algorithm is detailed and the algorithm evaluated. The CellSs scheduler takes an extension of the memory hierarchy for Cell/B.E. into account, with a cache memory shared between the SPEs. All new scheduling practices have been evaluated showing better behavior of our system.

  18. PINGU sensitivity to neutrino mass hierarchy

    International Nuclear Information System (INIS)

    Groß, Andreas

    2014-01-01

    Determination of the neutrino mass hierarchy (NMH) is among the most fundamental questions in particle physics. Recent measurements of 1) a large mixing angle between the first and the third neutrino mass eigenstates and 2) the first observation of atmospheric neutrino oscillations at tens of GeV with neutrino telescopes, open the intriguing new possibility to exploit matter effects in neutrino oscillation to determine the neutrino mass hierarchy. A further extension of IceCube/DeepCore called PINGU (Precision IceCube Next Generation Upgrade) has been recently envisioned with the ultimate goal to measure neutrino mass hierarchy. PINGU would consist of additional IceCube-like strings of detectors deployed in the deepest and cleanest ice in the center of IceCube. More densely deployed instrumentation would provide a threshold substantially below 10 GeV and enhance the sensitivity to the mass hierarchy signal in atmospheric neutrinos. Here we discuss an estimate of the PINGU sensitivity to the mass hierarchy determined using an approximation with an Asimov dataset and an oscillation parameter fit

  19. Boltzmann hierarchy for interacting neutrinos I: formalism

    International Nuclear Information System (INIS)

    Oldengott, Isabel M.; Rampf, Cornelius; Wong, Yvonne Y.Y.

    2015-01-01

    Starting from the collisional Boltzmann equation, we derive for the first time and from first principles the Boltzmann hierarchy for neutrinos including interactions with a scalar particle. Such interactions appear, for example, in majoron-like models of neutrino mass generation. We study two limits of the scalar mass: (i) An extremely massive scalar whose only role is to mediate an effective 4-fermion neutrino-neutrino interaction, and (ii) a massless scalar that can be produced in abundance and thus demands its own Boltzmann hierarchy. In contrast to, e.g., the first-order Boltzmann hierarchy for Thomson-scattering photons, our interacting neutrino/scalar Boltzmann hierarchies contain additional momentum-dependent collision terms arising from a non-negligible energy transfer in the neutrino-neutrino and neutrino-scalar interactions. This necessitates that we track each momentum mode of the phase space distributions individually, even if the particles were massless. Comparing our hierarchy with the commonly used (c eff 2 ,c vis 2 )-parameterisation, we find no formal correspondence between the two approaches, which raises the question of whether the latter parameterisation even has an interpretation in terms of particle scattering. Lastly, although we have invoked majoron-like models as a motivation for our study, our treatment is in fact generally applicable to all scenarios in which the neutrino and/or other ultrarelativistic fermions interact with scalar particles

  20. annot8r: GO, EC and KEGG annotation of EST datasets

    Directory of Open Access Journals (Sweden)

    Schmid Ralf

    2008-04-01

    Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non

  1. Ansatz for dynamical hierarchies

    DEFF Research Database (Denmark)

    Rasmussen, S.; Baas, N.A.; Mayer, B.

    2001-01-01

    Complex, robust functionalities can be generated naturally in at least two ways: by the assembly of structures and by the evolution of structures. This work is concerned with spontaneous formation of structures. We define the notion of dynamical hierarchies in natural systems and show...... the importance of this particular kind of organization for living systems. We then define a framework that enables us to formulate, investigate, and manipulate such dynamical hierarchies. This framework allows us to simultaneously investigate different levels of description together with them interrelationship...... three. Formulating this system as a simple two-dimensional molecular dynamics (MD) lattice gas allows us within one dynamical system to demonstrate the successive emergence of two higher levels (three levels all together) of robust structures with associated properties. Second, we demonstrate how...

  2. Hierarchy from baryogenesis

    International Nuclear Information System (INIS)

    Senatore, Leonardo

    2006-01-01

    We study a recently proposed mechanism to solve the hierarchy problem in the context of the landscape, where the solution of the hierarchy problem is connected to the requirement of having baryons in our Universe via electroweak baryogenesis. The phase transition is triggered by the fermion condensation of a new gauge sector which becomes strong at a scale Λ determined by dimensional transmutation, and it is mediated to the standard model by a new singlet field. In a 'friendly' neighborhood of the landscape, where only the relevant operators are ''scanned'' among the vacua, baryogenesis is effective only if the Higgs mass m h is comparable to this low scale Λ, forcing m h ∼Λ, and solving the hierarchy problem. A new CP violating phase is needed coupling the new singlet and the Higgs field to new matter fields. We study the constraints on this model given by baryogenesis and by the electron electric dipole moment (EDM), and we briefly comment on gauge coupling unification and on dark matter relic abundance. We find that next generation experiments on the EDM will be sensitive to essentially the entire viable region of the parameter space, so that absence of a signal would effectively rule out the model

  3. NoGOA: predicting noisy GO annotations using evidences and sparse representation.

    Science.gov (United States)

    Yu, Guoxian; Lu, Chang; Wang, Jun

    2017-07-21

    Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred. Although quality control techniques have been applied to ensure the quality of annotations, the community consistently report that there are still considerable noisy (or incorrect) annotations. Given the wide application of annotations, however, how to identify noisy annotations is an important but yet seldom studied open problem. We introduce a novel approach called NoGOA to predict noisy annotations. NoGOA applies sparse representation on the gene-term association matrix to reduce the impact of noisy annotations, and takes advantage of sparse representation coefficients to measure the semantic similarity between genes. Secondly, it preliminarily predicts noisy annotations of a gene based on aggregated votes from semantic neighborhood genes of that gene. Next, NoGOA estimates the ratio of noisy annotations for each evidence code based on direct annotations in GOA files archived on different periods, and then weights entries of the association matrix via estimated ratios and propagates weights to ancestors of direct annotations using GO hierarchy. Finally, it integrates evidence-weighted association matrix and aggregated votes to predict noisy annotations. Experiments on archived GOA files of six model species (H. sapiens, A. thaliana, S. cerevisiae, G. gallus, B. Taurus and M. musculus) demonstrate that NoGOA achieves significantly better results than other related methods and removing noisy annotations improves the performance of gene function prediction. The comparative study justifies the effectiveness of integrating evidence codes with sparse representation for predicting noisy GO annotations. Codes and datasets are available at http://mlda.swu.edu.cn/codes.php?name=NoGOA .

  4. Criteria for optimizing cortical hierarchies with continuous ranges

    Directory of Open Access Journals (Sweden)

    Antje Krumnack

    2010-03-01

    Full Text Available In a recent paper (Reid et al.; 2009, NeuroImage we introduced a method to calculate optimal hierarchies in the visual network that utilizes continuous, rather than discrete, hierarchical levels, and permits a range of acceptable values rather than attempting to fit fixed hierarchical distances. There, to obtain a hierarchy, the sum of deviations from the constraints that define the hierarchy was minimized using linear optimization. In the short time since publication of that paper we noticed that many colleagues misinterpreted the meaning of the term optimal hierarchy. In particular, a majority of them were under the impression that there was perhaps only one optimal hierarchy, but a substantial difficulty in finding that one. However, there is not only more than one optimal hierarchy but also more than one option for defining optimality. Continuing the line of this work we look at additional options for optimizing the visual hierarchy: minimizing the number of violated constraints and minimizing the maximal size of a constraint violation using linear optimization and mixed integer programming. The implementation of both optimization criteria is explained in detail. In addition, using constraint sets based on the data from Felleman and Van Essen, optimal hierarchies for the visual network are calculated for both optimization methods.

  5. Block (or Hamiltonian) Lie Symmetry of Dispersionless D-Type Drinfeld–Sokolov Hierarchy

    International Nuclear Information System (INIS)

    Li Chuan-Zhong; He Jing-Song; Su Yu-Cai

    2014-01-01

    In this paper, the dispersionless D-type Drinfeld–Sokolov hierarchy, i.e. a reduction of the dispersionless two-component BKP hierarchy, is studied. The additional symmetry flows of this hierarchy are presented. These flows form an infinite-dimensional Lie algebra of Block type as well as a Lie algebra of Hamiltonian type

  6. Symmetries of supersymmetric integrable hierarchies of KP type

    International Nuclear Information System (INIS)

    Nissimov, E.; Pacheva, S.

    2002-01-01

    This article is devoted to the systematic study of additional (non-isospectral) symmetries of constrained (reduced) supersymmetric integrable hierarchies of KP type--the so-called SKP (R;M B ,M F ) models. The latter are supersymmetric extensions of ordinary constrained KP hierarchies which contain as special cases basic integrable systems such as (m)KdV, AKNS, Fordy-Kulish, Yajima-Oikawa, etc. As a first main result it is shown that any SKP (R;M B ,M F ) hierarchy possesses two different mutually (anti-)commuting types of superloop superalgebra additional symmetries corresponding to the positive- and negative-grade parts of certain superloop superalgebras. The second main result is the systematic construction of the full algebra of additional Virasoro symmetries of SKP (R;M B ,M F ) hierarchies, which requires nontrivial modifications of the Virasoro flows known from the general case of unconstrained Manin-Radul super-KP hierarchies (the latter flows do not define symmetries for constrained SKP (R;M B ,M F ) hierarchies). As a third main result we provide systematic construction of the supersymmetric analogs of multi-component (matrix) KP hierarchies and show that the latter contain, among others, the supersymmetric version of the Davey-Stewartson system. Finally, we present an explicit derivation of the general Darboux-Baecklund solutions for the SKP (R;M B ,M F ) super-tau functions (supersymmetric 'soliton'-like solutions) which preserve the additional (non-isospectral) symmetries

  7. Gauge theories, duality relations and the tensor hierarchy

    International Nuclear Information System (INIS)

    Bergshoeff, Eric A.; Hohm, Olaf; Hartong, Jelle; Huebscher, Mechthild; OrtIn, Tomas

    2009-01-01

    We compute the complete 3- and 4-dimensional tensor hierarchies, i.e. sets of p-form fields, with 1 ≤ p ≤ D, which realize an off-shell algebra of bosonic gauge transformations. We show how these tensor hierarchies can be put on-shell by introducing a set of duality relations, thereby introducing additional scalars and a metric tensor. These so-called duality hierarchies encode the equations of motion of the bosonic part of the most general gauged supergravity theories in those dimensions, including the (projected) scalar equations of motion. We construct gauge-invariant actions that include all the fields in the tensor hierarchies. We elucidate the relation between the gauge transformations of the p-form fields in the action and those of the same fields in the tensor hierarchy.

  8. Annotating individual human genomes.

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J

    2011-10-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. ANNOTATING INDIVIDUAL HUMAN GENOMES*

    Science.gov (United States)

    Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.

    2014-01-01

    Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162

  10. Evaluation of three automated genome annotations for Halorhabdus utahensis.

    Directory of Open Access Journals (Sweden)

    Peter Bakke

    2009-07-01

    Full Text Available Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus ribosome-binding site. Additionally, we conducted laboratory experiments to test H. utahensis growth and enzyme activity. Current annotation practices need to improve in order to more accurately reflect a genome's biological potential. We make specific recommendations that could improve the quality of microbial annotation projects.

  11. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Deng Jixin

    2009-02-01

    Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

  12. GSV Annotated Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

    2010-09-14

    The following annotated bibliography was developed as part of the geospatial algorithm verification and validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Verification and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following five topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models. Many other papers were studied during the course of the investigation including. The annotations for these articles can be found in the paper "On the verification and validation of geospatial image analysis algorithms".

  13. Hierarchies in Coloured Petri Nets

    DEFF Research Database (Denmark)

    Huber, Peter; Jensen, Kurt; Shapiro, Robert M.

    1991-01-01

    constructs, and it illustrates them by means of two examples. The hierarchy constructs can be used for theoretical considerations, but their main use is to describe and analyse large real-world systems. All of the hierarchy constructs are supported by the editing and analysis facilities in the CPN Palette...

  14. Completing the land resource hierarchy

    Science.gov (United States)

    The Land Resource Hierarchy of the NRCS is a hierarchal landscape classification consisting of resource areas which represent both conceptual and spatially discrete landscape units stratifying agency programs and practices. The Land Resource Hierarchy (LRH) scales from discrete points (soil pedon an...

  15. Dominance Hierarchies in Young Children

    Science.gov (United States)

    Edelman, Murray S.; Omark, Donald R.

    1973-01-01

    This study uses the ethological approach of seeking species characteristics and phylogenetic continuities in an investigation of human behavior. Among primates a striking consistency is the presence of some form of dominance hierarchy in many species. The present study examines peer group dominance hierarchies as they are perceived by children in…

  16. Maslow's Hierarchy of Needs Revisited.

    Science.gov (United States)

    Frame, Douglas

    1996-01-01

    Reviews Maslow's hierarchy of needs and characterization of the self-actualizing personality, suggesting that since few people meet his self-actualization criteria, an educational system designed to produce such personalities may fail, with teachers attending only to the hierarchy's lower stages (self-esteem and self-actualization) which dilutes…

  17. Discovering gene annotations in biomedical text databases

    Directory of Open Access Journals (Sweden)

    Ozsoyoglu Gultekin

    2008-03-01

    Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

  18. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  19. Annotating Emotions in Meetings

    NARCIS (Netherlands)

    Reidsma, Dennis; Heylen, Dirk K.J.; Ordelman, Roeland J.F.

    We present the results of two trials testing procedures for the annotation of emotion and mental state of the AMI corpus. The first procedure is an adaptation of the FeelTrace method, focusing on a continuous labelling of emotion dimensions. The second method is centered around more discrete

  20. On the supersymmetric BKP hierarchy

    International Nuclear Information System (INIS)

    Ramos, Eduardo; Stanciu, Sonia

    1994-01-01

    We prove that the supersymmetric BKP-hierarchy of Yu (SBKP 2 ) is hamiltonian with respect to a nonlinear extension of the N=1 super-Virasoro algebra (W SBKP ) by fields of spin k, where k>[3]/[2] and 2k≡0,3 (mod 4). Moreover, we show how to associate in a similar manner an N=1 W-superalgebra with every integrable hierarchy of the SKdV-type. We also show using dressing transformations how to extend, in a way which is compatible with the hamiltonian structure, the SBKP 2 hierarchy by odd flows, as well as the equivalence of this extended hierarchy to the SBKP-hierarchy of Manin-Radul. ((orig.))

  1. An extended Harry Dym hierarchy

    International Nuclear Information System (INIS)

    Ma Wenxiu

    2010-01-01

    An extended Harry Dym hierarchy is constructed by using eigenfunctions and adjoint eigenfunctions of the spectral problems of the Harry Dym hierarchy associated with the pseudo-differential operator L = u∂ + u 0 + u 1 ∂ -1 + .... The corresponding Lax presentation possesses a self-consistent source involving squared eigenfunctions. The resulting extended Harry Dym hierarchy is reduced to the Harry Dym hierarchy with self-consistent sources under the n-reduction, L n = (L n ) ≥2 , and the k-constrained Harry Dym hierarchy under the k-constraint, L k = (L k ) ≥2 + Σ N i=1 q i ∂ -1 r i ∂ 2 . A few particular examples are computed, together with their Lax pairs.

  2. Reasoning with Annotations of Texts

    OpenAIRE

    Ma , Yue; Lévy , François; Ghimire , Sudeep

    2011-01-01

    International audience; Linguistic and semantic annotations are important features for text-based applications. However, achieving and maintaining a good quality of a set of annotations is known to be a complex task. Many ad hoc approaches have been developed to produce various types of annotations, while comparing those annotations to improve their quality is still rare. In this paper, we propose a framework in which both linguistic and domain information can cooperate to reason with annotat...

  3. First generation annotations for the fathead minnow (Pimephales promelas) genome

    Science.gov (United States)

    Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

  4. An Improved Semidefinite Programming Hierarchy for Testing Entanglement

    Science.gov (United States)

    Harrow, Aram W.; Natarajan, Anand; Wu, Xiaodi

    2017-06-01

    We present a stronger version of the Doherty-Parrilo-Spedalieri (DPS) hierarchy of approximations for the set of separable states. Unlike DPS, our hierarchy converges exactly at a finite number of rounds for any fixed input dimension. This yields an algorithm for separability testing that is singly exponential in dimension and polylogarithmic in accuracy. Our analysis makes use of tools from algebraic geometry, but our algorithm is elementary and differs from DPS only by one simple additional collection of constraints.

  5. GSV Annotated Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)

    2011-06-14

    The following annotated bibliography was developed as part of the Geospatial Algorithm Veri cation and Validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Veri cation and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following ve topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models.

  6. Dynamical hierarchies - A summary

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, S.; Barrett, C.L. [Los Alamos National Lab., NM (United States)]|[Santa Fe Institute, NM (United States); Olesen, M.W. [Los Alamos National Lab., NM (United States)] [and others

    1996-04-01

    This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems. In biological systems, higher order hyperstructures occur both in an intuitive and a formal sense: monomers, polymers, membranes, organelles, cells, tissues, organs, etc. constitute an observable hierarchy, apparently generated by the underlying biomolecular process. However, in models and simulations of these systems, it has turned out to be quite difficult to produce higher order emergent structures from first principles. The first problem is to agree on what a higher order structure is. An emergent structure can be defined through an introduction of an observational function. If a property can be observed in the dynamics, but not at the level of the fundamental first order interacting structures, we define it to be emergent. It is well known that second order structures occur relatively easy in simulation, so the problem is how to proceed to third and higher order without external interference. A third order structure is defined through the interaction of second order structures forming a new observable not found at the lower levels.

  7. Anarchy and hierarchy

    Energy Technology Data Exchange (ETDEWEB)

    Haba, Naoyuki; Murayama, Hitoshi

    2000-09-14

    We advocate a new approach to study models of fermion massesand mixings, namely anarchy proposed in hep-ph/9911341. In this approach,we scan the O(1) coefficients randomly. We argue that this is the correctapproach when the fundamental theory is sufficiently complicated.Assuming there is no physical distinction among three generations ofneutrinos, the probability distributions in MNS mixing angles can bepredicted independent of the choice of the measure. This is because themixing angles are distributed according to the Haar measure of the Liegroups whose elements diagonalize the mass matrices. The near-maximalmixings, as observed in the atmospheric neutrino data and as required inthe LMA solution to the solar neutrino problem, are highly probable. Asmall hierarchy between the Delta m2 for the atmospheric and the solarneutrinos is obtained very easily; the complex seesaw case gives ahierarchy of a factor of 20 as the most probable one, even though thisconclusion is more measure-dependent. U_e3 has to be just below thecurrent limit from the CHOOZ experiment. The CP-violating parameter sindelta is preferred to be maximal. We present a simple SU(5)-likeextension of anarchy to the charged-lepton and quark sectors which workswell phenomenologically.

  8. Feminist Praxis, Critical Theory and Informal Hierarchies

    Directory of Open Access Journals (Sweden)

    Eva Giraud

    2015-05-01

    Full Text Available This article draws on my experiences teaching across two undergraduate media modules in a UK research-intensive institution to explore tactics for combatting both institutional and informal hierarchies within university teaching contexts. Building on Sara Motta’s (2012 exploration of implementing critical pedagogic principles at postgraduate level in an elite university context, I discuss additional tactics for combatting these hierarchies in undergraduate settings, which were developed by transferring insights derived from informal workshops led by the University of Nottingham’s Feminism and Teaching network into the classroom. This discussion is framed in relation to the concepts of “cyborg pedagogies” and “political semiotics of articulation,” derived from the work of Donna Haraway, in order to theorize how these tactics can engender productive relationships between radical pedagogies and critical theory.

  9. Gauge-symmetry hierarchies revisited

    International Nuclear Information System (INIS)

    Gildener, E.

    1979-01-01

    It was shown by the author in a previous paper that in each order of perturbation theory there is an upper bound on the range of validity of a gauge hierarchy. Thus constructing a large hierarchy requires a fine-tuning of the scalar-field parameters. It was stated that the possibility of an inherent bound on the hierarchy exists, but the question of the actual existence of such a bound was left completely open. Since then several authors have addressed this problem. Some of what the author asserted was misunderstood, and incorrect conclusions have been drawn from recent computations. It has been claimed that the existence of large hierarchies has been demonstrated. It is the purpose of this paper to refute this claim, to help clarify the situation, and to explain why the status of this problem has in fact not really changed in recent years (author)

  10. Sato theory on the q-Toda hierarchy and its extension

    International Nuclear Information System (INIS)

    Li, Chuanzhong

    2015-01-01

    In this paper, we construct the Sato theory including the Hirota bilinear equations and tau function of a new q-deformed Toda hierarchy (QTH). Meanwhile the Block type additional symmetry and bi-Hamiltonian structure of this hierarchy are given. From Hamiltonian tau symmetry, we give another definition of tau function of this hierarchy. Afterwards, we extend the q-Toda hierarchy to an extended q-Toda hierarchy (EQTH) which satisfy a generalized Hirota quadratic equation in terms of generalized vertex operators. The Hirota quadratic equation might have further application in Gromov–Witten theory. The corresponding Sato theory including multi-fold Darboux transformations of this extended hierarchy is also constructed. At last, we construct the multicomponent extension of the q-Toda hierarchy and show the integrability including its bi-Hamiltonian structure, tau symmetry and conserved densities

  11. Principles of synchronous digital hierarchy

    CERN Document Server

    Jain, Rajesh Kumar

    2012-01-01

    The book presents the current standards of digital multiplexing, called synchronous digital hierarchy, including analog multiplexing technologies. It is aimed at telecommunication professionals who want to develop an understanding of digital multiplexing and synchronous digital hierarchy in particular and the functioning of practical telecommunication systems in general. The text includes all relevant fundamentals and provides a handy reference for problem solving or defining operations and maintenance strategies. The author covers digital conversion and TDM principles, line coding and digital

  12. Information slows down hierarchy growth.

    Science.gov (United States)

    Czaplicka, Agnieszka; Suchecki, Krzysztof; Miñano, Borja; Trias, Miquel; Hołyst, Janusz A

    2014-06-01

    We consider models of growing multilevel systems wherein the growth process is driven by rules of tournament selection. A system can be conceived as an evolving tree with a new node being attached to a contestant node at the best hierarchy level (a level nearest to the tree root). The proposed evolution reflects limited information on system properties available to new nodes. It can also be expressed in terms of population dynamics. Two models are considered: a constant tournament (CT) model wherein the number of tournament participants is constant throughout system evolution, and a proportional tournament (PT) model where this number increases proportionally to the growing size of the system itself. The results of analytical calculations based on a rate equation fit well to numerical simulations for both models. In the CT model all hierarchy levels emerge, but the birth time of a consecutive hierarchy level increases exponentially or faster for each new level. The number of nodes at the first hierarchy level grows logarithmically in time, while the size of the last, "worst" hierarchy level oscillates quasi-log-periodically. In the PT model, the occupations of the first two hierarchy levels increase linearly, but worse hierarchy levels either do not emerge at all or appear only by chance in the early stage of system evolution to further stop growing at all. The results allow us to conclude that information available to each new node in tournament dynamics restrains the emergence of new hierarchy levels and that it is the absolute amount of information, not relative, which governs such behavior.

  13. Quantify entanglement by concurrence hierarchy

    OpenAIRE

    Fan, Heng; Matsumoto, Keiji; Imai, Hiroshi

    2002-01-01

    We define the concurrence hierarchy as d-1 independent invariants under local unitary transformations in d-level quantum system. The first one is the original concurrence defined by Wootters et al in 2-level quantum system and generalized to d-level pure quantum states case. We propose to use this concurrence hierarchy as measurement of entanglement. This measurement does not increase under local quantum operations and classical communication.

  14. Information slows down hierarchy growth

    Science.gov (United States)

    Czaplicka, Agnieszka; Suchecki, Krzysztof; Miñano, Borja; Trias, Miquel; Hołyst, Janusz A.

    2014-06-01

    We consider models of growing multilevel systems wherein the growth process is driven by rules of tournament selection. A system can be conceived as an evolving tree with a new node being attached to a contestant node at the best hierarchy level (a level nearest to the tree root). The proposed evolution reflects limited information on system properties available to new nodes. It can also be expressed in terms of population dynamics. Two models are considered: a constant tournament (CT) model wherein the number of tournament participants is constant throughout system evolution, and a proportional tournament (PT) model where this number increases proportionally to the growing size of the system itself. The results of analytical calculations based on a rate equation fit well to numerical simulations for both models. In the CT model all hierarchy levels emerge, but the birth time of a consecutive hierarchy level increases exponentially or faster for each new level. The number of nodes at the first hierarchy level grows logarithmically in time, while the size of the last, "worst" hierarchy level oscillates quasi-log-periodically. In the PT model, the occupations of the first two hierarchy levels increase linearly, but worse hierarchy levels either do not emerge at all or appear only by chance in the early stage of system evolution to further stop growing at all. The results allow us to conclude that information available to each new node in tournament dynamics restrains the emergence of new hierarchy levels and that it is the absolute amount of information, not relative, which governs such behavior.

  15. Recommended HSE-7 documents hierarchy

    International Nuclear Information System (INIS)

    Klein, R.B.; Jennrich, E.A.; Lund, D.M.; Danna, J.G.; Davis, K.D.; Rutz, A.C.

    1990-01-01

    This report recommends a hierarchy of waste management documents at Los Alamos National Laboratory (LANL or ''Laboratory''). The hierarchy addresses documents that are required to plan, implement, and document waste management programs at Los Alamos. These documents will enable the waste management group and the six sections contained within that group to satisfy requirements that are imposed upon them by the US Department of Energy (DOE), DOE Albuquerque Operations, US Environmental Protection Agency, various State of New Mexico agencies, and Laboratory management

  16. Special polynomials associated with some hierarchies

    International Nuclear Information System (INIS)

    Kudryashov, Nikolai A.

    2008-01-01

    Special polynomials associated with rational solutions of a hierarchy of equations of Painleve type are introduced. The hierarchy arises by similarity reduction from the Fordy-Gibbons hierarchy of partial differential equations. Some relations for these special polynomials are given. Differential-difference hierarchies for finding special polynomials are presented. These formulae allow us to obtain special polynomials associated with the hierarchy studied. It is shown that rational solutions of members of the Schwarz-Sawada-Kotera, the Schwarz-Kaup-Kupershmidt, the Fordy-Gibbons, the Sawada-Kotera and the Kaup-Kupershmidt hierarchies can be expressed through special polynomials of the hierarchy studied

  17. Grassmannian approach to super-KP hierarchies

    International Nuclear Information System (INIS)

    Takama, Michiaki.

    1995-06-01

    We present a theory of 'maximal' super-KP (SKP) hierarchy whose flows are maximally extended to include all those of known SKP hierarchies, including, for example, the MRSKP hierarchy of Manin and Radul and the Jacobian SKP (JSKP) introduced by Mulase and Rabin. It is shown that SKP hierarchies has a natural field theoretic description in terms of the B-C system, in analogous way as the ordinary KP hierarchy. For this SKP hierarchy, we construct the vertex operators by using Kac-van de Leur superbosonization. The vertex operators act on the τ-function and then produce the wave function and the dual wave function of the hierarchy. Thereby we achieve the description of the 'maximal' SKP hierarchy in terms of the τ-function, which seemed to be lacking till now. Mutual relations among the SKP hierarchies are clarified. The MRSKP and the JSKP hierarchies are obtained as special cases when the time variables are appropriately restricted. (author)

  18. Recursion Operators for Dispersionless KP Hierarchy

    International Nuclear Information System (INIS)

    Cheng Qiusheng; He Jingsong

    2012-01-01

    Based on the corresponding theorem between dispersionless KP (dKP) hierarchy and ħ-dependent KP (ħKP) hierarchy, a general formal representation of the recursion operators for dKP hierarchy under n-reduction is given in a systematical way from the corresponding ħKP hierarchy. To illustrate this method, the recursion operators for dKP hierarchy under 2-reduction and 3-reduction are calculated in detail.

  19. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... and metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  20. Impingement: an annotated bibliography

    International Nuclear Information System (INIS)

    Uziel, M.S.; Hannon, E.H.

    1979-04-01

    This bibliography of 655 annotated references on impingement of aquatic organisms at intake structures of thermal-power-plant cooling systems was compiled from the published and unpublished literature. The bibliography includes references from 1928 to 1978 on impingement monitoring programs; impingement impact assessment; applicable law; location and design of intake structures, screens, louvers, and other barriers; fish behavior and swim speed as related to impingement susceptibility; and the effects of light, sound, bubbles, currents, and temperature on fish behavior. References are arranged alphabetically by author or corporate author. Indexes are provided for author, keywords, subject category, geographic location, taxon, and title

  1. Annotation-based enrichment of Digital Objects using open-source frameworks

    Directory of Open Access Journals (Sweden)

    Marcus Emmanuel Barnes

    2017-07-01

    Full Text Available The W3C Web Annotation Data Model, Protocol, and Vocabulary unify approaches to annotations across the web, enabling their aggregation, discovery and persistence over time. In addition, new javascript libraries provide the ability for users to annotate multi-format content. In this paper, we describe how we have leveraged these developments to provide annotation features alongside Islandora’s existing preservation, access, and management capabilities. We also discuss our experience developing with the Web Annotation Model as an open web architecture standard, as well as our approach to integrating mature external annotation libraries. The resulting software (the Web Annotation Utility Module for Islandora accommodates annotation across multiple formats. This solution can be used in various digital scholarship contexts.

  2. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty...

  3. Phylogenetic molecular function annotation

    International Nuclear Information System (INIS)

    Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

  4. Multiview Hessian regularization for image annotation.

    Science.gov (United States)

    Liu, Weifeng; Tao, Dacheng

    2013-07-01

    The rapid development of computer hardware and Internet technology makes large scale data dependent models computationally tractable, and opens a bright avenue for annotating images through innovative machine learning algorithms. Semisupervised learning (SSL) therefore received intensive attention in recent years and was successfully deployed in image annotation. One representative work in SSL is Laplacian regularization (LR), which smoothes the conditional distribution for classification along the manifold encoded in the graph Laplacian, however, it is observed that LR biases the classification function toward a constant function that possibly results in poor generalization. In addition, LR is developed to handle uniformly distributed data (or single-view data), although instances or objects, such as images and videos, are usually represented by multiview features, such as color, shape, and texture. In this paper, we present multiview Hessian regularization (mHR) to address the above two problems in LR-based image annotation. In particular, mHR optimally combines multiple HR, each of which is obtained from a particular view of instances, and steers the classification function that varies linearly along the data manifold. We apply mHR to kernel least squares and support vector machines as two examples for image annotation. Extensive experiments on the PASCAL VOC'07 dataset validate the effectiveness of mHR by comparing it with baseline algorithms, including LR and HR.

  5. Poisson hierarchy of discrete strings

    International Nuclear Information System (INIS)

    Ioannidou, Theodora; Niemi, Antti J.

    2016-01-01

    The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.

  6. The extended bigraded Toda hierarchy

    International Nuclear Information System (INIS)

    Carlet, Guido

    2006-01-01

    We generalize the Toda lattice hierarchy by considering N + M dependent variables. We construct roots and logarithms of the Lax operator which are uniquely defined operators with coefficients that are ε-series of differential polynomials in the dependent variables, and we use them to provide a Lax pair definition of the extended bigraded Toda hierarchy, generalizing [4]. Using R-matrix theory we give the bi-Hamiltonian formulation of this hierarchy and we prove the existence of a tau function for its solutions. Finally we study the dispersionless limit and its connection with a class of Frobenius manifolds on the orbit space of the extended affine Weyl groups W-tilde (N) (A N+M-1 ) of the A series, defined by Dubrovin and Zhang (1998 Compos. Math. 111 167)

  7. Poisson hierarchy of discrete strings

    Energy Technology Data Exchange (ETDEWEB)

    Ioannidou, Theodora, E-mail: ti3@auth.gr [Faculty of Civil Engineering, School of Engineering, Aristotle University of Thessaloniki, 54249, Thessaloniki (Greece); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2016-01-28

    The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.

  8. Mesotext. Framing and exploring annotations

    NARCIS (Netherlands)

    Boot, P.; Boot, P.; Stronks, E.

    2007-01-01

    From the introduction: Annotation is an important item on the wish list for digital scholarly tools. It is one of John Unsworth’s primitives of scholarship (Unsworth 2000). Especially in linguistics,a number of tools have been developed that facilitate the creation of annotations to source material

  9. THE DIMENSIONS OF COMPOSITION ANNOTATION.

    Science.gov (United States)

    MCCOLLY, WILLIAM

    ENGLISH TEACHER ANNOTATIONS WERE STUDIED TO DETERMINE THE DIMENSIONS AND PROPERTIES OF THE ENTIRE SYSTEM FOR WRITING CORRECTIONS AND CRITICISMS ON COMPOSITIONS. FOUR SETS OF COMPOSITIONS WERE WRITTEN BY STUDENTS IN GRADES 9 THROUGH 13. TYPESCRIPTS OF THE COMPOSITIONS WERE ANNOTATED BY CLASSROOM ENGLISH TEACHERS. THEN, 32 ENGLISH TEACHERS JUDGED…

  10. New supersymmetrizations of the generalized KDV hierarchies

    International Nuclear Information System (INIS)

    Figueroa-O'Farrill, J.M.; Stanciu, S.

    1993-03-01

    Recently we investigated a new supersymmetrization procedure for the KdV hierarchy inspired in some recent work on supersymmetric matrix models. We extend this procedure here for the generalized KdV hierarchies. The resulting supersymmetric hierarchies are generically nonlocal, expect for the case of Boussinesque which we treat in detail. The resulting supersymmetric hierarchy is integrable and bihamiltonian and contains the Boussinesque hierarchy as a subhierarchy. In a particular realization, we extend it by defining supersymmetric odd flows. We end with some comments on a slight modification of this supersymmetrization which yields local equations for any generalized KdV hierarchy. (orig.)

  11. The Hierarchy of Segment Reports

    Directory of Open Access Journals (Sweden)

    Danilo Dorović

    2015-05-01

    Full Text Available The article presents an attempt to find the connection between reports created for managers responsible for different business segments. With this purpose, the hierarchy of the business reporting segments is proposed. This can lead to better understanding of the expenses under common responsibility of more than one manager since these expenses should be in more than one report. The structure of cost defined per business segment hierarchy with the aim of new, unusual but relevant cost structure for management can be established. Both could potentially bring new information benefits for management in the context of profit reporting.

  12. Why and when hierarchy impacts team effectiveness: A meta-analytic integration.

    Science.gov (United States)

    Greer, Lindred L; de Jong, Bart A; Schouten, Maartje E; Dannals, Jennifer E

    2018-06-01

    Hierarchy has the potential to both benefit and harm team effectiveness. In this article, we meta-analytically investigate different explanations for why and when hierarchy helps or hurts team effectiveness, drawing on results from 54 prior studies (N = 13,914 teams). Our findings show that, on net, hierarchy negatively impacts team effectiveness (performance: ρ = -.08; viability: ρ = -.11), and that this effect is mediated by increased conflict-enabling states. Additionally, we show that the negative relationship between hierarchy and team performance is exacerbated by aspects of the team structure (i.e., membership instability, skill differentiation) and the hierarchy itself (i.e., mutability), which make hierarchical teams prone to conflict. The predictions regarding the positive effect of hierarchy on team performance as mediated by coordination-enabling processes, and the moderating roles of several aspects of team tasks (i.e., interdependence, complexity) and the hierarchy (i.e., form) were not supported, with the exception that task ambiguity enhanced the positive effects of hierarchy. Given that our findings largely support dysfunctional views on hierarchy, future research is needed to understand when and why hierarchy may be more likely to live up to its purported functional benefits. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  13. Hierarchy in directed random networks.

    Science.gov (United States)

    Mones, Enys

    2013-02-01

    In recent years, the theory and application of complex networks have been quickly developing in a markable way due to the increasing amount of data from real systems and the fruitful application of powerful methods used in statistical physics. Many important characteristics of social or biological systems can be described by the study of their underlying structure of interactions. Hierarchy is one of these features that can be formulated in the language of networks. In this paper we present some (qualitative) analytic results on the hierarchical properties of random network models with zero correlations and also investigate, mainly numerically, the effects of different types of correlations. The behavior of the hierarchy is different in the absence and the presence of giant components. We show that the hierarchical structure can be drastically different if there are one-point correlations in the network. We also show numerical results suggesting that the hierarchy does not change monotonically with the correlations and there is an optimal level of nonzero correlations maximizing the level of hierarchy.

  14. Void hierarchy and cosmic structure

    International Nuclear Information System (INIS)

    Weygaert, Rien van de; Ravi Sheth

    2004-01-01

    Within the context of hierarchical scenarios of gravitational structure formation we describe how an evolving hierarchy of voids evolves on the basis of two processes, the void-in-void process and the void-in-cloud process. The related analytical formulation in terms of a two-barrier excursion problem leads to a self-similarly evolving peaked void size distribution

  15. Maslow's Hierarchy and Student Retention.

    Science.gov (United States)

    Brookman, David M.

    1989-01-01

    Abraham Maslow's hierarchy of needs offers perspective on student motivation and a rationale for college retention programing. Student affairs and faculty interventions addressing student safety needs and engaging students' sense of purpose reinforce persistence. A mentor program is a possible cooperative effort between student personnel and…

  16. Integrable relativistic Toda type lattice hierarchies, associated coupling systems and the Darboux transformation

    International Nuclear Information System (INIS)

    Yang Hongxiang; Xu Xixiang; Sun Yepeng; Ding Haiyong

    2006-01-01

    Starting from a discrete isospectral problem, integrable positive and negative relativistic Toda type lattice hierarchies are derived. The two lattice hierarchies are proven to have discrete zero-curvature representations associated with a discrete spectral problem, and the positive and negative lattice hierarchies correspond to positive and negative power expansions of Lax operators with respect to the spectral parameter, respectively. The integrable positive and negative coupling systems of the resulting hierarchies are constructed through enlarging Lax pairs. In addition, with the help of gauge transformations of spectral problems, a Darboux transformation is established for the relativistic Toda type lattice. As an application, an exact solution is explicitly presented

  17. On an extended second Painlevé hierarchy

    Science.gov (United States)

    Gordoa, P. R.; Pickering, A.

    2017-10-01

    We present a new extension of the second Painlevé hierarchy and study its properties. In addition to Lax pairs, Bäcklund transformations, auto-Bäcklund transformations and basic special integrals, we also consider a new phenomenon whereby we obtain relations between systems of different orders but of the same form. The extension made here of the second Painlevé hierarchy is based on the use of non-isospectral scattering problems and so is quite general. We thus expect to be able to obtain similar extensions of other Painlevé hierarchies, including not only for continuous examples but also for discrete and differential-delay examples. We believe that our work is also of relevance for Painlevé classification, since it gives information about classes of equation that may be of interest and in addition provides a key to the possible identification of equations isolated in such a process.

  18. The problem of symmetry breaking hierarchy

    International Nuclear Information System (INIS)

    Natale, A.A.

    1983-01-01

    The problem of symmetry breaking hierarchy in grand unified theories is discussed, proving the impossibility to get a big hierarchy of interactions, in a natural way within the framework of perturbation theory. (L.C.) [pt

  19. Exact Solutions for Two Equation Hierarchies

    International Nuclear Information System (INIS)

    Song-Lin, Zhao; Da-Jun, Zhang; Jie, Ji

    2010-01-01

    Bilinear forms and double-Wronskian solutions are given for two hierarchies, the (2+1)-dimensional breaking Ablowitz–Kaup–Newell–Segur (AKNS) hierarchy and the negative order AKNS hierarchy. According to some choices of the coefficient matrix in the Wronskian condition equation set, we obtain some kinds of solutions for these two hierarchies, such as solitons, Jordan block solutions, rational solutions, complexitons and mixed solutions. (general)

  20. A note on the KP hierarchy

    International Nuclear Information System (INIS)

    Depireux, D.A.

    1992-01-01

    In this paper, given the two boson representation of the conformal algebra W ∞ , the second Hamiltonian structure of the KP hierarchy, the author constructs a bi-Hamiltonian hierarchy for the two associated currents. The KP hierarchy appears as a composite of this new and simpler system. The bi-Hamiltonian structure of the new hierarchy gives naturally all the Hamiltonian structures of the KP system

  1. A Hierarchy Model of Income Distribution

    OpenAIRE

    Fix, Blair

    2018-01-01

    Based on worldly experience, most people would agree that firms are hierarchically organized, and that pay tends to increase as one moves up the hierarchy. But how this hierarchical structure affects income distribution has not been widely studied. To remedy this situation, this paper presents a new model of income distribution that explores the effects of social hierarchy. This ‘hierarchy model’ takes the limited available evidence on the structure of firm hierarchies and generalizes it to c...

  2. Chado controller: advanced annotation management with a community annotation system.

    Science.gov (United States)

    Guignon, Valentin; Droc, Gaëtan; Alaux, Michael; Baurens, Franc-Christophe; Garsmeur, Olivier; Poiron, Claire; Carver, Tim; Rouard, Mathieu; Bocs, Stéphanie

    2012-04-01

    We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary data are available at Bioinformatics online.

  3. Displaying Annotations for Digitised Globes

    Science.gov (United States)

    Gede, Mátyás; Farbinger, Anna

    2018-05-01

    Thanks to the efforts of the various globe digitising projects, nowadays there are plenty of old globes that can be examined as 3D models on the computer screen. These globes usually contain a lot of interesting details that an average observer would not entirely discover for the first time. The authors developed a website that can display annotations for such digitised globes. These annotations help observers of the globe to discover all the important, interesting details. Annotations consist of a plain text title, a HTML formatted descriptive text and a corresponding polygon and are stored in KML format. The website is powered by the Cesium virtual globe engine.

  4. Generalized Miura transformations, two-bosons KP hierarchies and their reduction to KdV hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.; Ferreira, L.A.; Gomes, J.F.; Medeiros, R.T.; Zimerman, A.H.

    1993-02-01

    Bracket preserving gauge equivalence is established between several two-boson generated KP type of hierarchies. These KP hierarchies reduce under symplectic reduction (via Dirac constraints) to KdV and Schwarzian KdV hierarchies. Under this reduction the gauge equivalence is taking form of the conventional Miura maps between the above KdV type of hierarchies. (author). 16 refs

  5. Generalized Miura transformations, two-bosons KP hierarchies and their reduction to KdV hierarchies

    Energy Technology Data Exchange (ETDEWEB)

    Aratyn, H. [Illinois Univ., Chicago, IL (United States). Dept. of Physics; Ferreira, L.A.; Gomes, J.F.; Medeiros, R.T.; Zimerman, A.H.

    1993-02-01

    Bracket preserving gauge equivalence is established between several two-boson generated KP type of hierarchies. These KP hierarchies reduce under symplectic reduction (via Dirac constraints) to KdV and Schwarzian KdV hierarchies. Under this reduction the gauge equivalence is taking form of the conventional Miura maps between the above KdV type of hierarchies. (author). 16 refs.

  6. Generalized W-algebras and integrable hierarchies

    International Nuclear Information System (INIS)

    Burroughs, N.; De Groot, M.; Hollowood, T.; Miramontes, L.

    1992-01-01

    We report on generalizations of the KdV-type integrable hierarchies of Drinfel'd and Sokolov. These hierarchies lead to the existence of new classical W-algebras, which arise as the second hamiltonian structure of the hierarchies. In particular, we present a construction of the W n (l) -algebras. (orig.)

  7. BBGKY hierarchy and dynamics of correlations

    International Nuclear Information System (INIS)

    Polishchuk, D.O.

    2010-01-01

    We derive the BBGKY hierarchy for the Fermi and Bose many-particle systems, using the von Neumann hierarchy for the correlation operators. The solution of the Cauchy problem of the formulated hierarchy in the case of an n-body interaction potential is constructed in the space of sequences of trace-class operators.

  8. PCAS – a precomputed proteome annotation database resource

    Directory of Open Access Journals (Sweden)

    Luo Jingchu

    2003-11-01

    Full Text Available Abstract Background Many model proteomes or "complete" sets of proteins of given organisms are now publicly available. Much effort has been invested in computational annotation of those "draft" proteomes. Motif or domain based algorithms play a pivotal role in functional classification of proteins. Employing most available computational algorithms, mainly motif or domain recognition algorithms, we set up to develop an online proteome annotation system with integrated proteome annotation data to complement existing resources. Results We report here the development of PCAS (ProteinCentric Annotation System as an online resource of pre-computed proteome annotation data. We applied most available motif or domain databases and their analysis methods, including hmmpfam search of HMMs in Pfam, SMART and TIGRFAM, RPS-PSIBLAST search of PSSMs in CDD, pfscan of PROSITE patterns and profiles, as well as PSI-BLAST search of SUPERFAMILY PSSMs. In addition, signal peptide and TM are predicted using SignalP and TMHMM respectively. We mapped SUPERFAMILY and COGs to InterPro, so the motif or domain databases are integrated through InterPro. PCAS displays table summaries of pre-computed data and a graphical presentation of motifs or domains relative to the protein. As of now, PCAS contains human IPI, mouse IPI, and rat IPI, A. thaliana, C. elegans, D. melanogaster, S. cerevisiae, and S. pombe proteome. PCAS is available at http://pak.cbi.pku.edu.cn/proteome/gca.php Conclusion PCAS gives better annotation coverage for model proteomes by employing a wider collection of available algorithms. Besides presenting the most confident annotation data, PCAS also allows customized query so users can inspect statistically less significant boundary information as well. Therefore, besides providing general annotation information, PCAS could be used as a discovery platform. We plan to update PCAS twice a year. We will upgrade PCAS when new proteome annotation algorithms

  9. Annotation of selection strengths in viral genomes

    DEFF Research Database (Denmark)

    McCauley, Stephen; de Groot, Saskia; Mailund, Thomas

    2007-01-01

    Motivation: Viral genomes tend to code in overlapping reading frames to maximize information content. This may result in atypical codon bias and particular evolutionary constraints. Due to the fast mutation rate of viruses, there is additional strong evidence for varying selection between intra......- and intergenomic regions. The presence of multiple coding regions complicates the concept of Ka/Ks ratio, and thus begs for an alternative approach when investigating selection strengths. Building on the paper by McCauley & Hein (2006), we develop a method for annotating a viral genome coding in overlapping...... may thus achieve an annotation both of coding regions as well as selection strengths, allowing us to investigate different selection patterns and hypotheses. Results: We illustrate our method by applying it to a multiple alignment of four HIV2 sequences, as well as four Hepatitis B sequences. We...

  10. Annotating functional RNAs in genomes using Infernal.

    Science.gov (United States)

    Nawrocki, Eric P

    2014-01-01

    Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome's initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.

  11. A robust data-driven approach for gene ontology annotation.

    Science.gov (United States)

    Li, Yanpeng; Yu, Hong

    2014-01-01

    Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation. BioCreative IV GO annotation task aims to evaluate the performance of system that automatically assigns GO terms to genes based on the narrative sentences in biomedical literature. This article presents our work in this task as well as the experimental results after the competition. For the evidence sentence extraction subtask, we built a binary classifier to identify evidence sentences using reference distance estimator (RDE), a recently proposed semi-supervised learning method that learns new features from around 10 million unlabeled sentences, achieving an F1 of 19.3% in exact match and 32.5% in relaxed match. In the post-submission experiment, we obtained 22.1% and 35.7% F1 performance by incorporating bigram features in RDE learning. In both development and test sets, RDE-based method achieved over 20% relative improvement on F1 and AUC performance against classical supervised learning methods, e.g. support vector machine and logistic regression. For the GO term prediction subtask, we developed an information retrieval-based method to retrieve the GO term most relevant to each evidence sentence using a ranking function that combined cosine similarity and the frequency of GO terms in documents, and a filtering method based on high-level GO classes. The best performance of our submitted runs was 7.8% F1 and 22.2% hierarchy F1. We found that the incorporation of frequency information and hierarchy filtering substantially improved the performance. In the post-submission evaluation, we obtained a 10.6% F1 using a simpler setting. Overall, the experimental analysis showed our approaches were robust in both the two tasks. © The Author(s) 2014. Published by Oxford University Press.

  12. Creating New Medical Ontologies for Image Annotation A Case Study

    CERN Document Server

    Stanescu, Liana; Brezovan, Marius; Mihai, Cristian Gabriel

    2012-01-01

    Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.

  13. Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials.

    Science.gov (United States)

    Chalam, K V; Jain, P; Shah, V A; Shah, Gaurav Y

    2006-06-01

    An Internet browser-based annotation system can be used to identify and describe features in digitalized retinal images, in multicentric clinical trials, in real time. In this web-based annotation system, the user employs a mouse to draw and create annotations on a transparent layer, that encapsulates the observations and interpretations of a specific image. Multiple annotation layers may be overlaid on a single image. These layers may correspond to annotations by different users on the same image or annotations of a temporal sequence of images of a disease process, over a period of time. In addition, geometrical properties of annotated figures may be computed and measured. The annotations are stored in a central repository database on a server, which can be retrieved by multiple users in real time. This system facilitates objective evaluation of digital images and comparison of double-blind readings of digital photographs, with an identifiable audit trail. Annotation of ophthalmic images allowed clinically feasible and useful interpretation to track properties of an area of fundus pathology. This provided an objective method to monitor properties of pathologies over time, an essential component of multicentric clinical trials. The annotation system also allowed users to view stereoscopic images that are stereo pairs. This web-based annotation system is useful and valuable in monitoring patient care, in multicentric clinical trials, telemedicine, teaching and routine clinical settings.

  14. Global network structure of dominance hierarchy of ant workers.

    Science.gov (United States)

    Shimoji, Hiroyuki; Abe, Masato S; Tsuji, Kazuki; Masuda, Naoki

    2014-10-06

    Dominance hierarchy among animals is widespread in various species and believed to serve to regulate resource allocation within an animal group. Unlike small groups, however, detection and quantification of linear hierarchy in large groups of animals are a difficult task. Here, we analyse aggression-based dominance hierarchies formed by worker ants in Diacamma sp. as large directed networks. We show that the observed dominance networks are perfect or approximate directed acyclic graphs, which are consistent with perfect linear hierarchy. The observed networks are also sparse and random but significantly different from networks generated through thinning of the perfect linear tournament (i.e. all individuals are linearly ranked and dominance relationship exists between every pair of individuals). These results pertain to global structure of the networks, which contrasts with the previous studies inspecting frequencies of different types of triads. In addition, the distribution of the out-degree (i.e. number of workers that the focal worker attacks), not in-degree (i.e. number of workers that attack the focal worker), of each observed network is right-skewed. Those having excessively large out-degrees are located near the top, but not the top, of the hierarchy. We also discuss evolutionary implications of the discovered properties of dominance networks. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  15. COGNATE: comparative gene annotation characterizer.

    Science.gov (United States)

    Wilbrandt, Jeanne; Misof, Bernhard; Niehuis, Oliver

    2017-07-17

    The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https

  16. MODIFICATION OF THE ANALYTIC HIERARCHY PROCESS (AHP METHOD USING FUZZY LOGIC: FUZZY AHP APPROACH AS A SUPPORT TO THE DECISION MAKING PROCESS CONCERNING ENGAGEMENT OF THE GROUP FOR ADDITIONAL HINDERING

    Directory of Open Access Journals (Sweden)

    Darko Božanić

    2015-11-01

    Full Text Available This paper presents the modification of the AHP method, which takes into account the degree of suspense of decision maker, that is it allows that decision maker, with a certain degree of conviction (which is usually less than 100%, defines which linguistic expression corresponds to optimality criteria comparison. To determine the criteria weights and alternative values, fuzzy numbers are used since they are very suitable for the expression of vagueness and uncertainty. In this way, after applying the AHP method, we obtained values of criterion functions for each of the examined alternatives, which corresponds to the value determined by the degree of conviction. This provides that for different values of the degree of conviction can be made generation of different sets of criterion functions values. The set model was tested on choosing directions of action of the Group for additional hindering, as a procedure wich is often accompanied by greater or lesser degree of uncertainty of criteria that are necessary in relevant decision making

  17. Closed hierarchy of correlations in Markovian open quantum systems

    International Nuclear Information System (INIS)

    Žunkovič, Bojan

    2014-01-01

    We study the Lindblad master equation in the space of operators and provide simple criteria for closeness of the hierarchy of equations for correlations. We separately consider the time evolution of closed and open systems and show that open systems satisfying the closeness conditions are not necessarily of Gaussian type. In addition, we show that dissipation can induce the closeness of the hierarchy of correlations in interacting quantum systems. As an example we study an interacting optomechanical model, the Fermi–Hubbard model, and the Rabi model, all coupled to a fine-tuned Markovian environment and obtain exact analytic expressions for the time evolution of two-point correlations. (paper)

  18. Critical constraints on chiral hierarchies

    International Nuclear Information System (INIS)

    Chivukula, R.S.; Golden, M.; Simmons, E.H.

    1993-01-01

    Critical dynamics constrains models of dynamical electroweak symmetry breaking in which the scale of high-energy physics is far above 1 TeV. A big hierarchy requires the high-energy theory to have a second-order chiral phase transition, near which the theory is described by a low-energy effective Lagrangian with composite ''Higgs'' scalars. As scalar theories with more than one Φ 4 coupling can have a Coleman-Weinberg instability and a first-order transition, such dynamical EWSB models cannot always support a large hierarchy. If the large-N c Nambu--Jona-Lasinio model is a good approximation to the top-condensate and strong extended technicolor models, they will not produce acceptable EWSB

  19. Measuring Maslow's hierarchy of needs.

    Science.gov (United States)

    Lester, David

    2013-08-01

    Two scales have been proposed to measure Maslow's hierarchy of needs in college students, one by Lester (1990) and one by Strong and Fiebert (1987). In a sample of 51 college students, scores on the corresponding scales for the five needs did not correlate significantly and positively, except for the measures of physiological needs. Furthermore, there was limited support for Maslow's hypothesis that need deprivation would predict psychopathology (specifically, mania and depression).

  20. Hierarchy Measure for Complex Networks

    Science.gov (United States)

    Mones, Enys; Vicsek, Lilla; Vicsek, Tamás

    2012-01-01

    Nature, technology and society are full of complexity arising from the intricate web of the interactions among the units of the related systems (e.g., proteins, computers, people). Consequently, one of the most successful recent approaches to capturing the fundamental features of the structure and dynamics of complex systems has been the investigation of the networks associated with the above units (nodes) together with their relations (edges). Most complex systems have an inherently hierarchical organization and, correspondingly, the networks behind them also exhibit hierarchical features. Indeed, several papers have been devoted to describing this essential aspect of networks, however, without resulting in a widely accepted, converging concept concerning the quantitative characterization of the level of their hierarchy. Here we develop an approach and propose a quantity (measure) which is simple enough to be widely applicable, reveals a number of universal features of the organization of real-world networks and, as we demonstrate, is capable of capturing the essential features of the structure and the degree of hierarchy in a complex network. The measure we introduce is based on a generalization of the m-reach centrality, which we first extend to directed/partially directed graphs. Then, we define the global reaching centrality (GRC), which is the difference between the maximum and the average value of the generalized reach centralities over the network. We investigate the behavior of the GRC considering both a synthetic model with an adjustable level of hierarchy and real networks. Results for real networks show that our hierarchy measure is related to the controllability of the given system. We also propose a visualization procedure for large complex networks that can be used to obtain an overall qualitative picture about the nature of their hierarchical structure. PMID:22470477

  1. Information, Authority, and Corporate Hierarchies

    OpenAIRE

    Choe, Chongwoo; In-Uck, Park

    2010-01-01

    In a typical corporate hierarchy, the manager is delegated the authority to make strategic decisions, and to contract with other employees. By studying a model with one principal and two agents where one agent can gather information that is valuable for the principal's project choice and the other agent provides effort to the chosen project, we study when the principal can benefit from such delegation relative to centralization. We show that beneficial delegation is possible when complete con...

  2. Combinatorial solutions to integrable hierarchies

    Science.gov (United States)

    Kazarian, M. E.; Lando, S. K.

    2015-06-01

    This paper reviews modern approaches to the construction of formal solutions to integrable hierarchies of mathematical physics whose coefficients are answers to various enumerative problems. The relationship between these approaches and the combinatorics of symmetric groups and their representations is explained. Applications of the results to the construction of efficient computations in problems related to models of quantum field theories are described. Bibliography: 34 titles.

  3. A model of Yukawa hierarchies

    International Nuclear Information System (INIS)

    Elwood, J.K.; Irges, N.; Ramond, P.

    1997-05-01

    The authors present a model for the observed hierarchies among the Yukawa couplings of the standard model in the context of an effective low energy theory with an anomalous U(1) symmetry. This symmetry, a generic feature of superstring compactification, is a remnant of the Green-Schwarz anomaly cancellation mechanism. The gauge group is that of the standard model, augmented by X, the anomalous U(1), and two family-dependent phase symmetries Y (1) and Y (2) . The correct hierarchies are reproduced only when sin 2 θ w = 3/8 at the cut-off. To cancel anomalies, right-handed neutrinos and other standard model singlets must be introduced. Independently of the charges of the right-handed neutrinos, this model produces the same neutrino mixing matrix and an inverted hierarchy of neutrino masses. The heaviest is the electron neutrino with a mass ∼ 1 meV, and mixing of the order of λ c 3 with each of the other two neutrinos

  4. The (2+1)-dimensional nonisospectral relativistic Toda hierarchy related to the generalized discrete Painleve hierarchy

    International Nuclear Information System (INIS)

    Zhu Zuonong

    2007-01-01

    In this paper, we will concentrate on the topic of integrable discrete hierarchies in 2+1 dimensions, and their connection with discrete Painleve hierarchies. By considering a (2+1)-dimensional nonisospectral discrete linear problem, two new (2+1)-dimensional nonisospectral integrable lattice hierarchies-the 2+1 nonisospectral relativistic Toda lattice hierarchy and the 2+1 nonisospectral negative relativistic Toda lattice hierarchy-are constructed. It is shown that the reductions of the two new 2+1 nonisospectral lattice hierarchies lead to the (2+1)-dimensional nonisospectral Volterra lattice hierarchy and the (2+1)-dimensional nonisospectral negative Volterra lattice hierarchy. We also obtain two new (1+1)-dimensional nonisospectral integrable lattice hierarchies and two new ordinary difference hierarchies which are direct reductions of the two 2+1 nonisospectral integrable lattice hierarchies. One of the two difference hierarchies yields our previously obtained generalized discrete first Painleve (dP I ) hierarchy and another one yields a generalized alternative discrete second Painleve (alt-dP II ) hierarchy

  5. Objective-guided image annotation.

    Science.gov (United States)

    Mao, Qi; Tsang, Ivor Wai-Hung; Gao, Shenghua

    2013-04-01

    Automatic image annotation, which is usually formulated as a multi-label classification problem, is one of the major tools used to enhance the semantic understanding of web images. Many multimedia applications (e.g., tag-based image retrieval) can greatly benefit from image annotation. However, the insufficient performance of image annotation methods prevents these applications from being practical. On the other hand, specific measures are usually designed to evaluate how well one annotation method performs for a specific objective or application, but most image annotation methods do not consider optimization of these measures, so that they are inevitably trapped into suboptimal performance of these objective-specific measures. To address this issue, we first summarize a variety of objective-guided performance measures under a unified representation. Our analysis reveals that macro-averaging measures are very sensitive to infrequent keywords, and hamming measure is easily affected by skewed distributions. We then propose a unified multi-label learning framework, which directly optimizes a variety of objective-specific measures of multi-label learning tasks. Specifically, we first present a multilayer hierarchical structure of learning hypotheses for multi-label problems based on which a variety of loss functions with respect to objective-guided measures are defined. And then, we formulate these loss functions as relaxed surrogate functions and optimize them by structural SVMs. According to the analysis of various measures and the high time complexity of optimizing micro-averaging measures, in this paper, we focus on example-based measures that are tailor-made for image annotation tasks but are seldom explored in the literature. Experiments show consistency with the formal analysis on two widely used multi-label datasets, and demonstrate the superior performance of our proposed method over state-of-the-art baseline methods in terms of example-based measures on four

  6. Can nonstandard interactions jeopardize the hierarchy sensitivity of DUNE?

    Science.gov (United States)

    Deepthi, K. N.; Goswami, Srubabati; Nath, Newton

    2017-10-01

    We study the effect of nonstandard interactions (NSIs) on the propagation of neutrinos through the Earth's matter and how it affects the hierarchy sensitivity of the DUNE experiment. We emphasize the special case when the diagonal NSI parameter ɛe e=-1 , nullifying the standard matter effect. We show that if, in addition, C P violation is maximal then this gives rise to an exact intrinsic hierarchy degeneracy in the appearance channel, irrespective of the baseline and energy. Introduction of the off diagonal NSI parameter, ɛe τ, shifts the position of this degeneracy to a different ɛe e. Moreover the unknown magnitude and phases of the off diagonal NSI parameters can give rise to additional degeneracies. Overall, given the current model independent limits on NSI parameters, the hierarchy sensitivity of DUNE can get seriously impacted. However, a more precise knowledge of the NSI parameters, especially ɛe e, can give rise to an improved sensitivity. Alternatively, if a NSI exists in nature, and still DUNE shows hierarchy sensitivity, certain ranges of the NSI parameters can be excluded. Additionally, we briefly discuss the implications of ɛe e=-1 (in the Earth) on the Mikheyev-Smirnov-Wolfenstein effect in the Sun.

  7. A differential-difference hierarchy associated with relativistic Toda and Volterra hierarchies

    International Nuclear Information System (INIS)

    Fan Engui; Dai Huihui

    2008-01-01

    By embedding a free function into a compatible zero curvature equation, we enlarge the original differential-difference hierarchy into a new hierarchy with the free function which still admits zero curvature representation. The new hierarchy not only includes the original hierarchy, but also the well-known relativistic Toda hierarchy and the Volterra hierarchy as special reductions by properly choosing the free function. Infinitely many conservation laws and Darboux transformation for a representative differential-difference system are constructed based on its Lax representation. The exact solutions follow by applying the Darboux transformation

  8. Image annotation under X Windows

    Science.gov (United States)

    Pothier, Steven

    1991-08-01

    A mechanism for attaching graphic and overlay annotation to multiple bits/pixel imagery while providing levels of performance approaching that of native mode graphics systems is presented. This mechanism isolates programming complexity from the application programmer through software encapsulation under the X Window System. It ensures display accuracy throughout operations on the imagery and annotation including zooms, pans, and modifications of the annotation. Trade-offs that affect speed of display, consumption of memory, and system functionality are explored. The use of resource files to tune the display system is discussed. The mechanism makes use of an abstraction consisting of four parts; a graphics overlay, a dithered overlay, an image overly, and a physical display window. Data structures are maintained that retain the distinction between the four parts so that they can be modified independently, providing system flexibility. A unique technique for associating user color preferences with annotation is introduced. An interface that allows interactive modification of the mapping between image value and color is discussed. A procedure that provides for the colorization of imagery on 8-bit display systems using pixel dithering is explained. Finally, the application of annotation mechanisms to various applications is discussed.

  9. Neutrino mass matrix and hierarchy

    International Nuclear Information System (INIS)

    Kaus, Peter; Meshkov, Sydney

    2003-01-01

    We build a model to describe neutrinos based on strict hierarchy, incorporating as much as possible, the latest known data, for Δsol and Δatm, and for the mixing angles determined from neutrino oscillation experiments, including that from KamLAND. Since the hierarchy assumption is a statement about mass ratios, it lets us obtain all three neutrino masses. We obtain a mass matrix, Mν and a mixing matrix, U, where both Mν and U are given in terms of powers of Λ, the analog of the Cabibbo angle λ in the Wolfenstein representation, and two parameters, ρ and κ, each of order one. The expansion parameter, Λ, is defined by Λ2 = m2/m3 = √(Δsol/Δatm) ≅ 0.16, and ρ expresses our ignorance of the lightest neutrino mass m1, (m1 ρΛ4m3), while κ scales s13 to the experimental upper limit, s13 = κΛ2 ≅ 0.16κ. These matrices are similar in structure to those for the quark and lepton families, but with Λ about 1.6 times larger than the λ for the quarks and charged leptons. The upper limit for the effective neutrino mass in double β-decay experiments is 4 x 10-3eV if s13 = 0 and 6 x 10-3eV if s13 is maximal. The model, which is fairly unique, given the hierarchy assumption and the data, is compared to supersymmetric extension and texture zero models of mass generation

  10. Generalized NLS hierarchies from rational W algebras

    International Nuclear Information System (INIS)

    Toppan, F.

    1993-11-01

    Finite rational W algebras are very natural structures appearing in coset constructions when a Kac-Moody subalgebra is factored out. The problem of relating these algebras to integrable hierarchies of equations is studied by showing how to associate to a rational W algebra its corresponding hierarchy. Two examples are worked out, the sl(2)/U(1) coset, leading to the Non-Linear Schroedinger hierarchy, and the U(1) coset of the Polyakov-Bershadsky W algebra, leading to a 3-field representation of the KP hierarchy already encountered in the literature. In such examples a rational algebra appears as algebra of constraints when reducing a KP hierarchy to a finite field representation. This fact arises the natural question whether rational algebras are always associated to such reductions and whether a classification of rational algebras can lead to a classification of the integrable hierarchies. (author). 19 refs

  11. Neutrino mass hierarchy and matter effects

    OpenAIRE

    Smirnov, Alexei Yu.

    2013-01-01

    Matter effects modify the mixing and the effective masses of neutrinos in a way which depends on the neutrino mass hierarchy. Consequently, for normal and inverted hierarchies the oscillations and flavor conversion results are different. Sensitivity to the mass hierarchy appears whenever the matter effects on the 1-3 mixing and mass splitting become substantial. This happens in supernovae in wide energy range and in the matter of the Earth. The Earth density profile is a multi-layer medium wh...

  12. Hierarchy is Detrimental for Human Cooperation

    OpenAIRE

    Cronin, Katherine A.; Acheson, Daniel J.; Hernández, Penélope; Sánchez, Angel

    2016-01-01

    Studies of animal behavior consistently demonstrate that the social environment impacts cooperation, yet the effect of social dynamics has been largely excluded from studies of human cooperation. Here, we introduce a novel approach inspired by nonhuman primate research to address how social hierarchies impact human cooperation. Participants competed to earn hierarchy positions and then could cooperate with another individual in the hierarchy by investing in a common effort. Cooperation was ac...

  13. Hierarchy stability for spontaneously broken theories

    Energy Technology Data Exchange (ETDEWEB)

    Galvan, J B; Perez-Mercader, J; Sanchez, F J

    1987-04-16

    By using Weisberger's method for the integration of heavy degrees of freedom in multiscale theories, we show that tree level hierarchies are not destabilized byquantum corrections in a two-scale, two scalar field theory model where the heavy sector undergoes spontaneous symmetry breaking. We see explicitly the role played by the one-loop heavy log corrections to the effective parameters in maintaining the original tree level hierarchy and in keeping the theory free of hierarchy problems.

  14. A lattice hierarchy and its continuous limits

    International Nuclear Information System (INIS)

    Fan Engui

    2008-01-01

    By introducing a discrete spectral problem, we derive a lattice hierarchy which is integrable in Liouville's sense and possesses a multi-Hamiltonian structure. It is show that the discrete spectral problem converges to the well-known AKNS spectral problem under a certain continuous limit. In particular, we construct a sequence of equations in the lattice hierarchy which approximates the AKNS hierarchy as a continuous limit

  15. Hierarchy stability for spontaneously broken theories

    International Nuclear Information System (INIS)

    Galvan, J.B.; Perez-Mercader, J.; Sanchez, F.J.

    1987-01-01

    By using Weisberger's method for the integration of heavy degrees of freedom in multiscale theories, we show that tree level hierarchies are not destabilized byquantum corrections in a two-scale, two scalar field theory model where the heavy sector undergoes spontaneous symmetry breaking. We see explicitly the role played by the one-loop heavy log corrections to the effective parameters in maintaining the original tree level hierarchy and in keeping the theory free of hierarchy problems. (orig.)

  16. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

    Directory of Open Access Journals (Sweden)

    Dorrell Nick

    2007-06-01

    Full Text Available Abstract Background Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation. Results Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised. Conclusions Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.

  17. Riemann-Liouville integrals of fractional order and extended KP hierarchy

    International Nuclear Information System (INIS)

    Kamata, Masaru; Nakamula, Atsushi

    2002-01-01

    An attempt to formulate the extensions of the KP hierarchy by introducing fractional-order pseudo-differential operators is given. In the case of the extension with the half-order pseudo-differential operators, a system analogous to the supersymmetric extensions of the KP hierarchy is obtained. Unlike the supersymmetric extensions, no Grassmannian variable appears in the hierarchy considered here. More general hierarchies constructed by the 1/Nth-order pseudo-differential operators, their integrability and the reduction procedure are also investigated. In addition to finding the new extensions of the KP hierarchy, a brief introduction to the Riemann-Liouville integral is provided to yield a candidate for the fractional-order pseudo-differential operators

  18. Explicit flow equations and recursion operator of the ncKP hierarchy

    International Nuclear Information System (INIS)

    He, Jingsong; Wang, Lihong; Tu, Junyi; Li, Xiaodong

    2011-01-01

    The explicit expression of the flow equations of the noncommutative Kadomtsev–Petviashvili (ncKP) hierarchy is derived. Compared with the flow equations of the KP hierarchy, our result shows that the additional terms in the flow equations of the ncKP hierarchy indeed consist of commutators of dynamical coordinates {u i }. The recursion operator for the flow equations under n-reduction is presented. Further, under 2-reduction, we calculate a nonlocal recursion operator Φ(2) of the noncommutative Korteweg–de Vries(ncKdV) hierarchy, which generates a hierarchy of local, higher-order flows. Thus we solve the open problem proposed by Olver and Sokolov (1998 Commun. Math. Phys. 193 245–68)

  19. Alignment-Annotator web server: rendering and annotating sequence alignments.

    Science.gov (United States)

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Two New Multi-component BKP Hierarchies

    International Nuclear Information System (INIS)

    Wu Hongxia; Liu Xiaojun; Zeng Yunbo

    2009-01-01

    We firstly propose two kinds of new multi-component BKP (mcBKP) hierarchy based on the eigenfunction symmetry reduction and nonstandard reduction, respectively. The first one contains two types of BKP equation with self-consistent sources whose Lax representations are presented. The two mcBKP hierarchies both admit reductions to the k-constrained BKP hierarchy and to integrable (1+1)-dimensional hierarchy with self-consistent sources, which include two types of SK equation with self-consistent sources and of bi-directional SK equations with self-consistent sources.

  1. BAT: An open-source, web-based audio events annotation tool

    OpenAIRE

    Blai Meléndez-Catalan, Emilio Molina, Emilia Gómez

    2017-01-01

    In this paper we present BAT (BMAT Annotation Tool), an open-source, web-based tool for the manual annotation of events in audio recordings developed at BMAT (Barcelona Music and Audio Technologies). The main feature of the tool is that it provides an easy way to annotate the salience of simultaneous sound sources. Additionally, it allows to define multiple ontologies to adapt to multiple tasks and offers the possibility to cross-annotate audio data. Moreover, it is easy to install and deploy...

  2. Psychophysical "blinding" methods reveal a functional hierarchy of unconscious visual processing.

    Science.gov (United States)

    Breitmeyer, Bruno G

    2015-09-01

    Numerous non-invasive experimental "blinding" methods exist for suppressing the phenomenal awareness of visual stimuli. Not all of these suppressive methods occur at, and thus index, the same level of unconscious visual processing. This suggests that a functional hierarchy of unconscious visual processing can in principle be established. The empirical results of extant studies that have used a number of different methods and additional reasonable theoretical considerations suggest the following tentative hierarchy. At the highest levels in this hierarchy is unconscious processing indexed by object-substitution masking. The functional levels indexed by crowding, the attentional blink (and other attentional blinding methods), backward pattern masking, metacontrast masking, continuous flash suppression, sandwich masking, and single-flash interocular suppression, fall at progressively lower levels, while unconscious processing at the lowest levels is indexed by eye-based binocular-rivalry suppression. Although unconscious processing levels indexed by additional blinding methods is yet to be determined, a tentative placement at lower levels in the hierarchy is also given for unconscious processing indexed by Troxler fading and adaptation-induced blindness, and at higher levels in the hierarchy indexed by attentional blinding effects in addition to the level indexed by the attentional blink. The full mapping of levels in the functional hierarchy onto cortical activation sites and levels is yet to be determined. The existence of such a hierarchy bears importantly on the search for, and the distinctions between, neural correlates of conscious and unconscious vision. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Public Relations: Selected, Annotated Bibliography.

    Science.gov (United States)

    Demo, Penny

    Designed for students and practitioners of public relations (PR), this annotated bibliography focuses on recent journal articles and ERIC documents. The 34 citations include the following: (1) surveys of public relations professionals on career-related education; (2) literature reviews of research on measurement and evaluation of PR and…

  4. Persuasion: A Selected, Annotated Bibliography.

    Science.gov (United States)

    McDermott, Steven T.

    Designed to reflect the diversity of approaches to persuasion, this annotated bibliography cites materials selected for their contribution to that diversity as well as for being relatively current and/or especially significant representatives of particular approaches. The bibliography starts with a list of 17 general textbooks on approaches to…

  5. [Prescription annotations in Welfare Pharmacy].

    Science.gov (United States)

    Han, Yi

    2018-03-01

    Welfare Pharmacy contains medical formulas documented by the government and official prescriptions used by the official pharmacy in the pharmaceutical process. In the last years of Southern Song Dynasty, anonyms gave a lot of prescription annotations, made textual researches for the name, source, composition and origin of the prescriptions, and supplemented important historical data of medical cases and researched historical facts. The annotations of Welfare Pharmacy gathered the essence of medical theory, and can be used as precious materials to correctly understand the syndrome differentiation, compatibility regularity and clinical application of prescriptions. This article deeply investigated the style and form of the prescription annotations in Welfare Pharmacy, the name of prescriptions and the evolution of terminology, the major functions of the prescriptions, processing methods, instructions for taking medicine and taboos of prescriptions, the medical cases and clinical efficacy of prescriptions, the backgrounds, sources, composition and cultural meanings of prescriptions, proposed that the prescription annotations played an active role in the textual dissemination, patent medicine production and clinical diagnosis and treatment of Welfare Pharmacy. This not only helps understand the changes in the names and terms of traditional Chinese medicines in Welfare Pharmacy, but also provides the basis for understanding the knowledge sources, compatibility regularity, important drug innovations and clinical medications of prescriptions in Welfare Pharmacy. Copyright© by the Chinese Pharmaceutical Association.

  6. The surplus value of semantic annotations

    NARCIS (Netherlands)

    Marx, M.

    2010-01-01

    We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries,

  7. Systems Theory and Communication. Annotated Bibliography.

    Science.gov (United States)

    Covington, William G., Jr.

    This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

  8. Annotating images by mining image search results

    NARCIS (Netherlands)

    Wang, X.J.; Zhang, L.; Li, X.; Ma, W.Y.

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search

  9. On the robustness of Herlihy's hierarchy

    Science.gov (United States)

    Jayanti, Prasad

    1993-01-01

    A wait-free hierarchy maps object types to levels in Z(+) U (infinity) and has the following property: if a type T is at level N, and T' is an arbitrary type, then there is a wait-free implementation of an object of type T', for N processes, using only registers and objects of type T. The infinite hierarchy defined by Herlihy is an example of a wait-free hierarchy. A wait-free hierarchy is robust if it has the following property: if T is at level N, and S is a finite set of types belonging to levels N - 1 or lower, then there is no wait-free implementation of an object of type T, for N processes, using any number and any combination of objects belonging to the types in S. Robustness implies that there are no clever ways of combining weak shared objects to obtain stronger ones. Contrary to what many researchers believe, we prove that Herlihy's hierarchy is not robust. We then define some natural variants of Herlihy's hierarchy, which are also infinite wait-free hierarchies. With the exception of one, which is still open, these are not robust either. We conclude with the open question of whether non-trivial robust wait-free hierarchies exist.

  10. Models of neutrino masses: Anarchy versus hierarchy

    International Nuclear Information System (INIS)

    Altarelli, Guido; Feruglio, Ferruccio; Masina, Isabella

    2003-01-01

    We present a quantitative study of the ability of models with different levels of hierarchy to reproduce the solar neutrino solutions, in particular the LA solution. As a flexible testing ground we consider models based on SU(5)xU(1) F . In this context, we have made statistical simulations of models with different patterns from anarchy to various types of hierarchy: normal hierarchical models with and without automatic suppression of the 23 (sub)determinant and inverse hierarchy models. We find that, not only for the LOW or VO solutions, but even in the LA case, the hierarchical models have a significantly better success rate than those based on anarchy. The normal hierarchy and the inverse hierarchy models have comparable performances in models with see-saw dominance, while the inverse hierarchy models are particularly good in the no see-saw versions. As a possible distinction between these categories of models, the inverse hierarchy models favour a maximal solar mixing angle and their rate of success drops dramatically as the mixing angle decreases, while normal hierarchy models are far more stable in this respect. (author)

  11. Coupling Integrable Couplings of an Equation Hierarchy

    International Nuclear Information System (INIS)

    Wang Hui; Xia Tie-Cheng

    2013-01-01

    Based on a kind of Lie algebra G proposed by Zhang, one isospectral problem is designed. Under the framework of zero curvature equation, a new kind of integrable coupling of an equation hierarchy is generated using the methods proposed by Ma and Gao. With the help of variational identity, we get the Hamiltonian structure of the hierarchy. (general)

  12. A Suggested Modification to Maslow's Need Hierarchy

    Science.gov (United States)

    Groves, David L.; And Others

    1975-01-01

    Since its development, Maslow's need hierarchy has been criticized and applauded. This investigation was undertaken to explore a modification of the upper levels of the need hierarchy based upon the application of power, competition, and achievement to self, as well as the concept of "other directed." (Author)

  13. Solution of the gauge hierarchy problem

    International Nuclear Information System (INIS)

    Dimopoulos, S.; Georgi, H.

    1982-01-01

    We propose a novel solution to the gauge hierarchy problem in theories with softly broken supersymmetry. Quantum effects can resuscitate classically sick theories, producing the large scale from the small supersymmetry breaking scale. We use this mechanism to construct realistic SU(6) and SU(5) GUTs which do not suffer from gauge hierarchy or fine tuning problems. (orig.)

  14. q-Deformed KP Hierarchy and q-Deformed Constrained KP Hierarchy

    OpenAIRE

    He, Jingsong; Li, Yinghua; Cheng, Yi

    2006-01-01

    Using the determinant representation of gauge transformation operator, we have shown that the general form of $au$ function of the $q$-KP hierarchy is a $q$-deformed generalized Wronskian, which includes the $q$-deformed Wronskian as a special case. On the basis of these, we study the $q$-deformed constrained KP ($q$-cKP) hierarchy, i.e. $l$-constraints of $q$-KP hierarchy. Similar to the ordinary constrained KP (cKP) hierarchy, a large class of solutions of $q$-cKP hierarchy can be represent...

  15. A unified expressing model of the AKNS hierarchy and the KN hierarchy, as well as its integrable coupling system

    International Nuclear Information System (INIS)

    Guo Fukui; Zhang Yufeng

    2004-01-01

    A new subalgebra of loop algebra A-tilde 1 is first constructed. Then a new Lax pair is presented, whose compatibility gives rise to a new Liouville integrable system(called a major result), possessing bi-Hamiltonian structures. It is remarkable that two symplectic operators obtained in this paper are directly constructed in terms of the recurrence relations. As reduction cases of the new integrable system obtained, the famous AKNS hierarchy and the KN hierarchy are obtained, respectively. Second, we prove a conjugate operator of a recurrence operator is a hereditary symmetry. Finally, we construct a high dimension loop algebra G-bar to obtain an integrable coupling system of the major result by making use of Tu scheme. In addition, we find the major result obtained is a unified expressing integrable model of both the AKNS and KN hierarchies, of course, we may also regard the major result as an expanding integrable model of the AKNS and KN hierarchies. Thus, we succeed to find an example of expanding integrable models being Liouville integrable

  16. Is there a hierarchy of survival reflexes?

    Science.gov (United States)

    Macphail, Kieran

    2013-10-01

    A hierarchy of survival reflexes for prioritising assessment and treatment in patients with pain of insidious onset is hypothesised. The hierarchy asserts that some systems are more vital than others and that the central nervous system (CNS) prioritises systems based on their significance to survival. The hypothesis suggests that dysfunction in more important systems will cause compensation in less important systems. This paper presents studies examining these effects for each system, arguing that each section of the hierarchy may have effects on other systems within the hierarchy. This concept is untested empirically, highly speculative and substantial research is required to validate the suggested hierarchical prioritisation by the CNS. Nonetheless, the hierarchy does provide a theoretical framework to use to exclude contributing systems in patients with pain of insidious onset. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Constrained KP models as integrable matrix hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.; Ferreira, L.A.; Gomes, J.F.; Zimerman, A.H.

    1997-01-01

    We formulate the constrained KP hierarchy (denoted by cKP K+1,M ) as an affine [cflx sl](M+K+1) matrix integrable hierarchy generalizing the Drinfeld endash Sokolov hierarchy. Using an algebraic approach, including the graded structure of the generalized Drinfeld endash Sokolov hierarchy, we are able to find several new universal results valid for the cKP hierarchy. In particular, our method yields a closed expression for the second bracket obtained through Dirac reduction of any untwisted affine Kac endash Moody current algebra. An explicit example is given for the case [cflx sl](M+K+1), for which a closed expression for the general recursion operator is also obtained. We show how isospectral flows are characterized and grouped according to the semisimple non-regular element E of sl(M+K+1) and the content of the center of the kernel of E. copyright 1997 American Institute of Physics

  18. Resolution of ranking hierarchies in directed networks

    Science.gov (United States)

    Barucca, Paolo; Lillo, Fabrizio

    2018-01-01

    Identifying hierarchies and rankings of nodes in directed graphs is fundamental in many applications such as social network analysis, biology, economics, and finance. A recently proposed method identifies the hierarchy by finding the ordered partition of nodes which minimises a score function, termed agony. This function penalises the links violating the hierarchy in a way depending on the strength of the violation. To investigate the resolution of ranking hierarchies we introduce an ensemble of random graphs, the Ranked Stochastic Block Model. We find that agony may fail to identify hierarchies when the structure is not strong enough and the size of the classes is small with respect to the whole network. We analytically characterise the resolution threshold and we show that an iterated version of agony can partly overcome this resolution limit. PMID:29394278

  19. The Lax operator approach for the Virasoro and the W-constraints in the generalized KdV hierarchy

    International Nuclear Information System (INIS)

    Panda, S.; Roy, S.

    1992-08-01

    We show directly in the Lax operator approach how the Virasoro and W-constraints on the τ-function arise in the p-reduced KP hierarchy or Generalized KdV hierarchy. In particular, we consider the KdV and the Boussinesq hierarchy to show that the Virasoro and the W-constraints follow from the string equation by expanding the ''additional symmetry'' operator in terms of the Lax operator. We also mention how this method could be generalized for higher KdV hierarchies. (author). 34 refs

  20. Annotation of nerve cord transcriptome in earthworm Eisenia fetida

    Directory of Open Access Journals (Sweden)

    Vasanthakumar Ponesakki

    2017-12-01

    Full Text Available In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.

  1. An annotated corpus with nanomedicine and pharmacokinetic parameters

    Directory of Open Access Journals (Sweden)

    Lewinski NA

    2017-10-01

    Full Text Available Nastassja A Lewinski,1 Ivan Jimenez,1 Bridget T McInnes2 1Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, 2Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA Abstract: A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided. Keywords: nanotechnology, informatics, natural language processing, text mining, corpora

  2. Automatic annotation of lecture videos for multimedia driven pedagogical platforms

    Directory of Open Access Journals (Sweden)

    Ali Shariq Imran

    2016-12-01

    Full Text Available Today’s eLearning websites are heavily loaded with multimedia contents, which are often unstructured, unedited, unsynchronized, and lack inter-links among different multimedia components. Hyperlinking different media modality may provide a solution for quick navigation and easy retrieval of pedagogical content in media driven eLearning websites. In addition, finding meta-data information to describe and annotate media content in eLearning platforms is challenging, laborious, prone to errors, and time-consuming task. Thus annotations for multimedia especially of lecture videos became an important part of video learning objects. To address this issue, this paper proposes three major contributions namely, automated video annotation, the 3-Dimensional (3D tag clouds, and the hyper interactive presenter (HIP eLearning platform. Combining existing state-of-the-art SIFT together with tag cloud, a novel approach for automatic lecture video annotation for the HIP is proposed. New video annotations are implemented automatically providing the needed random access in lecture videos within the platform, and a 3D tag cloud is proposed as a new way of user interaction mechanism. A preliminary study of the usefulness of the system has been carried out, and the initial results suggest that 70% of the students opted for using HIP as their preferred eLearning platform at Gjøvik University College (GUC.

  3. An annotated corpus with nanomedicine and pharmacokinetic parameters.

    Science.gov (United States)

    Lewinski, Nastassja A; Jimenez, Ivan; McInnes, Bridget T

    2017-01-01

    A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration's Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the evaluation of nanomedicine entity extraction. The data were manually annotated for 21 entity mentions consisting of nanomedicine physicochemical characterization, exposure, and biologic response information of 41 Food and Drug Administration-approved nanomedicines. We evaluate the reliability of the manual annotations and demonstrate the use of the corpus by evaluating two state-of-the-art named entity extraction systems, OpenNLP and Stanford NER. The annotated corpus is available open source and, based on these results, guidelines and suggestions for future development of additional nanomedicine corpora are provided.

  4. Dictionary-driven protein annotation.

    Science.gov (United States)

    Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel

    2002-09-01

    Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were

  5. Shakespeare Is Alive and Well in Cyberspace: An Annotated Bibliography.

    Science.gov (United States)

    Hett, Dorothy Marie

    2002-01-01

    Suggests that in addition to using books and movies to enhance students' understanding of Shakespeare, teachers can add the World Wide Web to their repertoire to help students connect to Shakespeare. Presents annotations of 12 websites to use for teaching Shakespeare. (SG)

  6. Evaluating Hierarchical Structure in Music Annotations.

    Science.gov (United States)

    McFee, Brian; Nieto, Oriol; Farbood, Morwaread M; Bello, Juan Pablo

    2017-01-01

    Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for "flat" descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

  7. Evaluating Hierarchical Structure in Music Annotations

    Directory of Open Access Journals (Sweden)

    Brian McFee

    2017-08-01

    Full Text Available Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR, it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for “flat” descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.

  8. A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.

    Directory of Open Access Journals (Sweden)

    Lex Overmars

    Full Text Available The identification of translation initiation sites (TISs constitutes an important aspect of sequence-based genome analysis. An erroneous TIS annotation can impair the identification of regulatory elements and N-terminal signal peptides, and also may flaw the determination of descent, for any particular gene. We have formulated a reference-free method to score the TIS annotation quality. The method is based on a comparison of the observed and expected distribution of all TISs in a particular genome given prior gene-calling. We have assessed the TIS annotations for all available NCBI RefSeq microbial genomes and found that approximately 87% is of appropriate quality, whereas 13% needs substantial improvement. We have analyzed a number of factors that could affect TIS annotation quality such as GC-content, taxonomy, the fraction of genes with a Shine-Dalgarno sequence and the year of publication. The analysis showed that only the first factor has a clear effect. We have then formulated a straightforward Principle Component Analysis-based TIS identification strategy to self-organize and score potential TISs. The strategy is independent of reference data and a priori calculations. A representative set of 277 genomes was subjected to the analysis and we found a clear increase in TIS annotation quality for the genomes with a low quality score. The PCA-based annotation was also compared with annotation with the current tool of reference, Prodigal. The comparison for the model genome of Escherichia coli K12 showed that both methods supplement each other and that prediction agreement can be used as an indicator of a correct TIS annotation. Importantly, the data suggest that the addition of a PCA-based strategy to a Prodigal prediction can be used to 'flag' TIS annotations for re-evaluation and in addition can be used to evaluate a given annotation in case a Prodigal annotation is lacking.

  9. Training nuclei detection algorithms with simple annotations

    Directory of Open Access Journals (Sweden)

    Henning Kost

    2017-01-01

    Full Text Available Background: Generating good training datasets is essential for machine learning-based nuclei detection methods. However, creating exhaustive nuclei contour annotations, to derive optimal training data from, is often infeasible. Methods: We compared different approaches for training nuclei detection methods solely based on nucleus center markers. Such markers contain less accurate information, especially with regard to nuclear boundaries, but can be produced much easier and in greater quantities. The approaches use different automated sample extraction methods to derive image positions and class labels from nucleus center markers. In addition, the approaches use different automated sample selection methods to improve the detection quality of the classification algorithm and reduce the run time of the training process. We evaluated the approaches based on a previously published generic nuclei detection algorithm and a set of Ki-67-stained breast cancer images. Results: A Voronoi tessellation-based sample extraction method produced the best performing training sets. However, subsampling of the extracted training samples was crucial. Even simple class balancing improved the detection quality considerably. The incorporation of active learning led to a further increase in detection quality. Conclusions: With appropriate sample extraction and selection methods, nuclei detection algorithms trained on the basis of simple center marker annotations can produce comparable quality to algorithms trained on conventionally created training sets.

  10. Hierarchy is Detrimental for Human Cooperation

    Science.gov (United States)

    Cronin, Katherine A.; Acheson, Daniel J.; Hernández, Penélope; Sánchez, Angel

    2015-01-01

    Studies of animal behavior consistently demonstrate that the social environment impacts cooperation, yet the effect of social dynamics has been largely excluded from studies of human cooperation. Here, we introduce a novel approach inspired by nonhuman primate research to address how social hierarchies impact human cooperation. Participants competed to earn hierarchy positions and then could cooperate with another individual in the hierarchy by investing in a common effort. Cooperation was achieved if the combined investments exceeded a threshold, and the higher ranked individual distributed the spoils unless control was contested by the partner. Compared to a condition lacking hierarchy, cooperation declined in the presence of a hierarchy due to a decrease in investment by lower ranked individuals. Furthermore, hierarchy was detrimental to cooperation regardless of whether it was earned or arbitrary. These findings mirror results from nonhuman primates and demonstrate that hierarchies are detrimental to cooperation. However, these results deviate from nonhuman primate findings by demonstrating that human behavior is responsive to changing hierarchical structures and suggests partnership dynamics that may improve cooperation. This work introduces a controlled way to investigate the social influences on human behavior, and demonstrates the evolutionary continuity of human behavior with other primate species. PMID:26692287

  11. Hierarchy is Detrimental for Human Cooperation.

    Science.gov (United States)

    Cronin, Katherine A; Acheson, Daniel J; Hernández, Penélope; Sánchez, Angel

    2015-12-22

    Studies of animal behavior consistently demonstrate that the social environment impacts cooperation, yet the effect of social dynamics has been largely excluded from studies of human cooperation. Here, we introduce a novel approach inspired by nonhuman primate research to address how social hierarchies impact human cooperation. Participants competed to earn hierarchy positions and then could cooperate with another individual in the hierarchy by investing in a common effort. Cooperation was achieved if the combined investments exceeded a threshold, and the higher ranked individual distributed the spoils unless control was contested by the partner. Compared to a condition lacking hierarchy, cooperation declined in the presence of a hierarchy due to a decrease in investment by lower ranked individuals. Furthermore, hierarchy was detrimental to cooperation regardless of whether it was earned or arbitrary. These findings mirror results from nonhuman primates and demonstrate that hierarchies are detrimental to cooperation. However, these results deviate from nonhuman primate findings by demonstrating that human behavior is responsive to changing hierarchical structures and suggests partnership dynamics that may improve cooperation. This work introduces a controlled way to investigate the social influences on human behavior, and demonstrates the evolutionary continuity of human behavior with other primate species.

  12. Formal language theory: refining the Chomsky hierarchy.

    Science.gov (United States)

    Jäger, Gerhard; Rogers, James

    2012-07-19

    The first part of this article gives a brief overview of the four levels of the Chomsky hierarchy, with a special emphasis on context-free and regular languages. It then recapitulates the arguments why neither regular nor context-free grammar is sufficiently expressive to capture all phenomena in the natural language syntax. In the second part, two refinements of the Chomsky hierarchy are reviewed, which are both relevant to the extant research in cognitive science: the mildly context-sensitive languages (which are located between context-free and context-sensitive languages), and the sub-regular hierarchy (which distinguishes several levels of complexity within the class of regular languages).

  13. A quark interpretation of the combinatorial hierarchy

    International Nuclear Information System (INIS)

    Enqvist, Kari.

    1979-01-01

    We propose a physical interpretation of the second level of the combinatorial hierarchy in terms of three quarks, three antiquarks and the vacuum. This interpretation allows us to introduce a new quantum number, which measures electromagnetic mass splitting of the quarks. We extend our argument by analogue to baryons, and find some SU(3) and some new mass formulas for baryons. The generalization of our approach to other hierarchy levels is discussed. We present also an empirical mass formula for baryons, which seems to be loosely connected with the combinatorial hierarchy. (author)

  14. Use of Annotations for Component and Framework Interoperability

    Science.gov (United States)

    David, O.; Lloyd, W.; Carlson, J.; Leavesley, G. H.; Geter, F.

    2009-12-01

    The popular programming languages Java and C# provide annotations, a form of meta-data construct. Software frameworks for web integration, web services, database access, and unit testing now take advantage of annotations to reduce the complexity of APIs and the quantity of integration code between the application and framework infrastructure. Adopting annotation features in frameworks has been observed to lead to cleaner and leaner application code. The USDA Object Modeling System (OMS) version 3.0 fully embraces the annotation approach and additionally defines a meta-data standard for components and models. In version 3.0 framework/model integration previously accomplished using API calls is now achieved using descriptive annotations. This enables the framework to provide additional functionality non-invasively such as implicit multithreading, and auto-documenting capabilities while achieving a significant reduction in the size of the model source code. Using a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside of it. To study the effectiveness of an annotation based framework approach with other modeling frameworks, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A monthly water balance model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. In a next step, the PRMS model was implemented in OMS 3.0 and is currently being implemented for water supply forecasting in the

  15. Hierarchy of modular graph identities

    International Nuclear Information System (INIS)

    D’Hoker, Eric; Kaidi, Justin

    2016-01-01

    The low energy expansion of Type II superstring amplitudes at genus one is organized in terms of modular graph functions associated with Feynman graphs of a conformal scalar field on the torus. In earlier work, surprising identities between two-loop graphs at all weights, and between higher-loop graphs of weights four and five were constructed. In the present paper, these results are generalized in two complementary directions. First, all identities at weight six and all dihedral identities at weight seven are obtained and proven. Whenever the Laurent polynomial at the cusp is available, the form of these identities confirms the pattern by which the vanishing of the Laurent polynomial governs the full modular identity. Second, the family of modular graph functions is extended to include all graphs with derivative couplings and worldsheet fermions. These extended families of modular graph functions are shown to obey a hierarchy of inhomogeneous Laplace eigenvalue equations. The eigenvalues are calculated analytically for the simplest infinite sub-families and obtained by Maple for successively more complicated sub-families. The spectrum is shown to consist solely of eigenvalues s(s−1) for positive integers s bounded by the weight, with multiplicities which exhibit rich representation-theoretic patterns.

  16. Sniffing behavior communicates social hierarchy.

    Science.gov (United States)

    Wesson, Daniel W

    2013-04-08

    Sniffing is a specialized respiratory behavior that is essential for the acquisition of odors [1-4]. Perhaps not independent of this, sniffing is commonly displayed during motivated [5-7] and social behaviors [8, 9]. No measures of sniffing among interacting animals are available, however, calling into question the utility of this behavior in the social context. From radiotelemetry recordings of nasal respiration, I found that investigation by one rat toward the facial region of a conspecific often elicits a decrease in sniffing frequency in the conspecific. This reciprocal display of sniffing was found to be dependent upon the rat's social status in two separate paradigms, with subordinates reliably decreasing their sniffing frequency upon being investigated in the face by dominant rats. Failure of subordinates to decrease their sniffing frequency shortened the latency for agonistic behavior by dominant rats, reflecting that decreases in sniffing serve as appeasement signals during social interactions. Rats rendered unable to smell persisted in displaying reciprocal sniffing behavior, demonstrating the independence of this behavior from olfaction. Oxytocin treatment in rats with established social hierarchies abolished agonistic behaviors and reciprocal sniffing displays. Together, these findings demonstrate that rodents utilize sniffing behaviors communicatively, not only to collect [6, 10-14] but also to convey information. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Hierarchy of modular graph identities

    Energy Technology Data Exchange (ETDEWEB)

    D’Hoker, Eric; Kaidi, Justin [Mani L. Bhaumik Institute for Theoretical Physics, Department of Physics and Astronomy,University of California,Los Angeles, CA 90095 (United States)

    2016-11-09

    The low energy expansion of Type II superstring amplitudes at genus one is organized in terms of modular graph functions associated with Feynman graphs of a conformal scalar field on the torus. In earlier work, surprising identities between two-loop graphs at all weights, and between higher-loop graphs of weights four and five were constructed. In the present paper, these results are generalized in two complementary directions. First, all identities at weight six and all dihedral identities at weight seven are obtained and proven. Whenever the Laurent polynomial at the cusp is available, the form of these identities confirms the pattern by which the vanishing of the Laurent polynomial governs the full modular identity. Second, the family of modular graph functions is extended to include all graphs with derivative couplings and worldsheet fermions. These extended families of modular graph functions are shown to obey a hierarchy of inhomogeneous Laplace eigenvalue equations. The eigenvalues are calculated analytically for the simplest infinite sub-families and obtained by Maple for successively more complicated sub-families. The spectrum is shown to consist solely of eigenvalues s(s−1) for positive integers s bounded by the weight, with multiplicities which exhibit rich representation-theoretic patterns.

  18. Topological Strings and Integrable Hierarchies

    CERN Document Server

    Aganagic, M; Klemm, A D; Marino, M; Vafa, C; Aganagic, Mina; Dijkgraaf, Robbert; Klemm, Albrecht; Marino, Marcos; Vafa, Cumrun

    2006-01-01

    We consider the topological B-model on local Calabi-Yau geometries. We show how one can solve for the amplitudes by using W-algebra symmetries which encodes the symmetries of holomorphic diffeomorphisms of the Calabi-Yau. In the highly effective fermionic/brane formulation this leads to a free fermion description of the amplitudes. Furthermore we argue that topological strings on Calabi-Yau geometries provide a unifying picture connecting non-critical (super)strings, integrable hierarchies, and various matrix models. In particular we show how the ordinary matrix model, the double scaling limit of matrix models, and Kontsevich-like matrix model are all related and arise from studying branes in specific local Calabi-Yau three-folds. We also show how A-model topological string on P^1 and local toric threefolds (and in particular the topological vertex) can be realized and solved as B-model topological string amplitudes on a Calabi-Yau manifold.

  19. Fermion hierarchy from sfermion anarchy

    International Nuclear Information System (INIS)

    Altmannshofer, Wolfgang; Frugiuele, Claudia; Harnik, Roni

    2014-01-01

    We present a framework to generate the hierarchical flavor structure of Standard Model quarks and leptons from loops of superpartners. The simplest model consists of the minimal supersymmetric standard model with tree level Yukawa couplings for the third generation only and anarchic squark and slepton mass matrices. Agreement with constraints from low energy flavor observables, in particular Kaon mixing, is obtained for supersymmetric particles with masses at the PeV scale or above. In our framework both the second and the first generation fermion masses are generated at 1-loop. Despite this, a novel mechanism generates a hierarchy among the first and second generations without imposing a symmetry or small parameters. A second-to-first generation mass ratio of order 100 is typical. The minimal supersymmetric standard model thus includes all the necessary ingredients to realize a fermion spectrum that is qualitatively similar to observation, with hierarchical masses and mixing. The minimal framework produces only a few quantitative discrepancies with observation, most notably the muon mass is too low. Furthermore, we discuss simple modifications which resolve this and also investigate the compatibility of our model with gauge and Yukawa coupling Unification

  20. Semantic annotation in biomedicine: the current landscape.

    Science.gov (United States)

    Jovanović, Jelena; Bagheri, Ebrahim

    2017-09-22

    The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators.Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.

  1. Why we live in hierarchies? a quantitative treatise

    CERN Document Server

    Zafeiris, Anna

    2018-01-01

    This book systematically interprets and documents new, unifying principles and basic laws describing the most relevant aspects of hierarchy. To do so, it discusses recent experiments and models that are simple and realistic enough to reproduce the observations, and develops concepts for a better understanding of the complexity of systems consisting of many organisms. The book covers systems ranging from flocks of birds to groups of people.   Although it focuses on hierarchical collective behavior in general, two aspects pop up in the majority of cases: collective motion and dynamically changing, partially directed networks (and the natural relation between the two). In addition, it offers a brief description of the most relevant definitions and concepts involved in the context of hierarchies, presenting both a review of the current literature and a number of new experimental and computational results in more detail. It is a valuable resource for students and scholars pursuing research on the structure of in...

  2. Identifying the neutrino mass hierarchy with supernova neutrinos

    International Nuclear Information System (INIS)

    Tomas, Ricard

    2006-01-01

    We review how a high-statistics observation of the neutrino signal from a future galactic core-collapse supernova (SN) may be used to discriminate between different neutrino mixing scenarios. We discuss two complementary methods that allow for the positive identification of the mass hierarchy without knowledge of the emitted neutrino fluxes, provided that the 13-mixing angle is large, sin 2 θ 13 -5 . These two approaches are the observation of modulations in the neutrino spectra by Earth matter effects or by the passage of shock waves through the SN envelope. If the value of the 13-mixing angle is unknown, using additionally the information encoded in the prompt neutronization ν e burst-a robust feature found in all modern SN simulations-can be sufficient to fix both the neutrino hierarchy and to decide whether θ 13 is 'small' or 'large'

  3. Brane world model and hierarchy problem

    International Nuclear Information System (INIS)

    Alba, V.

    2007-01-01

    In this paper I wrote description of Kaluza-Klein model. Also I wrote how we can solve the hierarchy problem in Randall-Sundrum model. In fact, it's my motivation to study this part of theoretical physics

  4. Hierarchies of belief and interim rationalizability

    Directory of Open Access Journals (Sweden)

    Jeffrey C. Ely

    2006-03-01

    Full Text Available In games with incomplete information, conventional hierarchies of belief are incomplete as descriptions of the players' information for the purposes of determining a player's behavior. We show by example that this is true for a variety of solution concepts. We then investigate what is essential about a player's information to identify behavior. We specialize to two player games and the solution concept of interim rationalizability. We construct the universal type space for rationalizability and characterize the types in terms of their beliefs. Infinite hierarchies of beliefs over conditional beliefs, which we call Delta-hierarchies, are what turn out to matter. We show that any two types in any two type spaces have the same rationalizable sets in all games if and only if they have the same Delta-hierarchies.

  5. Probing Neutrino Mass Hierarchy with Supernova

    International Nuclear Information System (INIS)

    Chakraborty, Sovan

    2013-01-01

    The rise time of electron antineutrino lightcurve from a Galactic supernova (SN), observable at the IceCube Cherenkov detector, can provide signature of the neutrino mass hierarchy at “large” 1-3 leptonic mixing angle ϑ 13 . In the early accretion phase of the SN, the neutrino oscillations are nontrivial. Due to the matter suppression of collective effects at these early post bounce times, only the MSW resonances in the outer layers of the SN influence the neutrino flux. When the oscillations are taken into account, the signal in IceCube shows sufficiently fast rise time for the inverted mass hierarchy compared to the normal hierarchy. An investigation with an extensive set of stellar core-collapse simulations, provides both qualitative and quantitative robustness of these features. Thus opening another avenue to explore the neutrino mass hierarchy with the rise time of a supernova burst

  6. Planning hierarchy, modeling and sdvanced planning dystems

    OpenAIRE

    Meyr, Herbert Ottmar

    2003-01-01

    Planning hierarchy, modeling and sdvanced planning dystems / B. Fleischmann, H. Meyr. - In: Supply chain management / ed. by A. G. de Kok ... - Amsterdam u.a. : Elsevier, 2003. - (Handbooks in operations research and management science ; 11)

  7. The multi-component WKI hierarchy

    International Nuclear Information System (INIS)

    Yao Yuqin; Zhang Yufeng

    2005-01-01

    Firstly a new loop algebra G∼ M with 3M dimensions is constructed, which is devoted to establishing a new isospectral problem. Then the multi-component WKI hierarchy of soliton equations is obtained

  8. Improving Expression Power in Modeling OLAP Hierarchies

    Science.gov (United States)

    Malinowski, Elzbieta

    Data warehouses and OLAP systems form an integral part of modern decision support systems. In order to exploit both systems to their full capabilities hierarchies must be clearly defined. Hierarchies are important in analytical applications, since they provide users with the possibility to represent data at different abstraction levels. However, even though there are different kinds of hierarchies in real-world applications and some are already implemented in commercial tools, there is still a lack of a well-accepted conceptual model that allows decision-making users express their analysis needs. In this paper, we show how the conceptual multidimensional model can be used to facilitate the representation of complex hierarchies in comparison to their representation in the relational model and commercial OLAP tool, using as an example Microsoft Analysis Services.

  9. Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.

    Science.gov (United States)

    Krishnan, Arunkumar; Mustafa, Arshi; Almén, Markus Sällman; Fredriksson, Robert; Williams, Michael J; Schiöth, Helgi B

    2015-10-01

    Heterotrimeric G proteins perform a crucial role as molecular switches controlling various cellular responses mediated by G protein-coupled receptor (GPCR) signaling pathway. Recent data have shown that the vertebrate-like G protein families are found across metazoans and their closest unicellular relatives. However, an overall evolutionary hierarchy of vertebrate-like G proteins, including gene family annotations and in particular mapping individual gene gain/loss events across diverse holozoan lineages is still incomplete. Here, with more expanded invertebrate taxon sampling, we have reconstructed phylogenetic trees for each of the G protein classes/families and provide a robust classification and hierarchy of vertebrate-like heterotrimeric G proteins. Our results further extend the evidence that the common ancestor (CA) of holozoans had at least five ancestral Gα genes corresponding to all major vertebrate Gα classes and contain a total of eight genes including two Gβ and one Gγ. Our results also indicate that the GNAI/O-like gene likely duplicated in the last CA of metazoans to give rise to GNAI- and GNAO-like genes, which are conserved across invertebrates. Moreover, homologs of GNB1-4 paralogon- and GNB5 family-like genes are found in most metazoans and that the unicellular holozoans encode two ancestral Gβ genes. Similarly, most bilaterian invertebrates encode two Gγ genes which include a representative of the GNG gene cluster and a putative homolog of GNG13. Interestingly, our results also revealed key evolutionary events such as the Drosophila melanogaster eye specific Gβ subunit that is found conserved in most arthropods and several previously unidentified species specific expansions within Gαi/o, Gαs, Gαq, Gα12/13 classes and the GNB1-4 paralogon. Also, we provide an overall proposed evolutionary scenario on the expansions of all G protein families in vertebrate tetraploidizations. Our robust classification/hierarchy is essential to further

  10. A hierarchy of Ramsey-like cardinals

    OpenAIRE

    Holy, Peter; Schlicht, Philipp

    2017-01-01

    We introduce a hierarchy of large cardinals between weakly compact and measurable cardinals, that is closely related to the Ramsey-like cardinals introduced by Victoria Gitman, and is based on certain infinite filter games, however also has a range of equivalent characterizations in terms of elementary embeddings. The aim of this paper is to locate the Ramsey-like cardinals studied by Gitman, and other well-known large cardinal notions, in this hierarchy.

  11. Fermion mass hierarchies in theories of technicolor

    International Nuclear Information System (INIS)

    Peskin, M.E.

    1981-01-01

    Models in which light fermion masses result from dynamical symmetry breaking often produce these masses in a hierarchial pattern. The author exhibits two scenarios for obtaining such hierarchies and illustrates each with a simple model of mass generation. In the first scenario, the light fermion masses are separated by powers of a weak coupling constant; in the second scenario, they are separated by a ratio of large mass scales

  12. Hierarchy among Automata on Linear Orderings

    OpenAIRE

    Bruyère , Véronique; Carton , Olivier

    2005-01-01

    In a preceding paper, automata and rational expressions have been introduced for words indexed by linear orderings, together with a Kleene-like theorem. We here pursue this work by proposing a hierarchy among the rational sets. Each class of the hierarchy is defined by a subset of the rational operations that can be used. We then characterize any class by an appropriate class of automata, leading to a Kleene theorem inside the class. A characterization by particular classes of orderings is al...

  13. Shrinking population and the urban hierarchy

    OpenAIRE

    Kim, Ho Yeon

    2012-01-01

    This paper examines whether population shrinkage leads to changes in the urban hierarchy in terms of relative sizes of cities and their functions onomic geography. We work backwards in a racetrack economy with eight cities in a long-run equilibrium. Initial distribution of population is chosen to satisfy both the rank-size rule and central place hierarchy. We have a short-run equilibrium in which firms choose prices and consumers choose consumption taking the number of workers in each region ...

  14. Hierarchy generation in compactified supersymmetric models

    International Nuclear Information System (INIS)

    Ross, G.G.

    1988-01-01

    The problem of generating a large hierarchy in compactified supersymmetric models is re-examined. It is shown how, even for the class of models for which Str M 2 is non-vanishing, a combination of non-perturbative effects and radiative corrections may lead to an exponentially large hierarchy. A corollary is that the couplings of the effective field theory in the visible sector should be small, i.e., perturbation theory should be applicable. (orig.)

  15. Learning of Alignment Rules between Concept Hierarchies

    Science.gov (United States)

    Ichise, Ryutaro; Takeda, Hideaki; Honiden, Shinichi

    With the rapid advances of information technology, we are acquiring much information than ever before. As a result, we need tools for organizing this data. Concept hierarchies such as ontologies and information categorizations are powerful and convenient methods for accomplishing this goal, which have gained wide spread acceptance. Although each concept hierarchy is useful, it is difficult to employ multiple concept hierarchies at the same time because it is hard to align their conceptual structures. This paper proposes a rule learning method that inputs information from a source concept hierarchy and finds suitable location for them in a target hierarchy. The key idea is to find the most similar categories in each hierarchy, where similarity is measured by the κ(kappa) statistic that counts instances belonging to both categories. In order to evaluate our method, we conducted experiments using two internet directories: Yahoo! and LYCOS. We map information instances from the source directory into the target directory, and show that our learned rules agree with a human-generated assignment 76% of the time.

  16. Solutions of the bigraded Toda hierarchy

    International Nuclear Information System (INIS)

    Li Chuanzhong

    2011-01-01

    The (N, M)-bigraded Toda hierarchy is an extension of the original Toda lattice hierarchy. The pair of numbers (N, M) represents the band structure of the Lax matrix which has N upper and M lower diagonals, and the original one is referred to as the (1, 1)-bigraded Toda hierarchy. Because of this band structure, one can introduce M + N - 1 commuting flows which give a parametrization of a small phase space for a topological field theory. In this paper, first we show that there exists a natural symmetry between the (N, M)- and (M, N)-bigraded Toda hierarchies. We then derive the Hirota bilinear form for those commuting flows, which consist of two-dimensional Toda hierarchy, the discrete KP hierarchy and its Baecklund transformations. We also discuss the solution structure of the (N, M)-bigraded Toda equation in terms of the moment matrix defined via the wave operators associated with the Lax operator and construct some of the explicit solutions. In particular, we give the rational solutions which are expressed by the products of the Schur polynomials corresponding to the non-rectangular Young diagrams.

  17. Signaling hierarchy regulating human endothelial cell development.

    Science.gov (United States)

    Kelly, Melissa A; Hirschi, Karen K

    2009-05-01

    Our present knowledge of the regulation of mammalian endothelial cell differentiation has been largely derived from studies of mouse embryonic development. However, unique mechanisms and hierarchy of signals that govern human endothelial cell development are unknown and, thus, explored in these studies. Using human embryonic stem cells as a model system, we were able to reproducibly and robustly generate differentiated endothelial cells via coculture on OP9 marrow stromal cells. We found that, in contrast to studies in the mouse, bFGF and VEGF had no specific effects on the initiation of human vasculogenesis. However, exogenous Ihh promoted endothelial cell differentiation, as evidenced by increased production of cells with cobblestone morphology that coexpress multiple endothelial-specific genes and proteins, form lumens, and exhibit DiI-AcLDL uptake. Inhibition of BMP signaling using Noggin or BMP4, specifically, using neutralizing antibodies suppressed endothelial cell formation; whereas, addition of rhBMP4 to cells treated with the hedgehog inhibitor cyclopamine rescued endothelial cell development. Our studies revealed that Ihh promoted human endothelial cell differentiation from pluripotent hES cells via BMP signaling, providing novel insights applicable to modulating human endothelial cell formation and vascular regeneration for human clinical therapies.

  18. Linking human diseases to animal models using ontology-based phenotype annotation.

    Directory of Open Access Journals (Sweden)

    Nicole L Washington

    2009-11-01

    Full Text Available Scientists and clinicians who study genetic alterations and disease have traditionally described phenotypes in natural language. The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally tractable method to mine data resources for mutant phenotypes. In this study, we tested the hypothesis that ontological annotation of disease phenotypes will facilitate the discovery of new genotype-phenotype relationships within and across species. To describe phenotypes using ontologies, we used an Entity-Quality (EQ methodology, wherein the affected entity (E and how it is affected (Q are recorded using terms from a variety of ontologies. Using this EQ method, we annotated the phenotypes of 11 gene-linked human diseases described in Online Mendelian Inheritance in Man (OMIM. These human annotations were loaded into our Ontology-Based Database (OBD along with other ontology-based phenotype descriptions of mutants from various model organism databases. Phenotypes recorded with this EQ method can be computationally compared based on the hierarchy of terms in the ontologies and the frequency of annotation. We utilized four similarity metrics to compare phenotypes and developed an ontology of homologous and analogous anatomical structures to compare phenotypes between species. Using these tools, we demonstrate that we can identify, through the similarity of the recorded phenotypes, other alleles of the same gene, other members of a signaling pathway, and orthologous genes and pathway members across species. We conclude that EQ-based annotation of phenotypes, in conjunction with a cross-species ontology, and a variety of similarity metrics can identify biologically meaningful similarities between genes by comparing phenotypes alone. This annotation and search method provides a novel and efficient means to identify

  19. Annotating temporal information in clinical narratives.

    Science.gov (United States)

    Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem

    2013-12-01

    Temporal information in clinical narratives plays an important role in patients' diagnosis, treatment and prognosis. In order to represent narrative information accurately, medical natural language processing (MLP) systems need to correctly identify and interpret temporal information. To promote research in this area, the Informatics for Integrating Biology and the Bedside (i2b2) project developed a temporally annotated corpus of clinical narratives. This corpus contains 310 de-identified discharge summaries, with annotations of clinical events, temporal expressions and temporal relations. This paper describes the process followed for the development of this corpus and discusses annotation guideline development, annotation methodology, and corpus quality. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Estimating the annotation error rate of curated GO database sequence annotations

    Directory of Open Access Journals (Sweden)

    Brown Alfred L

    2007-05-01

    Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

  1. Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

    Science.gov (United States)

    Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young; Bada, Michael; Baumgartner, William A; Panteleyeva, Natalya; Verspoor, Karin; Palmer, Martha; Hunter, Lawrence E

    2017-08-17

    Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not

  2. ANNOTATION SUPPORTED OCCLUDED OBJECT TRACKING

    Directory of Open Access Journals (Sweden)

    Devinder Kumar

    2012-08-01

    Full Text Available Tracking occluded objects at different depths has become as extremely important component of study for any video sequence having wide applications in object tracking, scene recognition, coding, editing the videos and mosaicking. The paper studies the ability of annotation to track the occluded object based on pyramids with variation in depth further establishing a threshold at which the ability of the system to track the occluded object fails. Image annotation is applied on 3 similar video sequences varying in depth. In the experiment, one bike occludes the other at a depth of 60cm, 80cm and 100cm respectively. Another experiment is performed on tracking humans with similar depth to authenticate the results. The paper also computes the frame by frame error incurred by the system, supported by detailed simulations. This system can be effectively used to analyze the error in motion tracking and further correcting the error leading to flawless tracking. This can be of great interest to computer scientists while designing surveillance systems etc.

  3. Cognitive Hierarchy Theory and Two-Person Games

    Directory of Open Access Journals (Sweden)

    Carlos Gracia-Lázaro

    2017-01-01

    Full Text Available The outcome of many social and economic interactions, such as stock-market transactions, is strongly determined by the predictions that agents make about the behavior of other individuals. Cognitive hierarchy theory provides a framework to model the consequences of forecasting accuracy that has proven to fit data from certain types of game theory experiments, such as Keynesian beauty contests and entry games. Here, we focus on symmetric two-player-two-action games and establish an algorithm to find the players’ strategies according to the cognitive hierarchy approach. We show that the snowdrift game exhibits a pattern of behavior whose complexity grows as the cognitive levels of players increases. In addition to finding the solutions up to the third cognitive level, we demonstrate, in this theoretical frame, two new properties of snowdrift games: (i any snowdrift game can be characterized by only a parameter, its class; (ii they are anti-symmetric with respect to the diagonal of the pay-off’s space. Finally, we propose a model based on an evolutionary dynamics that captures the main features of the cognitive hierarchy theory.

  4. NegGOA: negative GO annotations selection using ontology structure.

    Science.gov (United States)

    Fu, Guangyuan; Wang, Jun; Yang, Bo; Yu, Guoxian

    2016-10-01

    Predicting the biological functions of proteins is one of the key challenges in the post-genomic era. Computational models have demonstrated the utility of applying machine learning methods to predict protein function. Most prediction methods explicitly require a set of negative examples-proteins that are known not carrying out a particular function. However, Gene Ontology (GO) almost always only provides the knowledge that proteins carry out a particular function, and functional annotations of proteins are incomplete. GO structurally organizes more than tens of thousands GO terms and a protein is annotated with several (or dozens) of these terms. For these reasons, the negative examples of a protein can greatly help distinguishing true positive examples of the protein from such a large candidate GO space. In this paper, we present a novel approach (called NegGOA) to select negative examples. Specifically, NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein to choose negative examples of the protein. We compare NegGOA with other negative examples selection algorithms and find that NegGOA produces much fewer false negatives than them. We incorporate the selected negative examples into an efficient function prediction model to predict the functions of proteins in Yeast, Human, Mouse and Fly. NegGOA also demonstrates improved accuracy than these comparing algorithms across various evaluation metrics. In addition, NegGOA is less suffered from incomplete annotations of proteins than these comparing methods. The Matlab and R codes are available at https://sites.google.com/site/guoxian85/neggoa gxyu@swu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Feeling Expression Using Avatars and Its Consistency for Subjective Annotation

    Science.gov (United States)

    Ito, Fuyuko; Sasaki, Yasunari; Hiroyasu, Tomoyuki; Miki, Mitsunori

    Consumer Generated Media(CGM) is growing rapidly and the amount of content is increasing. However, it is often difficult for users to extract important contents and the existence of contents recording their experiences can easily be forgotten. As there are no methods or systems to indicate the subjective value of the contents or ways to reuse them, subjective annotation appending subjectivity, such as feelings and intentions, to contents is needed. Representation of subjectivity depends on not only verbal expression, but also nonverbal expression. Linguistically expressed annotation, typified by collaborative tagging in social bookmarking systems, has come into widespread use, but there is no system of nonverbally expressed annotation on the web. We propose the utilization of controllable avatars as a means of nonverbal expression of subjectivity, and confirmed the consistency of feelings elicited by avatars over time for an individual and in a group. In addition, we compared the expressiveness and ease of subjective annotation between collaborative tagging and controllable avatars. The result indicates that the feelings evoked by avatars are consistent in both cases, and using controllable avatars is easier than collaborative tagging for representing feelings elicited by contents that do not express meaning, such as photos.

  6. The Ups and Downs of Hierarchy: the causes and consequences of hierarchy struggles and positional loss

    NARCIS (Netherlands)

    M.E. Schouten (Maartje)

    2016-01-01

    markdownabstractScholars have assumed that social hierarchies, the rank ordering of individuals with respect to a valued social dimension within a team, are stable over time. However, hierarchies change and the more changeable they are, the more likely they are to lead to conflicts and have other

  7. Constraints and Soliton Solutions for KdV Hierarchy and AKNS Hierarchy

    International Nuclear Information System (INIS)

    Li Nianhua; Li Yuqi

    2011-01-01

    It is well-known that the finite-gap solutions of the KdV equation can be generated by its recursion operator. We generalize the result to a special form of Lax pair, from which a method to constrain the integrable system to a lower-dimensional or fewer variable integrable system is proposed. A direct result is that the n-soliton solutions of the KdV hierarchy can be completely depicted by a series of ordinary differential equations (ODEs), which may be gotten by a simple but unfamiliar Lax pair. Furthermore the AKNS hierarchy is constrained to a series of univariate integrable hierarchies. The key is a special form of Lax pair for the AKNS hierarchy. It is proved that under the constraints all equations of the AKNS hierarchy are linearizable. (general)

  8. Automatically annotating topics in transcripts of patient-provider interactions via machine learning.

    Science.gov (United States)

    Wallace, Byron C; Laws, M Barton; Small, Kevin; Wilson, Ira B; Trikalinos, Thomas A

    2014-05-01

    Annotated patient-provider encounters can provide important insights into clinical communication, ultimately suggesting how it might be improved to effect better health outcomes. But annotating outpatient transcripts with Roter or General Medical Interaction Analysis System (GMIAS) codes is expensive, limiting the scope of such analyses. We propose automatically annotating transcripts of patient-provider interactions with topic codes via machine learning. We use a conditional random field (CRF) to model utterance topic probabilities. The model accounts for the sequential structure of conversations and the words comprising utterances. We assess predictive performance via 10-fold cross-validation over GMIAS-annotated transcripts of 360 outpatient visits (>230,000 utterances). We then use automated in place of manual annotations to reproduce an analysis of 116 additional visits from a randomized trial that used GMIAS to assess the efficacy of an intervention aimed at improving communication around antiretroviral (ARV) adherence. With respect to 6 topic codes, the CRF achieved a mean pairwise kappa compared with human annotators of 0.49 (range: 0.47-0.53) and a mean overall accuracy of 0.64 (range: 0.62-0.66). With respect to the RCT reanalysis, results using automated annotations agreed with those obtained using manual ones. According to the manual annotations, the median number of ARV-related utterances without and with the intervention was 49.5 versus 76, respectively (paired sign test P = 0.07). When automated annotations were used, the respective numbers were 39 versus 55 (P = 0.04). While moderately accurate, the predicted annotations are far from perfect. Conversational topics are intermediate outcomes, and their utility is still being researched. This foray into automated topic inference suggests that machine learning methods can classify utterances comprising patient-provider interactions into clinically relevant topics with reasonable accuracy.

  9. Hierarchy and social status in Budongo chimpanzees.

    Science.gov (United States)

    Newton-Fisher, Nicholas E

    2004-04-01

    The status hierarchy is fundamental in the lives of male chimpanzees. This study describes the dominance interactions and social status among adult male chimpanzees of the Sonso community in the Budongo Forest Reserve, Uganda, during the period that they were first studied (1994 and 1995). Social dominance is typically measured using the behaviour of either the subordinate or the dominant individual, but a relationship is dependent on the behaviour of both parties and this study explicitly used both subordinate and dominant behaviours to investigate the status hierarchy. Among adult males of the Sonso community, agonistic interactions occurred at a low rate and pant-grunts were rare, but males could be ranked into separate hierarchies of agonistic dominance and pant-grunting (labelled 'respect') using ratios of behaviour performed/behaviour received. These hierarchies were combined to form a single hierarchy of social status that divided the males among five distinct status levels. The highest status level was held by an alliance between two males who replaced the previous alpha male during the first part of the study. Neither male in this alliance partnership pant-grunted to the other, although the reason for cooperative behaviour was unclear. Although the nominally beta male was treated as such by other adult males, he achieved surprisingly little mating success. Budongo Forest chimpanzees do not warrant the sometimes-expressed view that they are non-aggressive and peaceable and the broad pattern of their status interactions matches with that seen in other chimpanzee populations.

  10. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    2015-01-01

    To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion...

  11. Ground Truth Annotation in T Analyst

    DEFF Research Database (Denmark)

    2015-01-01

    This video shows how to annotate the ground truth tracks in the thermal videos. The ground truth tracks are produced to be able to compare them to tracks obtained from a Computer Vision tracking approach. The program used for annotation is T-Analyst, which is developed by Aliaksei Laureshyn, Ph...

  12. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  13. Black English Annotations for Elementary Reading Programs.

    Science.gov (United States)

    Prasad, Sandre

    This report describes a program that uses annotations in the teacher's editions of existing reading programs to indicate the characteristics of black English that may interfere with the reading process of black children. The first part of the report provides a rationale for the annotation approach, explaining that the discrepancy between written…

  14. Harnessing Collaborative Annotations on Online Formative Assessments

    Science.gov (United States)

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  15. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

    Science.gov (United States)

    Brister, James Rodney; Bao, Yiming; Kuiken, Carla; Lefkowitz, Elliot J; Le Mercier, Philippe; Leplae, Raphael; Madupu, Ramana; Scheuermann, Richard H; Schobel, Seth; Seto, Donald; Shrivastava, Susmita; Sterk, Peter; Zeng, Qiandong; Klimke, William; Tatusova, Tatiana

    2010-10-01

    Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

  16. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

    Directory of Open Access Journals (Sweden)

    Qiandong Zeng

    2010-10-01

    Full Text Available Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

  17. Essential Requirements for Digital Annotation Systems

    Directory of Open Access Journals (Sweden)

    ADRIANO, C. M.

    2012-06-01

    Full Text Available Digital annotation systems are usually based on partial scenarios and arbitrary requirements. Accidental and essential characteristics are usually mixed in non explicit models. Documents and annotations are linked together accidentally according to the current technology, allowing for the development of disposable prototypes, but not to the support of non-functional requirements such as extensibility, robustness and interactivity. In this paper we perform a careful analysis on the concept of annotation, studying the scenarios supported by digital annotation tools. We also derived essential requirements based on a classification of annotation systems applied to existing tools. The analysis performed and the proposed classification can be applied and extended to other type of collaborative systems.

  18. MIPS bacterial genomes functional annotation benchmark dataset.

    Science.gov (United States)

    Tetko, Igor V; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Fobo, Gisela; Ruepp, Andreas; Antonov, Alexey V; Surmeli, Dimitrij; Mewes, Hans-Wernen

    2005-05-15

    Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation. BFAB is available at http://mips.gsf.de/proj/bfab

  19. Interoperable Multimedia Annotation and Retrieval for the Tourism Sector

    NARCIS (Netherlands)

    Chatzitoulousis, Antonios; Efraimidis, Pavlos S.; Athanasiadis, I.N.

    2015-01-01

    The Atlas Metadata System (AMS) employs semantic web annotation techniques in order to create an interoperable information annotation and retrieval platform for the tourism sector. AMS adopts state-of-the-art metadata vocabularies, annotation techniques and semantic web technologies.

  20. Ion implantation: an annotated bibliography

    International Nuclear Information System (INIS)

    Ting, R.N.; Subramanyam, K.

    1975-10-01

    Ion implantation is a technique for introducing controlled amounts of dopants into target substrates, and has been successfully used for the manufacture of silicon semiconductor devices. Ion implantation is superior to other methods of doping such as thermal diffusion and epitaxy, in view of its advantages such as high degree of control, flexibility, and amenability to automation. This annotated bibliography of 416 references consists of journal articles, books, and conference papers in English and foreign languages published during 1973-74, on all aspects of ion implantation including range distribution and concentration profile, channeling, radiation damage and annealing, compound semiconductors, structural and electrical characterization, applications, equipment and ion sources. Earlier bibliographies on ion implantation, and national and international conferences in which papers on ion implantation were presented have also been listed separately

  1. Teaching and Learning Communities through Online Annotation

    Science.gov (United States)

    van der Pluijm, B.

    2016-12-01

    What do colleagues do with your assigned textbook? What they say or think about the material? Want students to be more engaged in their learning experience? If so, online materials that complement standard lecture format provide new opportunity through managed, online group annotation that leverages the ubiquity of internet access, while personalizing learning. The concept is illustrated with the new online textbook "Processes in Structural Geology and Tectonics", by Ben van der Pluijm and Stephen Marshak, which offers a platform for sharing of experiences, supplementary materials and approaches, including readings, mathematical applications, exercises, challenge questions, quizzes, alternative explanations, and more. The annotation framework used is Hypothes.is, which offers a free, open platform markup environment for annotation of websites and PDF postings. The annotations can be public, grouped or individualized, as desired, including export access and download of annotations. A teacher group, hosted by a moderator/owner, limits access to members of a user group of teachers, so that its members can use, copy or transcribe annotations for their own lesson material. Likewise, an instructor can host a student group that encourages sharing of observations, questions and answers among students and instructor. Also, the instructor can create one or more closed groups that offers study help and hints to students. Options galore, all of which aim to engage students and to promote greater responsibility for their learning experience. Beyond new capacity, the ability to analyze student annotation supports individual learners and their needs. For example, student notes can be analyzed for key phrases and concepts, and identify misunderstandings, omissions and problems. Also, example annotations can be shared to enhance notetaking skills and to help with studying. Lastly, online annotation allows active application to lecture posted slides, supporting real-time notetaking

  2. A generative model for scientific concept hierarchies.

    Science.gov (United States)

    Datta, Srayan; Adar, Eytan

    2018-01-01

    In many scientific disciplines, each new 'product' of research (method, finding, artifact, etc.) is often built upon previous findings-leading to extension and branching of scientific concepts over time. We aim to understand the evolution of scientific concepts by placing them in phylogenetic hierarchies where scientific keyphrases from a large, longitudinal academic corpora are used as a proxy of scientific concepts. These hierarchies exhibit various important properties, including power-law degree distribution, power-law component size distribution, existence of a giant component and less probability of extending an older concept. We present a generative model based on preferential attachment to simulate the graphical and temporal properties of these hierarchies which helps us understand the underlying process behind scientific concept evolution and may be useful in simulating and predicting scientific evolution.

  3. On the Hierarchy of Neutrino Masses

    International Nuclear Information System (INIS)

    Jezabek, M.; Urban, P.

    2002-01-01

    We present a model of neutrino masses combining the seesaw mechanism and strong Dirac mass hierarchy and at the same time exhibiting a significantly reduced hierarchy at the level of active neutrino masses. The heavy Majorana masses are assumed to be degenerate. The suppression of the hierarchy is due to a symmetric and unitary operator R whose role is discussed. The model gives realistic mixing and mass spectrum. The mixing of atmospheric neutrinos is attributed to the charged lepton sector whereas the mixing of solar neutrinos is due to the neutrino sector. Small U e3 is a consequence of the model. The masses of the active neutrinos are given by μ 3 ≅ √(Δm 2 O ) and μ 1 /μ 2 = ≅ tan 2 (θ O ). (author)

  4. Cohesion and Hierarchy in Physically Abusive Families

    Directory of Open Access Journals (Sweden)

    Clarissa De Antoni

    2009-06-01

    Full Text Available This paper investigates cohesion (emotional bonding and hierarchy (powerstructure in families with abuse against their children. Twenty low-incomefamilies participated. Father, mother and child’s perspective of family relations(cohesion and hierarchy were evaluated by the Family System Test(FAST. The relationship between father-child, mother-child, couple, andamong siblings were evaluated at typical and conflictive situations. Resultsshow a significance regarding to cohesion in typical and conflictive situationfor father-child and mother-child dyads in all perspectives (by father, mother,and child. There is no significant differences regarding to hierarchy. Theseresults suggest that the families see the intrafamilial violence as a constant,since they cannot differentiate between both situations.

  5. A Global Mitigation Hierarchy for Nature Conservation

    Science.gov (United States)

    Bull, Joseph W; Addison, Prue F E; Burgass, Michael J; Gianuca, Dimas; Gorham, Taylor M; Jacob, Céline; Watson, James E M; Wilcox, Chris; Milner-Gulland, E J

    2018-01-01

    Abstract Efforts to conserve biodiversity comprise a patchwork of international goals, national-level plans, and local interventions that, overall, are failing. We discuss the potential utility of applying the mitigation hierarchy, widely used during economic development activities, to all negative human impacts on biodiversity. Evaluating all biodiversity losses and gains through the mitigation hierarchy could help prioritize consideration of conservation goals and drive the empirical evaluation of conservation investments through the explicit consideration of counterfactual trends and ecosystem dynamics across scales. We explore the challenges in using this framework to achieve global conservation goals, including operationalization and monitoring and compliance, and we discuss solutions and research priorities. The mitigation hierarchy's conceptual power and ability to clarify thinking could provide the step change needed to integrate the multiple elements of conservation goals and interventions in order to achieve successful biodiversity outcomes. PMID:29731513

  6. Formal language theory: refining the Chomsky hierarchy

    Science.gov (United States)

    Jäger, Gerhard; Rogers, James

    2012-01-01

    The first part of this article gives a brief overview of the four levels of the Chomsky hierarchy, with a special emphasis on context-free and regular languages. It then recapitulates the arguments why neither regular nor context-free grammar is sufficiently expressive to capture all phenomena in the natural language syntax. In the second part, two refinements of the Chomsky hierarchy are reviewed, which are both relevant to the extant research in cognitive science: the mildly context-sensitive languages (which are located between context-free and context-sensitive languages), and the sub-regular hierarchy (which distinguishes several levels of complexity within the class of regular languages). PMID:22688632

  7. A generative model for scientific concept hierarchies

    Science.gov (United States)

    Adar, Eytan

    2018-01-01

    In many scientific disciplines, each new ‘product’ of research (method, finding, artifact, etc.) is often built upon previous findings–leading to extension and branching of scientific concepts over time. We aim to understand the evolution of scientific concepts by placing them in phylogenetic hierarchies where scientific keyphrases from a large, longitudinal academic corpora are used as a proxy of scientific concepts. These hierarchies exhibit various important properties, including power-law degree distribution, power-law component size distribution, existence of a giant component and less probability of extending an older concept. We present a generative model based on preferential attachment to simulate the graphical and temporal properties of these hierarchies which helps us understand the underlying process behind scientific concept evolution and may be useful in simulating and predicting scientific evolution. PMID:29474409

  8. Automatic annotation of head velocity and acceleration in Anvil

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2012-01-01

    We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements....... The annotations are a useful supplement to manual annotations and may help human annotators to quickly and reliably determine onset of head movements and to suggest which kind of head movement is taking place....

  9. Grass buffers for playas in agricultural landscapes: An annotated bibliography

    Science.gov (United States)

    Melcher, Cynthia P.; Skagen, Susan K.

    2005-01-01

    This bibliography and associated literature synthesis (Melcher and Skagen, 2005) was developed for the Playa Lakes Joint Venture (PLJV). The PLJV sought compilation and annotation of the literature on grass buffers for protecting playas from runoff containing sediments, nutrients, pesticides, and other contaminants. In addition, PLJV sought information regarding the extent to which buffers may attenuate the precipitation runoff needed to fill playas, and avian use of buffers. We emphasize grass buffers, but we also provide information on other buffer types.

  10. PENGGUNAAN METODE ANALYTICAL HIERARCHY PROCESS DALAM PEMILIHAN LOKASI MANGROVE PARK

    Directory of Open Access Journals (Sweden)

    Mustika Mustika

    2017-02-01

    Full Text Available Demak district is a district that has quite a lot of mangrove forests, beautiful expanse of mangrove is a natural potential that can be developed as a regional tourism assets. Mangrove Park is one of the utilization of conservation area into tourism areas of education and recreation The Selection of Planning site locations required an appropriate location in the terms of land use, The appropriate land is a land that has a Mangrove area which still leafy, natural (unprocessed and intended as a tourism area, an easy accessibility, the network infrastructure is also needed in the election of location in order to support the available facilities in the building. In addition, the view of the inside and outside of the site that will be a tourism place attraction. Decision Support System can be used as a tool to help the site selection process that involves many criteria. Analytical Hierarchy Process (AHP can be used to analyze which support the decision to choose a location. Phases of AHP used in this research is the identification of causes, preparation of hierarchy, prioritization, consistency, and the priority weight. From the Implementation of the method on the study case successfully find the best location for mangrove park, it is in the village Bedono it has the highest total global priorities 1.2349. Keywords: Site Location, Analytical Hierarchy Process, Mangrove Park Kabupaten Demak adalah kabupaten yang memiliki hutan mangrove yang cukup banyak, hamparan mangrove yang indah merupakan potensi alam yang dapat dikembangkan sebagai aset pariwisata daerah. Mangrove Park adalah salah satu bentuk pemanfaatan kawasan konservasi menjadi kawasan wisata edukasi dan rekreasi. Pemilihan lokasi tapak perencanaan diperlukan sebuah lokasi yang tepat dari segi peruntukan lahan, lahan yang tepat adalah lahan yang memiliki area Mangrove yang masih rimbun, alami (belum diolah dan diperuntukkan sebagai kawasan wisata, aksebilitas yang mudah dijangkau, jaringan

  11. On self-dual Yang-Mills hierarchy

    International Nuclear Information System (INIS)

    Nakamura, Yoshimasa

    1989-01-01

    In this note, motivated by the Kadomtsev-Petviashvili (KP) hierarchy of integrable nonlinear evolution equations, a GL(n,C) self-dual Yang-Mills (SDYM) hierarchy is presented; it is an infinite system of SDYM equations having an infinite number of independent variables and being outside of the KP hierarchy. A relationship between the KP hierarchy and the SDYM hierarchy is discussed. It is also shown that GL(∞) SDYM equations introduced in this note are reduced to the GL(n,C) SDYM hierarchy by imposing an algebraic constraint. (orig.)

  12. An Operational Investigation of the CPS Hierarchy

    DEFF Research Database (Denmark)

    Danvy, Olivier; Yang, Zhe

    1999-01-01

    We explore the hierarchy of control induced by successive transformations into continuation-passing style (CPS) in the presence of “control delimiters ” and “composable continuations ”. Specifically, we investigate the structural operational semantics associated with the CPS hierarchy. To this end......, we characterize an operational notion of continuation semantics. We relate it to the traditional CPS transformation and we use it to account for the control operator shift and the control delimiter reset operationally. We then transcribe the resulting continuation semantics in ML, thus obtaining...

  13. An Operational Investigation of the CPS Hierarchy

    DEFF Research Database (Denmark)

    Danvy, Olivier; Yang, Zhe

    1998-01-01

    We explore the hierarchy of control induced by successive transformations into continuation-passing style (CPS) in the presence of “control delimiters ” and “composable continuations ”. Specifically, we investigate the structural operational semantics associated with the CPS hierarchy. To this end......, we characterize an operational notion of continuation semantics. We relate it to the traditional CPS transformation and we use it to account for the control operator shift and the control delimiter reset operationally. We then transcribe the resulting continuation semantics in ML, thus obtaining...

  14. Contrastive hierarchies, privative features, and Portuguese vowels

    Directory of Open Access Journals (Sweden)

    Joaquim Brandão de Carvalho

    2011-01-01

    Full Text Available Dresher’s (2009 Contrastive hierarchy theory (CHT is intended to provide a unified account of both sides of phonological primes: contrastivity and behaviour. This article explores the point and the possibility of extending CHT, which is based on binary features, to a system of monovalent elements that is much indebted to Schane’s (1984 Particle Phonology. It shows how several aspects of the phonology of European Portuguese nuclei that seem prima facie independent from one another – such as reduction patterns and the inventory of diphthongs and nasal vowels – are constrained by element hierarchy, and, thus, receive a unitary account.

  15. MOS modeling hierarchy including radiation effects

    International Nuclear Information System (INIS)

    Alexander, D.R.; Turfler, R.M.

    1975-01-01

    A hierarchy of modeling procedures has been developed for MOS transistors, circuit blocks, and integrated circuits which include the effects of total dose radiation and photocurrent response. The models were developed for use with the SCEPTRE circuit analysis program, but the techniques are suitable for other modern computer aided analysis programs. The modeling hierarchy permits the designer or analyst to select the level of modeling complexity consistent with circuit size, parametric information, and accuracy requirements. Improvements have been made in the implementation of important second order effects in the transistor MOS model, in the definition of MOS building block models, and in the development of composite terminal models for MOS integrated circuits

  16. Program information architecture/document hierarchy

    International Nuclear Information System (INIS)

    Woods, T.W.

    1991-09-01

    The Nuclear Waste Management System (NWMS) Management Systems Improvement Strategy (MSIS) (DOE 1990) requires that the information within the computer program and information management system be ordered into a precedence hierarchy for consistency. Therefore, the US Department of Energy (DOE). Office of Civilian Radioactive Waste Management (OCRWM) requested Westinghouse Hanford Company to develop a plan for NWMS program information which the MSIS calls a document hierarchy. This report provides the results of that effort and describes the management system as a ''program information architecture.'' 3 refs., 3 figs

  17. Do experiments suggest a hierarchy problem?

    International Nuclear Information System (INIS)

    Vissani, F.

    1997-09-01

    The hierarchy problem of the scalar sector of the standard model is reformulated, emphasizing the role of experimental facts that may suggest the existence of a new physics large mass scale, for instance indications of the instability of the matter, or indications in favor of massive neutrinos. In the see-saw model for the neutrino masses a hierarchy problem arises if the mass of the right-handed neutrinos is larger than approximatively 10 7 GeV: this problem, and its possible solutions, are discussed. (author)

  18. An open annotation ontology for science on web 3.0.

    Science.gov (United States)

    Ciccarese, Paolo; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Tim

    2011-05-17

    There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for

  19. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

    Directory of Open Access Journals (Sweden)

    Mazo Ilya

    2007-07-01

    Full Text Available Abstract Background Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more likely to interact with each other than with proteins with other functions. However, since functional annotation and protein network topology are often studied separately, the direct relationship between them has not been comprehensively demonstrated. In addition to having the general biological significance, such demonstration would further validate the data extraction and processing methods used to compose protein annotation and protein-protein interactions datasets. Results We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP technology. For the protein annotation extracted from the entire PubMed, we evaluated the precision and recall rates, and compared the performance of the automatic extraction technology to that of manual curation used in public Gene Ontology (GO annotation. In the second part of our presentation, we reported a large-scale investigation into the correspondence between communities in the literature-based protein networks and GO annotation groups of functionally related proteins. We found a comprehensive two-way match: proteins within biological annotation groups form significantly denser linked network clusters than expected by chance and, conversely, densely linked network communities exhibit a pronounced non-random overlap with GO groups. We also expanded the publicly available GO biological process annotation using the relations extracted by our NLP technology

  20. Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

    Science.gov (United States)

    Balhoff, James P; Dahdul, Wasila M; Dececchi, T Alexander; Lapp, Hilmar; Mabee, Paula M; Vision, Todd J

    2014-01-01

    Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.

  1. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  2. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a......) language drift on Twitter is significant, and while off-the-shelf systems have been reported to perform well on in-sample data, they often perform poorly on new samples of tweets, (b) state-of-the-art performance across various datasets can beobtained from crowdsourced annotations, making it more feasible...

  3. Fuzzy Logic and Arithmetical Hierarchy III

    Czech Academy of Sciences Publication Activity Database

    Hájek, Petr

    2001-01-01

    Roč. 68, č. 1 (2001), s. 129-142 ISSN 0039-3215 R&D Projects: GA AV ČR IAA1030004 Institutional research plan: AV0Z1030915 Keywords : fuzzy logic * basic fuzzy logic * Lukasiewicz logic * Godel logic * product logic * arithmetical hierarchy Subject RIV: BA - General Mathematics

  4. Large hierarchies from approximate R symmetries

    International Nuclear Information System (INIS)

    Kappl, Rolf; Ratz, Michael; Vaudrevange, Patrick K.S.

    2008-12-01

    We show that hierarchically small vacuum expectation values of the superpotential in supersymmetric theories can be a consequence of an approximate R symmetry. We briefly discuss the role of such small constants in moduli stabilization and understanding the huge hierarchy between the Planck and electroweak scales. (orig.)

  5. The hamiltonian structures of the KP hierarchy

    International Nuclear Information System (INIS)

    Das, A.; Panda, S.; Huang Wenjui

    1991-01-01

    We obtain the two hamiltonian structures of the KP hierarchy following the method of Drinfeld and Sokolov. We point out how the second structure of Drinfeld and Sokolov needs to be modified in the present case. We briefly comment on the connection between these structures and the W 1+∞ algebra. (orig.)

  6. A note on the substructural hierarchy

    Czech Academy of Sciences Publication Activity Database

    Jeřábek, Emil

    2016-01-01

    Roč. 62, 1-2 (2016), s. 102-110 ISSN 0942-5616 EU Projects: European Commission(XE) 339691 - FEALORA Institutional support: RVO:67985840 Keywords : substructural hierarchy * full Lambek calculus * extension variables Subject RIV: BA - General Mathematics Impact factor: 0.250, year: 2016 http://dx.doi.org/10.1002/malq.201500066

  7. Signaling hierarchy regulating human endothelial cell development

    Science.gov (United States)

    Our present knowledge of the regulation of mammalian endothelial cell differentiation has been largely derived from studies of mouse embryonic development. However, unique mechanisms and hierarchy of signals that govern human endothelial cell development are unknown and, thus, explored in these stud...

  8. The Analytic Hierarchy Process and Participatory Decisionmaking

    Science.gov (United States)

    Daniel L. Schmoldt; Daniel L. Peterson; Robert L. Smith

    1995-01-01

    Managing natural resource lands requires social, as well as biophysical, considerations. Unfortunately, it is extremely difficult to accurately assess and quantify changing social preferences, and to aggregate conflicting opinions held by diverse social groups. The Analytic Hierarchy Process (AHP) provides a systematic, explicit, rigorous, and robust mechanism for...

  9. Using Analytic Hierarchy Process in Textbook Evaluation

    Science.gov (United States)

    Kato, Shigeo

    2014-01-01

    This study demonstrates the application of the analytic hierarchy process (AHP) in English language teaching materials evaluation, focusing in particular on its potential for systematically integrating different components of evaluation criteria in a variety of teaching contexts. AHP is a measurement procedure wherein pairwise comparisons are made…

  10. The Hamiltonian structures of the KP hierarchy

    International Nuclear Information System (INIS)

    Das, A.; Panda, S.; Huang Wenjui

    1991-08-01

    We obtain the two Hamiltonian structures of the KP hierarchy following the method of Drinfeld and Sokolov. We point out how the second structure of Drinfeld and Sokolov needs to be modified in the present case. We briefly comment on the connection between these structures and the W 1+∞ algebra. (author). 18 refs

  11. A hierarchy of systems of nonlinear equations

    International Nuclear Information System (INIS)

    Falkensteiner, P.; Grosse, H.

    1985-01-01

    Imposing isospectral invariance for the one-dimensional Dirac operator yields an infinite hierarchy of systems of chiral invariant nonlinear partial differential equations. The same system is obtained through a Lax pair construction and finally a formulation in terms of Kac-Moody generators is given. (Author)

  12. New solutions to the hierarchy problem

    International Nuclear Information System (INIS)

    Burdman, Gustavo

    2007-01-01

    After summarizing the status of the Standard Model, we focus on the Hierarchy Problem and why we believe this strongly suggests the need for new physics at the TeV scale. We then concentrate on theories with extra dimensions and their possible manifestations at this scale. (author)

  13. Prioritization of Programmer's Productivity Using Analytic Hierarchy ...

    African Journals Online (AJOL)

    This paper focuses on the application of Analytic Hierarchy Process (AHP) model in the context of prioritizing programmer's productivity in University of Benin, Benin City Nigeria. This is achieved by evaluating the way in which the AHP model can be used to select the best programmer for the purpose of developing software ...

  14. Dark energy and the hierarchy problem

    International Nuclear Information System (INIS)

    Chen, Pisin

    2007-01-01

    The well-known hierarchy between the Planck scale (∼10 19 GeV) and the TeV scale, namely a ratio of ∼10 16 between the two, is coincidentally repeated in a inverted order between the TeV scale and the dark energy scale at ∼10 -3 eV implied by the observations. We argue that this is not a numerical coincidence. The same brane-world setups to address the first hierarchy problem may also in principle address this second hierarchy issue. Specifically, we consider supersymmetry in the bulk and its breaking on the brane and resort to the Casimir energy induced by the bulk graviton-gravitino mass-shift on the brane as the dark energy. For the ADD model we found that our notion is sensible only if the number of extra dimension n=2. We extend our study to the Randall-Sundrum model. Invoking the chirality-flip on the boundaries for SUSY-breaking, the zero-mode gravitino contribution to the Casimir energy does give rise to the double hierarchy. Unfortunately since the higher Kaluza-Klein modes acquire relative mass-shifts at the TeV level, the zero-mode contribution to Casimir energy is overshadowed

  15. Classification hierarchies for product data modelling

    NARCIS (Netherlands)

    Pels, H.J.

    2006-01-01

    Abstraction is an essential element in data modelling that appears mainly in one of the following forms: generalisation, classification or aggregation. In the design of complex products classification hierarchies can be found product families that are viewed as classes of product types, while

  16. Stress amplifies memory for social hierarchy.

    Science.gov (United States)

    Cordero, María Isabel; Sandi, Carmen

    2007-11-01

    Individuals differ in their social status and societies in the extent of social status differences among their members. There is great interest in understanding the key factors that contribute to the establishment of social dominance structures. Given that stress can affect behavior and cognition, we hypothesized that, given equal opportunities to become either dominant or submissive, stress experienced by one of the individuals during their first encounter would determine the long-term establishment of a social hierarchy by acting as a two-stage rocket: (1) by influencing the rank achieved after a social encounter and (2) by facilitating and/or promoting a long-term memory for the specific hierarchy. Using a novel model for the assessment of long-term dominance hierarchies in rats, we present here the first evidence supporting such hypothesis. In control conditions, the social rank established through a first interaction and food competition test between two male rats is not maintained when animals are confronted 1 week later. However, if one of the rats is stressed just before their first encounter, the dominance hierarchy developed on day 1 is still clearly observed 1 week later, with the stressed animal becoming submissive (i.e., looser in competition tests) in both social interactions. Our findings also allow us to propose that stress potentiates a hierarchy-linked recognition memory between "specific" individuals through mechanisms that involve de novo protein synthesis. These results implicate stress among the key mechanisms contributing to create social imbalance and highlight memory mechanisms as key mediators of stress-induced long-term establishment of social rank.

  17. Stress amplifies memory for social hierarchy

    Directory of Open Access Journals (Sweden)

    María I Cordero

    2007-10-01

    Full Text Available Individuals differ in their social status and societies in the extent of social status differences among their members. There is great interest in understanding the key factors that contribute to the establishment of social dominance structures. Given that stress can affect behavior and cognition, we hypothesized that, given equal opportunities to become either dominant or submissive, stress experienced by one of the individuals during their first encounter would determine the long-term establishment of a social hierarchy by acting as a two-stage rocket: (1 by influencing the rank achieved after a social encounter and (2 by facilitating and/or promoting a long-term memory for the specific hierarchy. Using a novel model for the assessment of long-term dominance hierarchies in rats, we present here the first evidence supporting such hypothesis. In control conditions, the social rank established through a first interaction and food competition test between two male rats is not maintained when animals are confronted 1 week later. However, if one of the rats is stressed just before their first encounter, the dominance hierarchy developed on day 1 is still clearly observed 1 week later, with the stressed animal becoming submissive (i.e., looser in competition tests in both social interactions. Our findings also allow us to propose that stress potentiates a hierarchy-linked recognition memory between “specific” individuals through mechanisms that involve de novo protein synthesis. These results implicate stress among the key mechanisms contributing to create social imbalance and highlight memory mechanisms as key mediators of stress-induced long-term establishment of social rank.

  18. Annotations to quantum statistical mechanics

    CERN Document Server

    Kim, In-Gee

    2018-01-01

    This book is a rewritten and annotated version of Leo P. Kadanoff and Gordon Baym’s lectures that were presented in the book Quantum Statistical Mechanics: Green’s Function Methods in Equilibrium and Nonequilibrium Problems. The lectures were devoted to a discussion on the use of thermodynamic Green’s functions in describing the properties of many-particle systems. The functions provided a method for discussing finite-temperature problems with no more conceptual difficulty than ground-state problems, and the method was equally applicable to boson and fermion systems and equilibrium and nonequilibrium problems. The lectures also explained nonequilibrium statistical physics in a systematic way and contained essential concepts on statistical physics in terms of Green’s functions with sufficient and rigorous details. In-Gee Kim thoroughly studied the lectures during one of his research projects but found that the unspecialized method used to present them in the form of a book reduced their readability. He st...

  19. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  20. The Helmholtz Hierarchy: Phase Space Statistics of Cold Dark Matter

    OpenAIRE

    Tassev, Svetlin

    2010-01-01

    We present a new formalism to study large-scale structure in the universe. The result is a hierarchy (which we call the "Helmholtz Hierarchy") of equations describing the phase space statistics of cold dark matter (CDM). The hierarchy features a physical ordering parameter which interpolates between the Zel'dovich approximation and fully-fledged gravitational interactions. The results incorporate the effects of stream crossing. We show that the Helmholtz hierarchy is self-consistent and obeys...

  1. Special polynomials associated with rational solutions of some hierarchies

    International Nuclear Information System (INIS)

    Kudryashov, Nikolai A.

    2009-01-01

    New special polynomials associated with rational solutions of the Painleve hierarchies are introduced. The Hirota relations for these special polynomials are found. Differential-difference hierarchies to find special polynomials are presented. These formulae allow us to search special polynomials associated with the hierarchies. It is shown that rational solutions of the Caudrey-Dodd-Gibbon, the Kaup-Kupershmidt and the modified hierarchy for these ones can be obtained using new special polynomials.

  2. Method and System for Making OLAP Hierarchies Summarisable

    DEFF Research Database (Denmark)

    2002-01-01

    Field of Invention: The present invention relates to computer databases, in particular to a method and system for transforming general OLAP hierarchies into summarizable hierarchies. This enables fast query response times for aggregation queries without excessive storage use even when the hierarc......Field of Invention: The present invention relates to computer databases, in particular to a method and system for transforming general OLAP hierarchies into summarizable hierarchies. This enables fast query response times for aggregation queries without excessive storage use even when...

  3. Operator approach to solutions of the constrained BKP hierarchy

    International Nuclear Information System (INIS)

    Shen, Hsin-Fu; Lee, Niann-Chern; Tu, Ming-Hsien

    2011-01-01

    The operator formalism to the vector k-constrained BKP hierarchy is presented. We solve the Hirota bilinear equations of the vector k-constrained BKP hierarchy via the method of neutral free fermion. In particular, by choosing suitable group element of O(∞), we construct rational and soliton solutions of the vector k-constrained BKP hierarchy.

  4. The influence of annotation in graphical organizers

    NARCIS (Netherlands)

    Bezdan, Eniko; Kester, Liesbeth; Kirschner, Paul A.

    2013-01-01

    Bezdan, E., Kester, L., & Kirschner, P. A. (2012, 29-31 August). The influence of annotation in graphical organizers. Poster presented at the biannual meeting of the EARLI Special Interest Group Comprehension of Text and Graphics, Grenoble, France.

  5. An Informally Annotated Bibliography of Sociolinguistics.

    Science.gov (United States)

    Tannen, Deborah

    This annotated bibliography of sociolinguistics is divided into the following sections: speech events, ethnography of speaking and anthropological approaches to analysis of conversation; discourse analysis (including analysis of conversation and narrative), ethnomethodology and nonverbal communication; sociolinguistics; pragmatics (including…

  6. The Community Junior College: An Annotated Bibliography.

    Science.gov (United States)

    Rarig, Emory W., Jr., Ed.

    This annotated bibliography on the junior college is arranged by topic: research tools, history, functions and purposes, organization and administration, students, programs, personnel, facilities, and research. It covers publications through the fall of 1965 and has an author index. (HH)

  7. WormBase: Annotating many nematode genomes.

    Science.gov (United States)

    Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W

    2012-01-01

    WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.

  8. Annotated Tsunami bibliography: 1962-1976

    International Nuclear Information System (INIS)

    Pararas-Carayannis, G.; Dong, B.; Farmer, R.

    1982-08-01

    This compilation contains annotated citations to nearly 3000 tsunami-related publications from 1962 to 1976 in English and several other languages. The foreign-language citations have English titles and abstracts

  9. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    HEISS, ANN M.; AND OTHERS

    THIS ANNOTATED BIBLIOGRAPHY CONTAINS REFERENCES TO GENERAL GRADUATE EDUCATION AND TO EDUCATION FOR THE FOLLOWING PROFESSIONAL FIELDS--ARCHITECTURE, BUSINESS, CLINICAL PSYCHOLOGY, DENTISTRY, ENGINEERING, LAW, LIBRARY SCIENCE, MEDICINE, NURSING, SOCIAL WORK, TEACHING, AND THEOLOGY. (HW)

  10. Contributions to In Silico Genome Annotation

    KAUST Repository

    Kalkatawi, Manal M.

    2017-11-30

    Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation, while identifying functions of these regions is considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and timeconsuming. This study contributes to genome annotation by introducing several novel bioinformatics methods, some based on machine learning (ML) approaches. First, we present Dragon PolyA Spotter (DPS), a method for accurate identification of the polyadenylation signals (PAS) within human genomic DNA sequences. For this, we derived a novel feature-set able to characterize properties of the genomic region surrounding the PAS, enabling development of high accuracy optimized ML predictive models. DPS considerably outperformed the state-of-the-art results. The second contribution concerns developing generic models for structural annotation, i.e., the recognition of different genomic signals and regions (GSR) within eukaryotic DNA. We developed DeepGSR, a systematic framework that facilitates generating ML models to predict GSR with high accuracy. To the best of our knowledge, no available generic and automated method exists for such task that could facilitate the studies of newly sequenced organisms. The prediction module of DeepGSR uses deep learning algorithms to derive highly abstract features that depend mainly on proper data representation and hyperparameters calibration. DeepGSR, which was evaluated on recognition of PAS and translation initiation sites (TIS) in different organisms, yields a simpler and more precise representation of the problem under study, compared to some other hand-tailored models, while producing high accuracy prediction results. Finally

  11. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... to layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  12. Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees.

    Science.gov (United States)

    Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.

  13. Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

    Science.gov (United States)

    Wang, Qinghua; Arighi, Cecilia N.; King, Benjamin L.; Polson, Shawn W.; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F.; Page, Shallee T.; Farnum Rendino, Marc; Thomas, William Kelley; Udwary, Daniel W.; Wu, Cathy H.

    2012-01-01

    Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome. PMID:22434832

  14. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  15. Annotating the human genome with Disease Ontology

    Science.gov (United States)

    Osborne, John D; Flatow, Jared; Holko, Michelle; Lin, Simon M; Kibbe, Warren A; Zhu, Lihua (Julie); Danila, Maria I; Feng, Gang; Chisholm, Rex L

    2009-01-01

    Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. Conclusion The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome. PMID:19594883

  16. Fluid inclusions in salt: an annotated bibliography

    International Nuclear Information System (INIS)

    Isherwood, D.J.

    1979-01-01

    An annotated bibliography is presented which was compiled while searching the literature for information on fluid inclusions in salt for the Nuclear Regulatory Commission's study on the deep-geologic disposal of nuclear waste. The migration of fluid inclusions in a thermal gradient is a potential hazard to the safe disposal of nuclear waste in a salt repository. At the present time, a prediction as to whether this hazard precludes the use of salt for waste disposal can not be made. Limited data from the Salt-Vault in situ heater experiments in the early 1960's (Bradshaw and McClain, 1971) leave little doubt that fluid inclusions can migrate towards a heat source. In addition to the bibliography, there is a brief summary of the physical and chemical characteristics that together with the temperature of the waste will determine the chemical composition of the brine in contact with the waste canister, the rate of fluid migration, and the brine-canister-waste interactions

  17. Annotating Human P-Glycoprotein Bioassay Data.

    Science.gov (United States)

    Zdrazil, Barbara; Pinto, Marta; Vasanthanathan, Poongavanam; Williams, Antony J; Balderud, Linda Zander; Engkvist, Ola; Chichester, Christine; Hersey, Anne; Overington, John P; Ecker, Gerhard F

    2012-08-01

    Huge amounts of small compound bioactivity data have been entering the public domain as a consequence of open innovation initiatives. It is now the time to carefully analyse existing bioassay data and give it a systematic structure. Our study aims to annotate prominent in vitro assays used for the determination of bioactivities of human P-glycoprotein inhibitors and substrates as they are represented in the ChEMBL and TP-search open source databases. Furthermore, the ability of data, determined in different assays, to be combined with each other is explored. As a result of this study, it is suggested that for inhibitors of human P-glycoprotein it is possible to combine data coming from the same assay type, if the cell lines used are also identical and the fluorescent or radiolabeled substrate have overlapping binding sites. In addition, it demonstrates that there is a need for larger chemical diverse datasets that have been measured in a panel of different assays. This would certainly alleviate the search for other inter-correlations between bioactivity data yielded by different assay setups.

  18. A STUDY ON THE HIERARCHY OF MANAGEMENT ELEMENTS

    Science.gov (United States)

    Suzuki, Nobuyuki; Watanabe, Tadashi

    Compared to the late 20th century, the Japanese construction industry has drastically changed its business methodology, outlook and approach in response to global issues and the incredible advances in technology. Such influences, non-exhaustively include the; WTO Government procurement agreement, updating conditions of tendering and contracting, client demands for cost reduction and the rapid penetration of ICT (Information and Communication Technology) into modern society. These days, the significance of controlling Quality, Cost and Time (the so-called QCT) has been recognized as an eternal-triangle by almost all countries, Government organizations and the private sector. However, as the construction industry is exposed to , and influenced by, more and more internal and external dynamic factors, continued reliance on managing and controlling QCT elements on their own is no longer adequate in meeting the growing demands and expectations, and as such control of additional management elements is now essential to avoid problems, or minimize their potential impacts should they occur. This paper utilizes the results of a survey carried out amongst construction managers and consultants in Japan and overseas to develop a spatial network that defines the interaction of management factors as a weighted graphical model. The calculated closeness centrality index of the developed management network model is adopted to identify the initialelement hierarchy, which is then further analyzed using the minimum distance of independent relationships of management elements (Warshall-Floyd algorism methodology), to identify the optimum potential hierarchy for effective construction management. A key result of the analysis is the significance of "Human Resource" in the construction industry management element hierarchy alongside the traditional QCT elements.

  19. CAUSAL INFERENCE WITH A GRAPHICAL HIERARCHY OF INTERVENTIONS.

    Science.gov (United States)

    Shpitser, Ilya; Tchetgen, Eric Tchetgen

    2016-12-01

    Identifying causal parameters from observational data is fraught with subtleties due to the issues of selection bias and confounding. In addition, more complex questions of interest, such as effects of treatment on the treated and mediated effects may not always be identified even in data where treatment assignment is known and under investigator control, or may be identified under one causal model but not another. Increasingly complex effects of interest, coupled with a diversity of causal models in use resulted in a fragmented view of identification. This fragmentation makes it unnecessarily difficult to determine if a given parameter is identified (and in what model), and what assumptions must hold for this to be the case. This, in turn, complicates the development of estimation theory and sensitivity analysis procedures. In this paper, we give a unifying view of a large class of causal effects of interest, including novel effects not previously considered, in terms of a hierarchy of interventions, and show that identification theory for this large class reduces to an identification theory of random variables under interventions from this hierarchy. Moreover, we show that one type of intervention in the hierarchy is naturally associated with queries identified under the Finest Fully Randomized Causally Interpretable Structure Tree Graph (FFRCISTG) model of Robins (via the extended g-formula), and another is naturally associated with queries identified under the Non-Parametric Structural Equation Model with Independent Errors (NPSEM-IE) of Pearl, via a more general functional we call the edge g-formula. Our results motivate the study of estimation theory for the edge g-formula, since we show it arises both in mediation analysis, and in settings where treatment assignment has unobserved causes, such as models associated with Pearl's front-door criterion.

  20. Gene coexpression network analysis as a source of functional annotation for rice genes.

    Directory of Open Access Journals (Sweden)

    Kevin L Childs

    Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

  1. The Helmholtz Hierarchy: phase space statistics of cold dark matter

    International Nuclear Information System (INIS)

    Tassev, Svetlin V.

    2011-01-01

    We present a new formalism to study large-scale structure in the universe. The result is a hierarchy (which we call the ''Helmholtz Hierarchy'') of equations describing the phase space statistics of cold dark matter (CDM). The hierarchy features a physical ordering parameter which interpolates between the Zel'dovich approximation and fully-fledged gravitational interactions. The results incorporate the effects of stream crossing. We show that the Helmholtz hierarchy is self-consistent and obeys causality to all orders. We present an interpretation of the hierarchy in terms of effective particle trajectories

  2. Aspect of Fermion Mass Hierarchy within Flavor Democracy for Yukawa Couplings

    Science.gov (United States)

    Higuchi, Katsuichi; Yamamoto, Katsuji

    We discuss the fermion mass hierarchy by including vector-like fermions which are accommodated in E6 GUTs within flavor democracy for Yukawa couplings. In this framework, all Yukawa couplings for the standard Higgs doublet have the same strength, and all Yukawa couplings for the singlet Higgs have the same strength (New ansatz). In addition, singlet Higgs and right-handed neutrinos exist. Under this condition, the mass hierarchy mt ≫ mb ˜ mτ as well as mt ≫ mc, mu can be naturally explained.

  3. Small molecule annotation for the Protein Data Bank.

    Science.gov (United States)

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. © The Author(s) 2014. Published by Oxford University Press.

  4. An Imperative Type Hierarchy with Partial Products

    DEFF Research Database (Denmark)

    Schwartzbach, Michael Ignatieff; Schmidt, Erik Meineche

    1989-01-01

    notation for defining recursive types, that is superior to traditional type sums and products. We show how the ordering on types extends to an ordering on types with invariants. We allow the use of least upper bounds in type definitions and show how to compute upper bounds of invariants.......A type hierarchy for a programming language defines an ordering on the types such that any application for small types may be reused for all larger types. The imperative facet makes this non-trivial; the straight-forward definitions will yield an inconsistent system. We introduce a new type...... constructor, the partial product, and show how to define a consistent hierarchy in the context of fully recursive types. A simple polymorphism is derived by introducing a notion of placeholder types. By extending the partial product types to include structural invariants we obtain a particularly appropriate...

  5. Scale hierarchy in high-temperature QCD

    CERN Document Server

    Akerlund, Oscar

    2013-01-01

    Because of asymptotic freedom, QCD becomes weakly interacting at high temperature: this is the reason for the transition to a deconfined phase in Yang-Mills theory at temperature $T_c$. At high temperature $T \\gg T_c$, the smallness of the running coupling $g$ induces a hierachy betwen the "hard", "soft" and "ultrasoft" energy scales $T$, $g T$ and $g^2 T$. This hierarchy allows for a very successful effective treatment where the "hard" and the "soft" modes are successively integrated out. However, it is not clear how high a temperature is necessary to achieve such a scale hierarchy. By numerical simulations, we show that the required temperatures are extremely high. Thus, the quantitative success of the effective theory down to temperatures of a few $T_c$ appears surprising a posteriori.

  6. Generalized non-linear Schroedinger hierarchy

    International Nuclear Information System (INIS)

    Aratyn, H.; Gomes, J.F.; Zimerman, A.H.

    1994-01-01

    The importance in studying the completely integrable models have became evident in the last years due to the fact that those models present an algebraic structure extremely rich, providing the natural scenery for solitons description. Those models can be described through non-linear differential equations, pseudo-linear operators (Lax formulation), or a matrix formulation. The integrability implies in the existence of a conservation law associated to each of degree of freedom. Each conserved charge Q i can be associated to a Hamiltonian, defining a time evolution related to to a time t i through the Hamilton equation ∂A/∂t i =[A,Q i ]. Particularly, for a two-dimensions field theory, infinite degree of freedom exist, and consequently infinite conservation laws describing the time evolution in space of infinite times. The Hamilton equation defines a hierarchy of models which present a infinite set of conservation laws. This paper studies the generalized non-linear Schroedinger hierarchy

  7. Inverted radiative hierarchy of quark masses

    International Nuclear Information System (INIS)

    Berezhiani, Z.G.; Rattazzi, R.

    1992-01-01

    Inverted radiative hierarchy of quark masses is investigated. The authors suggest that the mass hierarchy is first generated in a sector of heavy isosinglet fermions due to radiative effects and then projected in the inverted way to the usual quarks by means of a universal seesaw. The simple left-right symmetric gauge model is presented with the P- and CP-parities and the exact isotopical symmetry which are softly (or spontaneously) broken in the Higgs potential. This approach naturally explains the observed pattern of quark masses and mixing, providing the quantitatively correct formula for the Cabibbo angle. Top quark is predicted to be in the 90-150 GeV range

  8. Explorations of the extended ncKP hierarchy

    International Nuclear Information System (INIS)

    Dimakis, Aristophanes; Mueller-Hoissen, Folkert

    2004-01-01

    A recently obtained extension (xncKP) of the Moyal-deformed KP hierarchy (ncKP hierarchy) by a set of evolution equations in the Moyal-deformation parameters is further explored. Formulae are derived to compute these equations efficiently. Reductions of the xncKP hierarchy are treated, in particular to the extended ncKdV and ncBoussinesq hierarchies. Furthermore, a good part of the Sato formalism for the KP hierarchy is carried over to the generalized framework. In particular, the well-known bilinear identity theorem for the KP hierarchy, expressed in terms of the (formal) Baker-Akhiezer function, extends to the xncKP hierarchy. Moreover, it is demonstrated that N-soliton solutions of the ncKP equation are also solutions of the first few deformation equations. This is shown to be related to the existence of certain families of algebraic identities

  9. Affine Lie algebraic origin of constrained KP hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.; Gomes, J.F.; Zimerman, A.H.

    1994-07-01

    It is presented an affine sl(n+1) algebraic construction of the basic constrained KP hierarchy. This hierarchy is analyzed using two approaches, namely linear matrix eigenvalue problem on hermitian symmetric space and constrained KP Lax formulation and we show that these approaches are equivalent. The model is recognized to be generalized non-linear Schroedinger (GNLS) hierarchy and it is used as a building block for a new class of constrained KP hierarchies. These constrained KP hierarchies are connected via similarity-Backlund transformations and interpolate between GNLS and multi-boson KP-Toda hierarchies. The construction uncovers origin of the Toda lattice structure behind the latter hierarchy. (author). 23 refs

  10. Gauge equivalence between two-boson KP hierarchies

    International Nuclear Information System (INIS)

    Aratyn, H.

    1994-01-01

    In this paper it is explained the status of the two-boson KP hierarchy, which appears in this setting as an invariant subspace of the coadjoint orbit within the KP l=1 hierarchy. We will work with two main cases of two-boson KP hierarchies, one defined within KP l=1 hierarchy will be called Faa di Bruno KP hierarchy, while the second defined within KP hierarchy for a quadratic two-boson KP hierarchy. It will be established for them the gauge invariance playing the role of generalized Miura transformations. It is emphasized the symplectic character of equivalence of KP l=1 and KP. It is also made a point that the gauge equivalence established for two-boson systems is valid for an arbitrary n-th Poisson bracket structure and not only the first Poisson bracket structure. (author). 7 refs

  11. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  12. Hierarchy of on-orbit servicing interfaces

    Science.gov (United States)

    Moe, Rud V.

    1989-01-01

    A series of equipment interfaces is involved in on-orbit servicing operations. The end-to-end hierarchy of servicing interfaces is presented. The interface concepts presented include structure and handling, and formats for transfer of resources (power, data, fluids, etc.). Consequences on cost, performance, and service ability of the use of standard designs or unique designs with interface adapters are discussed. Implications of the interface designs compatibility with remote servicing using telerobotic servicers are discussed.

  13. Gauge hierarchy and long range forces

    International Nuclear Information System (INIS)

    Pal, P.B.; Keung, Wai-Yee; Chang, D.

    1990-01-01

    With the aid of simple examples, we show how a long range attractive force can arise in a gauge theory with a hierarchy. The force is due to the exchange of a Higgs boson whose mass and matter couplings are both naturally suppressed by the hierarchical mass ratio. Such bosons appear if there is an accidental global symmetry in the low-energy renormalizable Lagrangian after the high energy symmetry breaking. 6 refs

  14. Do Convolutional Neural Networks Learn Class Hierarchy?

    Science.gov (United States)

    Bilal, Alsallakh; Jourabloo, Amin; Ye, Mao; Liu, Xiaoming; Ren, Liu

    2018-01-01

    Convolutional Neural Networks (CNNs) currently achieve state-of-the-art accuracy in image classification. With a growing number of classes, the accuracy usually drops as the possibilities of confusion increase. Interestingly, the class confusion patterns follow a hierarchical structure over the classes. We present visual-analytics methods to reveal and analyze this hierarchy of similar classes in relation with CNN-internal data. We found that this hierarchy not only dictates the confusion patterns between the classes, it furthermore dictates the learning behavior of CNNs. In particular, the early layers in these networks develop feature detectors that can separate high-level groups of classes quite well, even after a few training epochs. In contrast, the latter layers require substantially more epochs to develop specialized feature detectors that can separate individual classes. We demonstrate how these insights are key to significant improvement in accuracy by designing hierarchy-aware CNNs that accelerate model convergence and alleviate overfitting. We further demonstrate how our methods help in identifying various quality issues in the training data.

  15. Integral equation hierarchy for continuum percolation

    International Nuclear Information System (INIS)

    Given, J.A.

    1988-01-01

    In this thesis a projection operator technique is presented that yields hierarchies of integral equations satisfied exactly by the n-point connectedness functions in a continuum version of the site-bond percolation problem. The n-point connectedness functions carry the same structural information for a percolation problem as then-point correlation functions do for a thermal problem. This method extends the Potts model mapping of Fortuin and Kastelyn to the continuum by exploiting an s-state generalization of the Widom-Rowlinson model, a continuum model for phase separation. The projection operator technique is used to produce an integral equation hierarchy for percolation similar to the Born-Green heirarchy. The Kirkwood superposition approximation (SA) is extended to percolation in order to close this hierarchy and yield a nonlinear integral equation for the two-point connectedness function. The fact that this function, in the SA, is the analytic continuation to negative density of the two-point correlation function in a corresponding thermal problem is discussed. The BGY equation for percolation is solved numerically, both by an expansion in powers of the density, and by an iterative technique due to Kirkwood. It is argued both analytically and numerically, that the BYG equation for percolation, unlike its thermal counterpart, shows non-classical critical behavior, with η = 1 and γ = 0.05 ± .1. Finally a sequence of refinements to the superposition approximations based in the theory of fluids by Rice and Lekner is discussed

  16. Determining the neutrino mass hierarchy with cosmology

    International Nuclear Information System (INIS)

    De Bernardis, Francesco; Kitching, Thomas D.; Heavens, Alan; Melchiorri, Alessandro

    2009-01-01

    The combination of current large-scale structure and cosmic microwave background anisotropies data can place strong constraints on the sum of the neutrino masses. Here we show that future cosmic shear experiments, in combination with cosmic microwave background constraints, can provide the statistical accuracy required to answer questions about differences in the mass of individual neutrino species. Allowing for the possibility that masses are nondegenerate we combine Fisher matrix forecasts for a weak lensing survey like Euclid with those for the forthcoming Planck experiment. Under the assumption that neutrino mass splitting is described by a normal hierarchy we find that the combination Planck and Euclid will possibly reach enough sensitivity to put a constraint on the mass of a single species. Using a Bayesian evidence calculation we find that such future experiments could provide strong evidence for either a normal or an inverted neutrino hierarchy. Finally we show that if a particular neutrino hierarchy is assumed then this could bias cosmological parameter constraints, for example, the dark energy equation of state parameter, by > or approx. 1σ, and the sum of masses by 2.3σ. We finally discuss the impact of uncertainties on the theoretical modeling of nonlinearities. The results presented in this analysis are obtained under an approximation to the nonlinear power spectrum. This significant source of uncertainty needs to be addressed in future work.

  17. Collaborative hierarchy maintains cooperation in asymmetric games.

    Science.gov (United States)

    Antonioni, Alberto; Pereda, María; Cronin, Katherine A; Tomassini, Marco; Sánchez, Angel

    2018-03-29

    The interplay of social structure and cooperative behavior is under much scrutiny lately as behavior in social contexts becomes increasingly relevant for everyday life. Earlier experimental work showed that the existence of a social hierarchy, earned through competition, was detrimental for the evolution of cooperative behaviors. Here, we study the case in which individuals are ranked in a hierarchical structure based on their performance in a collective effort by having them play a Public Goods Game. In the first treatment, participants are ranked according to group earnings while, in the second treatment, their rankings are based on individual earnings. Subsequently, participants play asymmetric Prisoner's Dilemma games where higher-ranked players gain more than lower ones. Our experiments show that there are no detrimental effects of the hierarchy formed based on group performance, yet when ranking is assigned individually we observe a decrease in cooperation. Our results show that different levels of cooperation arise from the fact that subjects are interpreting rankings as a reputation which carries information about which subjects were cooperators in the previous phase. Our results demonstrate that noting the manner in which a hierarchy is established is essential for understanding its effects on cooperation.

  18. Semi-Semantic Annotation: A guideline for the URDU.KON-TB treebank POS annotation

    Directory of Open Access Journals (Sweden)

    Qaiser ABBAS

    2016-12-01

    Full Text Available This work elaborates the semi-semantic part of speech annotation guidelines for the URDU.KON-TB treebank: an annotated corpus. A hierarchical annotation scheme was designed to label the part of speech and then applied on the corpus. This raw corpus was collected from the Urdu Wikipedia and the Jang newspaper and then annotated with the proposed semi-semantic part of speech labels. The corpus contains text of local & international news, social stories, sports, culture, finance, religion, traveling, etc. This exercise finally contributed a part of speech annotation to the URDU.KON-TB treebank. Twenty-two main part of speech categories are divided into subcategories, which conclude the morphological, and semantical information encoded in it. This article reports the annotation guidelines in major; however, it also briefs the development of the URDU.KON-TB treebank, which includes the raw corpus collection, designing & employment of annotation scheme and finally, its statistical evaluation and results. The guidelines presented as follows, will be useful for linguistic community to annotate the sentences not only for the national language Urdu but for the other indigenous languages like Punjab, Sindhi, Pashto, etc., as well.

  19. Fluxes, hierarchies, and metastable vacua in supersymmetric field theories

    International Nuclear Information System (INIS)

    Bruemmer, F.

    2008-01-01

    This thesis concerns topics both in low-energy effective field theories from type IIB superstring flux compactifications and in four-dimensional, rigidly supersymmetric gauge theories. We introduce flux compactifications with so-called ''warped throat'' regions, which lead to large hierarchies of scales in the effective four-dimensional theory. The correspondence between a particular such throat and a five-dimensional Randall-Sundrum-like model is established. We shown how certain string-theoretic features of the compactification, such as moduli stabilization by fluxes or the presence of an unstabilized Kaehler modulus, are incorporated in the five-dimensional picture. The KKLT construction for metastable de Sitter vacua is reviewed, as well as some possible modifications involving spontaneous F-term supersymmetry breaking. For KKLT-like models with their hidden sector localized inside a throat, the mediation of supersymmetry breaking to the visible sector is investigated. We review the mechanism of mixed modulus-anomaly mediation, and show that there can be additional equally important gravity-mediated contributions. We finally turn to the ISS model of metastable dynamical supersymmetry breaking in four dimensions, and present a renormalizable extension which generates a large hierarchy naturally. We also recapitulate how the ISS model may be obtained from a type IIB superstring model. (orig.)

  20. Fluxes, hierarchies, and metastable vacua in supersymmetric field theories

    Energy Technology Data Exchange (ETDEWEB)

    Bruemmer, F.

    2008-02-06

    This thesis concerns topics both in low-energy effective field theories from type IIB superstring flux compactifications and in four-dimensional, rigidly supersymmetric gauge theories. We introduce flux compactifications with so-called ''warped throat'' regions, which lead to large hierarchies of scales in the effective four-dimensional theory. The correspondence between a particular such throat and a five-dimensional Randall-Sundrum-like model is established. We shown how certain string-theoretic features of the compactification, such as moduli stabilization by fluxes or the presence of an unstabilized Kaehler modulus, are incorporated in the five-dimensional picture. The KKLT construction for metastable de Sitter vacua is reviewed, as well as some possible modifications involving spontaneous F-term supersymmetry breaking. For KKLT-like models with their hidden sector localized inside a throat, the mediation of supersymmetry breaking to the visible sector is investigated. We review the mechanism of mixed modulus-anomaly mediation, and show that there can be additional equally important gravity-mediated contributions. We finally turn to the ISS model of metastable dynamical supersymmetry breaking in four dimensions, and present a renormalizable extension which generates a large hierarchy naturally. We also recapitulate how the ISS model may be obtained from a type IIB superstring model. (orig.)

  1. Maslow and the motivation hierarchy: measuring satisfaction of the needs.

    Science.gov (United States)

    Taormina, Robert J; Gao, Jennifer H

    2013-01-01

    For each of the 5 needs in Maslow's motivational hierarchy (physiological, safety-security, belongingness, esteem, and self-actualization), operational definitions were developed from Maslow's theory of motivation. New measures were created based on the operational definitions (1) to assess the satisfaction of each need, (2) to assess their expected correlations (a) with each of the other needs and (b) with four social and personality measures (i.e., family support, traditional values, anxiety/worry, and life satisfaction), and (3) to test the ability of the satisfaction level of each need to statistically predict the satisfaction level of the next higher-level need. Psychometric tests of the scales conducted on questionnaire results from 386 adult respondents from the general population lent strong support for the validity and reliability of all 5 needs measures. Significant positive correlations among the scales were also found; that is, the more each lower-level need was satisfied, the more the next higher-level need was satisfied. Additionally, as predicted, family support, traditional values, and life satisfaction had significant positive correlations with the satisfaction of all 5 needs, and the anxiety/worry facet of neuroticism had significant negative correlations with the satisfaction of all the needs. Multiple regression analyses revealed that the satisfaction of each higher-level need was statistically predicted by the satisfaction of the need immediately below it in the hierarchy, as expected from Maslow's theory.

  2. Organizing product innovation: hierarchy, market or triple-helix networks?

    Science.gov (United States)

    Fitjar, Rune Dahl; Gjelsvik, Martin; Rodríguez-Pose, Andrés

    This paper assesses the extent to which the organization of the innovation effort in firms, as well as the geographical scale at which this effort is pursued, affects the capacity to benefit from product innovations. Three alternative modes of organization are studied: hierarchy, market and triple-helix-type networks. Furthermore, we consider triple-helix networks at three geographical scales: local, national and international. These relationships are tested on a random sample of 763 firms located in five urban regions of Norway which reported having introduced new products or services during the preceding 3 years. The analysis shows that firms exploiting internal hierarchy or triple-helix networks with a wide range of partners managed to derive a significantly higher share of their income from new products, compared to those that mainly relied on outsourcing within the market. In addition, the analysis shows that the geographical scale of cooperation in networks, as well as the type of partner used, matters for the capacity of firms to benefit from product innovation. In particular, firms that collaborate in international triple-helix-type networks involving suppliers, customers and R&D institutions extract a higher share of their income from product innovations, regardless of whether they organize the processes internally or through the network.

  3. Active learning reduces annotation time for clinical concept extraction.

    Science.gov (United States)

    Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

    2017-10-01

    To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2011-07-01

    Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

  5. Multi-Label Classification Based on Low Rank Representation for Image Annotation

    Directory of Open Access Journals (Sweden)

    Qiaoyu Tan

    2017-01-01

    Full Text Available Annotating remote sensing images is a challenging task for its labor demanding annotation process and requirement of expert knowledge, especially when images can be annotated with multiple semantic concepts (or labels. To automatically annotate these multi-label images, we introduce an approach called Multi-Label Classification based on Low Rank Representation (MLC-LRR. MLC-LRR firstly utilizes low rank representation in the feature space of images to compute the low rank constrained coefficient matrix, then it adapts the coefficient matrix to define a feature-based graph and to capture the global relationships between images. Next, it utilizes low rank representation in the label space of labeled images to construct a semantic graph. Finally, these two graphs are exploited to train a graph-based multi-label classifier. To validate the performance of MLC-LRR against other related graph-based multi-label methods in annotating images, we conduct experiments on a public available multi-label remote sensing images (Land Cover. We perform additional experiments on five real-world multi-label image datasets to further investigate the performance of MLC-LRR. Empirical study demonstrates that MLC-LRR achieves better performance on annotating images than these comparing methods across various evaluation criteria; it also can effectively exploit global structure and label correlations of multi-label images.

  6. A multi-ontology approach to annotate scientific documents based on a modularization technique.

    Science.gov (United States)

    Gomes, Priscilla Corrêa E Castro; Moura, Ana Maria de Carvalho; Cavalcanti, Maria Cláudia

    2015-12-01

    Scientific text annotation has become an important task for biomedical scientists. Nowadays, there is an increasing need for the development of intelligent systems to support new scientific findings. Public databases available on the Web provide useful data, but much more useful information is only accessible in scientific texts. Text annotation may help as it relies on the use of ontologies to maintain annotations based on a uniform vocabulary. However, it is difficult to use an ontology, especially those that cover a large domain. In addition, since scientific texts explore multiple domains, which are covered by distinct ontologies, it becomes even more difficult to deal with such task. Moreover, there are dozens of ontologies in the biomedical area, and they are usually big in terms of the number of concepts. It is in this context that ontology modularization can be useful. This work presents an approach to annotate scientific documents using modules of different ontologies, which are built according to a module extraction technique. The main idea is to analyze a set of single-ontology annotations on a text to find out the user interests. Based on these annotations a set of modules are extracted from a set of distinct ontologies, and are made available for the user, for complementary annotation. The reduced size and focus of the extracted modules tend to facilitate the annotation task. An experiment was conducted to evaluate this approach, with the participation of a bioinformatician specialist of the Laboratory of Peptides and Proteins of the IOC/Fiocruz, who was interested in discovering new drug targets aiming at the combat of tropical diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Minimal string theories and integrable hierarchies

    Science.gov (United States)

    Iyer, Ramakrishnan

    Well-defined, non-perturbative formulations of the physics of string theories in specific minimal or superminimal model backgrounds can be obtained by solving matrix models in the double scaling limit. They provide us with the first examples of completely solvable string theories. Despite being relatively simple compared to higher dimensional critical string theories, they furnish non-perturbative descriptions of interesting physical phenomena such as geometrical transitions between D-branes and fluxes, tachyon condensation and holography. The physics of these theories in the minimal model backgrounds is succinctly encoded in a non-linear differential equation known as the string equation, along with an associated hierarchy of integrable partial differential equations (PDEs). The bosonic string in (2,2m-1) conformal minimal model backgrounds and the type 0A string in (2,4 m) superconformal minimal model backgrounds have the Korteweg-de Vries system, while type 0B in (2,4m) backgrounds has the Zakharov-Shabat system. The integrable PDE hierarchy governs flows between backgrounds with different m. In this thesis, we explore this interesting connection between minimal string theories and integrable hierarchies further. We uncover the remarkable role that an infinite hierarchy of non-linear differential equations plays in organizing and connecting certain minimal string theories non-perturbatively. We are able to embed the type 0A and 0B (A,A) minimal string theories into this single framework. The string theories arise as special limits of a rich system of equations underpinned by an integrable system known as the dispersive water wave hierarchy. We find that there are several other string-like limits of the system, and conjecture that some of them are type IIA and IIB (A,D) minimal string backgrounds. We explain how these and several other string-like special points arise and are connected. In some cases, the framework endows the theories with a non

  8. MPEG-7 based video annotation and browsing

    Science.gov (United States)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

    The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

  9. ACID: annotation of cassette and integron data

    Directory of Open Access Journals (Sweden)

    Stokes Harold W

    2009-04-01

    Full Text Available Abstract Background Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms. Description By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided. Conclusion ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.

  10. Hierarchy, Dominance, and Deliberation: Egalitarian Values Require Mental Effort.

    Science.gov (United States)

    Van Berkel, Laura; Crandall, Christian S; Eidelman, Scott; Blanchar, John C

    2015-09-01

    Hierarchy and dominance are ubiquitous. Because social hierarchy is early learned and highly rehearsed, the value of hierarchy enjoys relative ease over competing egalitarian values. In six studies, we interfere with deliberate thinking and measure endorsement of hierarchy and egalitarianism. In Study 1, bar patrons' blood alcohol content was correlated with hierarchy preference. In Study 2, cognitive load increased the authority/hierarchy moral foundation. In Study 3, low-effort thought instructions increased hierarchy endorsement and reduced equality endorsement. In Study 4, ego depletion increased hierarchy endorsement and caused a trend toward reduced equality endorsement. In Study 5, low-effort thought instructions increased endorsement of hierarchical attitudes among those with a sense of low personal power. In Study 6, participants' thinking quickly allocated more resources to high-status groups. Across five operationalizations of impaired deliberative thought, hierarchy endorsement increased and egalitarianism receded. These data suggest hierarchy may persist in part because it has a psychological advantage. © 2015 by the Society for Personality and Social Psychology, Inc.

  11. Annotating Logical Forms for EHR Questions.

    Science.gov (United States)

    Roberts, Kirk; Demner-Fushman, Dina

    2016-05-01

    This paper discusses the creation of a semantically annotated corpus of questions about patient data in electronic health records (EHRs). The goal is to provide the training data necessary for semantic parsers to automatically convert EHR questions into a structured query. A layered annotation strategy is used which mirrors a typical natural language processing (NLP) pipeline. First, questions are syntactically analyzed to identify multi-part questions. Second, medical concepts are recognized and normalized to a clinical ontology. Finally, logical forms are created using a lambda calculus representation. We use a corpus of 446 questions asking for patient-specific information. From these, 468 specific questions are found containing 259 unique medical concepts and requiring 53 unique predicates to represent the logical forms. We further present detailed characteristics of the corpus, including inter-annotator agreement results, and describe the challenges automatic NLP systems will face on this task.

  12. A health hierarchy of effects model: a synthesis of advertising and health hierarchy conceptualizations.

    Science.gov (United States)

    Rouse, R A

    1991-01-01

    Work by both advertising and health researchers has independently yielded hierarchy of effects models which can be used to predict campaign success. Unfortunately, however, previous work has been criticized as "common sense" approaches which are more "assumed" than "proven." This analysis argues that much of the problem is due to the lack of precision often associated with over-simplified "uni-dimensional" models. Instead, this perspective synthesized a "two-dimensional" health hierarchy of effects model and outlines a pragmatic strategy for campaign measurement.

  13. Annotating images by mining image search results.

    Science.gov (United States)

    Wang, Xin-Jing; Zhang, Lei; Li, Xirong; Ma, Wei-Ying

    2008-11-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results. Some 2.4 million images with their surrounding text are collected from a few photo forums to support this approach. The entire process is formulated in a divide-and-conquer framework where a query keyword is provided along with the uncaptioned image to improve both the effectiveness and efficiency. This is helpful when the collected data set is not dense everywhere. In this sense, our approach contains three steps: 1) the search process to discover visually and semantically similar search results, 2) the mining process to identify salient terms from textual descriptions of the search results, and 3) the annotation rejection process to filter out noisy terms yielded by Step 2. To ensure real-time annotation, two key techniques are leveraged-one is to map the high-dimensional image visual features into hash codes, the other is to implement it as a distributed system, of which the search and mining processes are provided as Web services. As a typical result, the entire process finishes in less than 1 second. Since no training data set is required, our approach enables annotating with unlimited vocabulary and is highly scalable and robust to outliers. Experimental results on both real Web images and a benchmark image data set show the effectiveness and efficiency of the proposed algorithm. It is also worth noting that, although the entire approach is illustrated within the divide-and conquer framework, a query keyword is not crucial to our current implementation. We provide experimental results to prove this.

  14. Towards the VWO Annotation Service: a Success Story of the IMAGE RPI Expert Rating System

    Science.gov (United States)

    Reinisch, B. W.; Galkin, I. A.; Fung, S. F.; Benson, R. F.; Kozlov, A. V.; Khmyrov, G. M.; Garcia, L. N.

    2010-12-01

    Interpretation of Heliophysics wave data requires specialized knowledge of wave phenomena. Users of the virtual wave observatory (VWO) will greatly benefit from a data annotation service that will allow querying of data by phenomenon type, thus helping accomplish the VWO goal to make Heliophysics wave data searchable, understandable, and usable by the scientific community. Individual annotations can be sorted by phenomenon type and reduced into event lists (catalogs). However, in contrast to the event lists, annotation records allow a greater flexibility of collaborative management by more easily admitting operations of addition, revision, or deletion. They can therefore become the building blocks for an interactive Annotation Service with a suitable graphic user interface to the VWO middleware. The VWO Annotation Service vision is an interactive, collaborative sharing of domain expert knowledge with fellow scientists and students alike. An effective prototype of the VWO Annotation Service has been in operation at the University of Massachusetts Lowell since 2001. An expert rating system (ERS) was developed for annotating the IMAGE radio plasma imager (RPI) active sounding data containing 1.2 million plasmagrams. The RPI data analysts can use ERS to submit expert ratings of plasmagram features, such as presence of echo traces resulted from reflected RPI signals from distant plasma structures. Since its inception in 2001, the RPI ERS has accumulated 7351 expert plasmagram ratings in 16 phenomenon categories, together with free-text descriptions and other metadata. In addition to human expert ratings, the system holds 225,125 ratings submitted by the CORPRAL data prospecting software that employs a model of the human pre-attentive vision to select images potentially containing interesting features. The annotation records proved to be instrumental in a number of investigations where manual data exploration would have been prohibitively tedious and expensive

  15. Motion lecture annotation system to learn Naginata performances

    Science.gov (United States)

    Kobayashi, Daisuke; Sakamoto, Ryota; Nomura, Yoshihiko

    2013-12-01

    This paper describes a learning assistant system using motion capture data and annotation to teach "Naginata-jutsu" (a skill to practice Japanese halberd) performance. There are some video annotation tools such as YouTube. However these video based tools have only single angle of view. Our approach that uses motion-captured data allows us to view any angle. A lecturer can write annotations related to parts of body. We have made a comparison of effectiveness between the annotation tool of YouTube and the proposed system. The experimental result showed that our system triggered more annotations than the annotation tool of YouTube.

  16. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  17. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  18. Software for computing and annotating genomic ranges.

    Science.gov (United States)

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  19. Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

    Science.gov (United States)

    Feuermann, Marc; Gaudet, Pascale; Mi, Huaiyu; Lewis, Suzanna E; Thomas, Paul D

    2016-01-01

    We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo. © The Author(s) 2016. Published by Oxford University Press.

  20. Physical interpretation of the combinatorial hierarchy

    International Nuclear Information System (INIS)

    Bastin, T.; Noyes, H.P.

    1978-01-01

    The combinatorial hierarchy model for base particle processes is compared and contrasted with the Ur-theory as developed at the Tutzing Conferences. It agrees with Ur-theory about a finite basis, the ''fixed past--uncertain future'' aspects of physics, and the necessity of dropping Bohr's requirement of reduction to the haptic language of commonsense and classical physics. However, it retains a constructive, hierarchial approach with can yield only an approximate and discrete ''space time'', and introduces the observation metaphysic at the start. Concrete interpretation of the four levels of the hierarchy (with cardinals 3, 7, 127, 2 127 -1 approx. =10 38 ) associates the three levels which map up and down with three absolute conservation laws (charge, baryon number, lepton number) and the spin dichotomy. The first level represents +, -, and +- unit charge. The second has the quantum nubmers of a baryon--antibaryon pair and associated charged meson (e.g., n anti n, p anti n, p anti p, n anti p, π + , π 0 , π - ). The third level associates this pair, now including four spin states as well as four charge states, with a neutral lepton--antilepton pair (e anti e or ν anti ν) in four spin states (total, 64 states): three charged spinless, three charged spin-1, and neutral spin-1 mesons (15 states), and a neutral vector boson associated with the leptons; this gives 3 + 15 + 3 x 15 = 63 possible boson states, so a total correct count of 63 + 64 = 127 states. Something like SU 2 X SU 3 and other indications of quark quantum numbers can occur as substructures at the fourth (unstable) level. A slight extension gives the usual static approximation to the building energy of the hydrogen atom, α 2 m/sub e/c 2 . Cosmological implications of the theory are in accord with current experience. A beginning in the physical interpretation of a theory which could eventually encompass all branches of physics was made. 3 figures, 6 tables

  1. Solar Tutorial and Annotation Resource (STAR)

    Science.gov (United States)

    Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

    2009-12-01

    We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven

  2. The Hierarchy of Proinflammatory Cytokines in Ocular Inflammation.

    Science.gov (United States)

    Da Cunha, A P; Zhang, Q; Prentiss, M; Wu, X Q; Kainz, V; Xu, Y Y; Vrouvlianis, J; Li, H; Rangaswamy, N; Leehy, B; McGee, T L; Bell, C L; Bigelow, C E; Kansara, V; Medley, Q; Huang, Q; Wu, H Y

    2018-04-01

    The concept of tissue-dependent cytokine hierarchy has been demonstrated in a number of diseases, but it has not been investigated in ophthalmic diseases. Here, we evaluated the functional hierarchy of interleukin-1β (IL-1β), IL-6, IL-17A, and tumor necrosis factor (TNF) in the induction of ocular inflammation. We delivered adeno-associated virus (AAV) vectors expressing IL-1β, IL-6, IL-17A, or TNF intravitreally in naïve C57/BL6 mice and compared and contrasted the inflammatory effects in the eye 5 weeks after AAV-mediated gene transfer. We also used an in vitro human system to test the effect of cytokines on barrier function. We found that IL-1β had the highest ability to initiate ocular inflammation. The continuous overexpression of IL-1β resulted in a significant upregulation of additional proinflammatory mediators in the eye. Using scanning laser ophthalmoscope and optical coherence tomography imaging techniques, we showed that a low dose of AAVIL-1β was sufficient and was as pathogenic as a high dose of TNF in inducing vascular leakage, retinal degeneration, and cellular infiltration. Furthermore, only a marginal increase in IL-1β was enough to cause cellular infiltration, thus confirming the highly pathogenic nature of IL-1β in the eye. Contrary to our expectation, IL-6 or IL-17A had minimal or no effect in the eye. To examine the clinical relevance of our findings, we used an impedance assay to show that IL-1β alone or TNF alone was able to cause primary human retinal endothelial cell barrier dysfunction in vitro. Again, IL-6 alone or IL-17A alone had no effect on barrier function; however, in the presence of IL-1β or TNF, IL-17A but not IL-6 may provide additive proinflammatory effects. Our studies demonstrate the existence of a functional hierarchy of proinflammatory cytokines in the eye, and we show that IL-1β is the most pathogenic when it is continuously expressed in the eye.

  3. Asymptotic density and the Ershov hierarchy

    OpenAIRE

    Downey, Rod; Jockusch, Carl; McNicholl, Timothy H.; Schupp, Paul

    2013-01-01

    We classify the asymptotic densities of the $\\Delta^0_2$ sets according to their level in the Ershov hierarchy. In particular, it is shown that for $n \\geq 2$, a real $r \\in [0,1]$ is the density of an $n$-c.e.\\ set if and only if it is a difference of left-$\\Pi_2^0$ reals. Further, we show that the densities of the $\\omega$-c.e.\\ sets coincide with the densities of the $\\Delta^0_2$ sets, and there are $\\omega$-c.e.\\ sets whose density is not the density of an $n$-c.e. set for any $n \\in \\ome...

  4. From fusion hierarchy to excited state TBA

    International Nuclear Information System (INIS)

    Juettner, G.; Kluemper, A.

    1998-01-01

    Functional relations among the fusion hierarchy of quantum transfer matrices give a novel derivation of the TBA equations, namely without string hypothesis. This is demonstrated for two important models of 1D highly correlated electron systems, the supersymmetric t-J model and the supersymmetric extended Hubbard model. As a consequence, ''the excited state TBA'' equations, which characterize correlation lengths, are explicitly derived for the t-J model. To the authors' knowledge, this is the first explicit derivation of excited state TBA equations for 1D lattice electron systems. (orig.)

  5. Revaluing the hierarchy of paper recycling

    International Nuclear Information System (INIS)

    Samakovlis, Eva

    2004-01-01

    This article revalues the hierarchy of paper waste management policies in a dynamic general equilibrium model. Incineration, material recycling and the distinction between non-renewable fossil fuels and renewable forest assets are incorporated. By comparing the first order conditions from the command optimum with the conditions from the market model, it is discovered that the unregulated market fails to create an optimal resource allocation. To see how the market behaves, in absence of environmental policy, compared to the first best solution a numerical model is used. Pigouvian taxes and subsidies are derived to correct for the externalities

  6. A Machian solution of the hierarchy problem

    International Nuclear Information System (INIS)

    Gogberashvili, M.

    2008-01-01

    The new interpretation of Mach's principle of mass of a particle being a measure of the interactions of this particle with all other gravitating particles inside its causal spheres is introduced. It is shown that within some alternative model of gravitation that incorporates this principle, the Machian influence of the universe can reduce Planck's scale to the electro-weak scale and the large number that is needed to explain the hierarchy between the scales is the amount of gravitating particles inside the universe horizon. Our model can lead to new observable effects at cosmological distances and close to the sources of a strong gravitational field. (orig.)

  7. Stability of mass hierarchy in models with a sliding singlet

    International Nuclear Information System (INIS)

    Smirnov, A.Yu.; Tainov, E.A.

    1986-01-01

    In the broad class of models with a heavy sliding singlet and softly broken supersymmetry (e.g. by the effects of N=1 supergravity) it is shown that the doublet-triplet hierarchy obtained at the tree level is not destroyed by quantum correction at any loop order. As an example the simplest SU(5) model with a stable doublet-triplet hierarchy is proposed. The necessary and sufficient conditions of the hierarchy stability are discussed. (orig.)

  8. Baecklund transformation of the noncommutative Gelfand-Dickey hierarchy

    International Nuclear Information System (INIS)

    Zheng Zhong; He Jingsong; Cheng Yi

    2004-01-01

    We study the Baecklund transformation of the noncommutative Gelfand-Dickey(ncGD) hierarchy. By factorizing its Lax operator into the multiplication form of first order differential operator, the noncommutative modified KdV(ncMKdV) hierarchy and the Miura transformations are defined. Our results show that the ncMKdV equations are invariant under the cyclic permutation, and hence induces the Baecklund transformation of the ncGD hierarchy. (author)

  9. Self-organizing dominance hierarchies in a wild primate population

    OpenAIRE

    Franz, Mathias; McLean, Emily; Tung, Jenny; Altmann, Jeanne; Alberts, Susan C.

    2015-01-01

    Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The ‘prior attributes hypothesis’ posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the ‘social d...

  10. A hierarchy of Liouville integrable discrete Hamiltonian equations

    Energy Technology Data Exchange (ETDEWEB)

    Xu Xixiang [College of Science, Shandong University of Science and Technology, Qingdao 266510 (China)], E-mail: xixiang_xu@yahoo.com.cn

    2008-05-12

    Based on a discrete four-by-four matrix spectral problem, a hierarchy of Lax integrable lattice equations with two potentials is derived. Two Hamiltonian forms are constructed for each lattice equation in the resulting hierarchy by means of the discrete variational identity. A strong symmetry operator of the resulting hierarchy is given. Finally, it is shown that the resulting lattice equations are all Liouville integrable discrete Hamiltonian systems.

  11. The Theory of Ratio Scale Estimation: Saaty's Analytic Hierarchy Process

    OpenAIRE

    Patrick T. Harker; Luis G. Vargas

    1987-01-01

    The Analytic Hierarchy Process developed by Saaty (Saaty, T. L. 1980. The Analytic Hierarchy Process. McGraw-Hill, New York.) has proven to be an extremely useful method for decision making and planning. However, some researchers in these areas have raised concerns over the theoretical basis underlying this process. This paper addresses currently debated issues concerning the theoretical foundations of the Analytic Hierarchy Process. We also illustrate through proof and through examples the v...

  12. When Do Types Induce the Same Belief Hierarchy?

    Directory of Open Access Journals (Sweden)

    Andrés Perea

    2016-10-01

    Full Text Available Type structures are a simple device to describe higher-order beliefs. However, how can we check whether two types generate the same belief hierarchy? This paper generalizes the concept of a type morphism and shows that one type structure is contained in another if and only if the former can be mapped into the other using a generalized type morphism. Hence, every generalized type morphism is a hierarchy morphism and vice versa. Importantly, generalized type morphisms do not make reference to belief hierarchies. We use our results to characterize the conditions under which types generate the same belief hierarchy.

  13. The Toda lattice hierarchy and deformation of conformal field theories

    International Nuclear Information System (INIS)

    Fukuma, M.

    1990-01-01

    In this paper, the authors point out that the Toda lattice hierarchy known in soliton theory is relevant for the description of the deformations of conformal field theories while the KP hierarchy describes unperturbed conformal theories. It is shown that the holomorphic parts of the conserved currents in the perturbed system (the Toda lattice hierarchy) coincide with the conserved currents in the KP hierarchy and can be written in terms of the W-algebraic currents. Furthermore, their anti-holomorphic counterparts are obtained

  14. On Recursion Operator of the q -KP Hierarchy

    International Nuclear Information System (INIS)

    Tian Ke-Lei; Zhu Xiao-Ming; He Jing-Song

    2016-01-01

    It is the aim of the present article to give a general expression of flow equations of the q-KP hierarchy. The distinct difference between the q-KP hierarchy and the KP hierarchy is due to q-binomial and the action of q-shift operator θ, which originates from the Leibnitz rule of the quantum calculus. We further show that the n-reduction leads to a recursive scheme for these flow equations. The recursion operator for the flow equations of the q-KP hierarchy under the n-reduction is also derived. (paper)

  15. An extended integrable fractional-order KP soliton hierarchy

    International Nuclear Information System (INIS)

    Li Li

    2011-01-01

    In this Letter, we consider the modified derivatives and integrals of fractional-order pseudo-differential operators. A sequence of Lax KP equations hierarchy and extended fractional KP (fKP) hierarchy are introduced, and the fKP hierarchy has Lax presentations with the extended Lax operators. In the case of the extension with the half-order pseudo-differential operators, a new integrable fKP hierarchy is obtained. A few particular examples of fractional order will be listed, together with their Lax pairs.

  16. The analytic hierarchy process as a support for decision making

    Directory of Open Access Journals (Sweden)

    Filipović Milanka

    2007-01-01

    Full Text Available The first part of this text deals with a convention site selection as one of the most lucrative areas in the tourism industry. The second part gives a further description of a method for decision making - the analytic hierarchy process. The basic characteristics: hierarchy constructions and pair wise comparison on the given level of the hierarchy are allured. The third part offers an example of application. This example is solved using the Super - Decision software, which is developed as a computer support for the analytic hierarchy process. This indicates that the AHP approach is a useful tool to help support a decision of convention site selection. .

  17. An extended integrable fractional-order KP soliton hierarchy

    Energy Technology Data Exchange (ETDEWEB)

    Li Li, E-mail: li07099@163.co [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China)

    2011-01-17

    In this Letter, we consider the modified derivatives and integrals of fractional-order pseudo-differential operators. A sequence of Lax KP equations hierarchy and extended fractional KP (fKP) hierarchy are introduced, and the fKP hierarchy has Lax presentations with the extended Lax operators. In the case of the extension with the half-order pseudo-differential operators, a new integrable fKP hierarchy is obtained. A few particular examples of fractional order will be listed, together with their Lax pairs.

  18. A hardness result for core stability in additive hedonic games

    NARCIS (Netherlands)

    Woeginger, G.J.

    2013-01-01

    We investigate the computational complexity of a decision problem in hedonic coalition formation games. We prove that core stability in additive hedonic games is complete for the second level of the polynomial hierarchy.

  19. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Science.gov (United States)

    Oellrich, Anika; Collier, Nigel; Smedley, Damian; Groza, Tudor

    2015-01-01

    Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES), the National Center for Biomedical Ontology (NCBO) Annotator, the Biomedical Concept Annotation System (BeCAS) and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74%) and their quality (best F1-measure of 33%), independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%), the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content of the Sh

  20. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Directory of Open Access Journals (Sweden)

    Anika Oellrich

    Full Text Available Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES, the National Center for Biomedical Ontology (NCBO Annotator, the Biomedical Concept Annotation System (BeCAS and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74% and their quality (best F1-measure of 33%, independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%, the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content

  1. Legal Information Sources: An Annotated Bibliography.

    Science.gov (United States)

    Conner, Ronald C.

    This 25-page annotated bibliography describes the legal reference materials in the special collection of a medium-sized public library. Sources are listed in 12 categories: cases, dictionaries, directories, encyclopedias, forms, references for the lay person, general, indexes, laws and legislation, legal research aids, periodicals, and specialized…

  2. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  3. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  4. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  5. Just-in-time : on strategy annotations

    NARCIS (Netherlands)

    J.C. van de Pol (Jaco)

    2001-01-01

    textabstractA simple kind of strategy annotations is investigated, giving rise to a class of strategies, including leftmost-innermost. It is shown that under certain restrictions, an interpreter can be written which computes the normal form of a term in a bottom-up traversal. The main contribution

  6. Argumentation Theory. [A Selected Annotated Bibliography].

    Science.gov (United States)

    Benoit, William L.

    Materials dealing with aspects of argumentation theory are cited in this annotated bibliography. The 50 citations are organized by topic as follows: (1) argumentation; (2) the nature of argument; (3) traditional perspectives on argument; (4) argument diagrams; (5) Chaim Perelman's theory of rhetoric; (6) the evaluation of argument; (7) argument…

  7. Annotated Bibliography of EDGE2D Use

    Energy Technology Data Exchange (ETDEWEB)

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  8. Nutrition & Adolescent Pregnancy: A Selected Annotated Bibliography.

    Science.gov (United States)

    National Agricultural Library (USDA), Washington, DC.

    This annotated bibliography on nutrition and adolescent pregnancy is intended to be a source of technical assistance for nurses, nutritionists, physicians, educators, social workers, and other personnel concerned with improving the health of teenage mothers and their babies. It is divided into two major sections. The first section lists selected…

  9. Great Basin Experimental Range: Annotated bibliography

    Science.gov (United States)

    E. Durant McArthur; Bryce A. Richardson; Stanley G. Kitchen

    2013-01-01

    This annotated bibliography documents the research that has been conducted on the Great Basin Experimental Range (GBER, also known as the Utah Experiment Station, Great Basin Station, the Great Basin Branch Experiment Station, Great Basin Experimental Center, and other similar name variants) over the 102 years of its existence. Entries were drawn from the original...

  10. Evaluating automatically annotated treebanks for linguistic research

    NARCIS (Netherlands)

    Bloem, J.; Bański, P.; Kupietz, M.; Lüngen, H.; Witt, A.; Barbaresi, A.; Biber, H.; Breiteneder, E.; Clematide, S.

    2016-01-01

    This study discusses evaluation methods for linguists to use when employing an automatically annotated treebank as a source of linguistic evidence. While treebanks are usually evaluated with a general measure over all the data, linguistic studies often focus on a particular construction or a group

  11. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis

    2015-01-01

    This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups...

  12. Annotated Bibliography of EDGE2D Use

    International Nuclear Information System (INIS)

    Strachan, J.D.; Corrigan, G.

    2005-01-01

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  13. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  14. Book Reviews, Annotation, and Web Technology.

    Science.gov (United States)

    Schulze, Patricia

    From reading texts to annotating web pages, grade 6-8 students rely on group cooperation and individual reading and writing skills in this research project that spans six 50-minute lessons. Student objectives for this project are that they will: read, discuss, and keep a journal on a book in literature circles; understand the elements of and…

  15. Snap: an integrated SNP annotation platform

    DEFF Research Database (Denmark)

    Li, Shengting; Ma, Lijia; Li, Heng

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...

  16. Annotating State of Mind in Meeting Data

    NARCIS (Netherlands)

    Heylen, Dirk K.J.; Reidsma, Dennis; Ordelman, Roeland J.F.; Devillers, L.; Martin, J-C.; Cowie, R.; Batliner, A.

    We discuss the annotation procedure for mental state and emotion that is under development for the AMI (Augmented Multiparty Interaction) corpus. The categories that were found to be most appropriate relate not only to emotions but also to (meta-)cognitive states and interpersonal variables. The

  17. ePNK Applications and Annotations

    DEFF Research Database (Denmark)

    Kindler, Ekkart

    2017-01-01

    newapplicationsfor the ePNK and, in particular, visualizing the result of an application in the graphical editor of the ePNK by singannotations, and interacting with the end user using these annotations. In this paper, we give an overview of the concepts of ePNK applications by discussing the implementation...

  18. Retribution as hierarchy regulation: Hierarchy preferences moderate the effect of offender socioeconomic status on support for retribution.

    Science.gov (United States)

    Redford, Liz; Ratliff, Kate A

    2018-01-01

    People punish others for various reasons, including deterring future crime, incapacitating the offender, and retribution, or payback. The current research focuses on retribution, testing whether support for retribution is motivated by the desire to maintain social hierarchies. If so, then the retributive tendencies of hierarchy enhancers or hierarchy attenuators should depend on whether offenders are relatively lower or higher in status, respectively. Three studies showed that hierarchy attenuators were more retributive against high-status offenders than for low-status offenders, that hierarchy enhancers showed a stronger orientation towards retributive justice, and that relationship was stronger for low-status, rather than high-status, criminal offenders. These findings clarify the purpose and function of retributive punishment. They also reveal how hierarchy-regulating motives underlie retribution, motives which, if allowed to influence judgements, may contribute to biased or ineffective justice systems. © 2017 The British Psychological Society.

  19. Special Issue: Annotated Bibliography for Volumes XIX-XXXII.

    Science.gov (United States)

    Pullin, Richard A.

    1998-01-01

    This annotated bibliography lists 310 articles from the "Journal of Cooperative Education" from Volumes XIX-XXXII, 1983-1997. Annotations are presented in the order they appear in the journal; author and subject indexes are provided. (JOW)

  20. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  1. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  2. On hierarchical solutions to the BBGKY hierarchy

    Science.gov (United States)

    Hamilton, A. J. S.

    1988-01-01

    It is thought that the gravitational clustering of galaxies in the universe may approach a scale-invariant, hierarchical form in the small separation, large-clustering regime. Past attempts to solve the Born-Bogoliubov-Green-Kirkwood-Yvon (BBGKY) hierarchy in this regime have assumed a certain separable hierarchical form for the higher order correlation functions of galaxies in phase space. It is shown here that such separable solutions to the BBGKY equations must satisfy the condition that the clustered component of the solution has cluster-cluster correlations equal to galaxy-galaxy correlations to all orders. The solutions also admit the presence of an arbitrary unclustered component, which plays no dyamical role in the large-clustering regime. These results are a particular property of the specific separable model assumed for the correlation functions in phase space, not an intrinsic property of spatially hierarchical solutions to the BBGKY hierarchy. The observed distribution of galaxies does not satisfy the required conditions. The disagreement between theory and observation may be traced, at least in part, to initial conditions which, if Gaussian, already have cluster correlations greater than galaxy correlations.

  3. Hierarchies without symmetries from extra dimensions

    International Nuclear Information System (INIS)

    Arkani-Hamed, Nima; Schmaltz, Martin

    2000-01-01

    It is commonly thought that small couplings in a low-energy theory, such as those needed for the fermion mass hierarchy or proton stability, must originate from symmetries in a high-energy theory. We show that this expectation is violated in theories where the standard model fields are confined to a thick wall in extra dimensions, with the fermions ''stuck'' at different points in the wall. Couplings between them are then suppressed due to the exponentially small overlaps of their wave functions. This provides a framework for understanding both the fermion mass hierarchy and proton stability without imposing symmetries, but rather in terms of higher dimensional geography. A model independent prediction of this scenario is non-universal couplings of the standard model fermions to the ''Kaluza-Klein'' excitations of the gauge fields. This allows a measurement of the fermion locations in the extra dimensions at the CERN LHC or NLC if the wall thickness is close to the TeV scale. (c) 2000 The American Physical Society

  4. Hierarchies Without Symmetries from Extra Dimensions

    International Nuclear Information System (INIS)

    Arkani-Hamed, Nima

    1999-01-01

    It is commonly thought that small couplings in a low-energy theory, such as those needed for the fermion mass hierarchy or proton stability, must originate from symmetries in a high-energy theory. We show that this expectation is violated in theories where the Standard Model fields are confined to a thick wall in extra dimensions, with the fermions ''stuck'' at different points in the wall. Couplings between them are then suppressed due to the exponentially small overlaps of their wave functions. This provides a framework for understanding both the fermion mass hierarchy and proton stability without imposing symmetries, but rather in terms of higher dimensional geography. A model independent prediction of this scenario is non-universal couplings of the Standard Model fermions to the ''Kaluza-Klein'' excitations of the gauge fields. This allows a measurement of the fermion locations in the extra dimensions at the LHC or NLC if the wall thickness is close to the TeV scale

  5. A color hierarchy for automatic target selection.

    Directory of Open Access Journals (Sweden)

    Illia Tchernikov

    Full Text Available Visual processing of color starts at the cones in the retina and continues through ventral stream visual areas, called the parvocellular pathway. Motion processing also starts in the retina but continues through dorsal stream visual areas, called the magnocellular system. Color and motion processing are functionally and anatomically discrete. Previously, motion processing areas MT and MST have been shown to have no color selectivity to a moving stimulus; the neurons were colorblind whenever color was presented along with motion. This occurs when the stimuli are luminance-defined versus the background and is considered achromatic motion processing. Is motion processing independent of color processing? We find that motion processing is intrinsically modulated by color. Color modulated smooth pursuit eye movements produced upon saccading to an aperture containing a surface of coherently moving dots upon a black background. Furthermore, when two surfaces that differed in color were present, one surface was automatically selected based upon a color hierarchy. The strength of that selection depended upon the distance between the two colors in color space. A quantifiable color hierarchy for automatic target selection has wide-ranging implications from sports to advertising to human-computer interfaces.

  6. Gauge hierarchy problem in grand unified theories

    International Nuclear Information System (INIS)

    Alhendi, H.A.A.

    1982-01-01

    In grand unification schemes, several mass scales are to be introduced, with some of them much larger than all the others, to cope with experimental observations, in which elementary particles of higher masses require higher energy to observe them than elementary particles of lower masses. There have been controversial arguments in the literature on such hierarchical scale structure, when radiative corrections are taken into account. It has been asserted that the gauge hierarchy depends on the choice of the subtraction point (in the classical field space), of the four-point function at zero external momentum. It also has been asserted that the gauge hierarchy problem whenever it is possible to be maintained in one sector of particles, it also is possible to be maintained in the other sectors. These two problems have been studied in a prototype model, namely an 0(3)-model with two triplets of real scalar Higgs fields. Our analysis shows that, within ordinary perturbation theory, none of these two problems is quite correct

  7. Adapting Memory Hierarchies for Emerging Datacenter Interconnects

    Institute of Scientific and Technical Information of China (English)

    江涛; 董建波; 侯锐; 柴琳; 张立新; 孙凝晖; 田斌

    2015-01-01

    Efficient resource utilization requires that emerging datacenter interconnects support both high performance communication and efficient remote resource sharing. These goals require that the network be more tightly coupled with the CPU chips. Designing a new interconnection technology thus requires considering not only the interconnection itself, but also the design of the processors that will rely on it. In this paper, we study memory hierarchy implications for the design of high-speed datacenter interconnects—particularly as they affect remote memory access—and we use PCIe as the vehicle for our investigations. To that end, we build three complementary platforms: a PCIe-interconnected prototype server with which we measure and analyze current bottlenecks; a software simulator that lets us model microarchitectural and cache hierarchy changes;and an FPGA prototype system with a streamlined switchless customized protocol Thunder with which we study hardware optimizations outside the processor. We highlight several architectural modifications to better support remote memory access and communication, and quantify their impact and limitations.

  8. Natural gauge hierarchy in SO(10)

    International Nuclear Information System (INIS)

    Babu, K.S.; Barr, S.M.

    1994-01-01

    It is shown that a natural gauge hierarchy and doublet-triplet splitting can be achieved in SO(10) using the Dimopoulos-Wilczek mechanism. Artificial cancellations (fine-tuning) and arbitrary forms of the superpotential are avoided, the superpotential being the most general compatible with a symmetry. It is shown by example that the Dimopoulos-Wilczek mechanism can be protected against the effects of higher-dimension operators possibly induced by Planck-scale physics. Natural implementation of the mechanisms leads to an automatic Peccei-Quinn symmetry. The same local symmetries that would protect the gauge hierarchy against Planck-scale effects tend to protect the axion also. How realistic quark and lepton masses might arise in this framework is discussed. It is shown how the theory may remain perturbative up to the Planck scale. It is also argued that ''weak suppression'' of proton decay can be implemented more economically than can ''strong suppression,'' offering some grounds to hope [in the context of SO(10)] that proton decay could be seen at SuperKamiokande

  9. BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

    Science.gov (United States)

    Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

    2015-08-18

    Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  10. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  11. Quick Pad Tagger : An Efficient Graphical User Interface for Building Annotated Corpora with Multiple Annotation Layers

    OpenAIRE

    Marc Schreiber; Kai Barkschat; Bodo Kraft; Albert Zundorf

    2015-01-01

    More and more domain specific applications in the internet make use of Natural Language Processing (NLP) tools (e. g. Information Extraction systems). The output quality of these applications relies on the output quality of the used NLP tools. Often, the quality can be increased by annotating a domain specific corpus. However, annotating a corpus is a time consuming and exhaustive task. To reduce the annota tion time we present...

  12. nGASP - the nematode genome annotation assessment project

    Energy Technology Data Exchange (ETDEWEB)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

  13. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    Energy Technology Data Exchange (ETDEWEB)

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  14. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.

    Science.gov (United States)

    Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  15. Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?

    Science.gov (United States)

    Czégel, Dániel; Palla, Gergely

    2015-01-01

    Signs of hierarchy are prevalent in a wide range of systems in nature and society. One of the key problems is quantifying the importance of hierarchical organisation in the structure of the network representing the interactions or connections between the fundamental units of the studied system. Although a number of notable methods are already available, their vast majority is treating all directed acyclic graphs as already maximally hierarchical. Here we propose a hierarchy measure based on random walks on the network. The novelty of our approach is that directed trees corresponding to multi level pyramidal structures obtain higher hierarchy scores compared to directed chains and directed stars. Furthermore, in the thermodynamic limit the hierarchy measure of regular trees is converging to a well defined limit depending only on the branching number. When applied to real networks, our method is computationally very effective, as the result can be evaluated with arbitrary precision by subsequent multiplications of the transition matrix describing the random walk process. In addition, the tests on real world networks provided very intuitive results, e.g., the trophic levels obtained from our approach on a food web were highly consistent with former results from ecology. PMID:26657012

  16. Durable and mass producible polymer surface structures with different combinations of micro–micro hierarchy

    International Nuclear Information System (INIS)

    Jiang, Yu; Suvanto, Mika; Pakkanen, Tapani A

    2016-01-01

    Extensive studies have been performed with the aim of fabricating hierarchical surface structures inspired by nature. However, synthetic hierarchical structures have to sacrifice mechanical resistance to functionality by introducing finer scaled structures. Therefore, surfaces are less durable. Surface micro–micro hierarchy has been proven to be effective in replacing micro–nano hierarchy in the sense of superhydrophobicity. However, less attention has been paid to the combined micro–micro hierarchies with surface pillars and pits incorporated together. The fabrication of this type of hierarchy may be less straightforward, with the possibility of being a complicated multi-step process. In this study, we present a simple yet mass producible fabrication method for hierarchical structures with different combinations of surface pillars and pits. The fabrication was based on only one aluminum (Al) mold with sequential mountings. The fabricated structures exhibit high mechanical durability and structural stabilities with a normal load up to 100 kg. In addition, the theoretical estimation of the wetting state shows a promising way of stabilizing a water droplet on the surface pit structures with a more stable Cassie–Baxter state. (paper)

  17. Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?

    Science.gov (United States)

    Czégel, Dániel; Palla, Gergely

    2015-12-10

    Signs of hierarchy are prevalent in a wide range of systems in nature and society. One of the key problems is quantifying the importance of hierarchical organisation in the structure of the network representing the interactions or connections between the fundamental units of the studied system. Although a number of notable methods are already available, their vast majority is treating all directed acyclic graphs as already maximally hierarchical. Here we propose a hierarchy measure based on random walks on the network. The novelty of our approach is that directed trees corresponding to multi level pyramidal structures obtain higher hierarchy scores compared to directed chains and directed stars. Furthermore, in the thermodynamic limit the hierarchy measure of regular trees is converging to a well defined limit depending only on the branching number. When applied to real networks, our method is computationally very effective, as the result can be evaluated with arbitrary precision by subsequent multiplications of the transition matrix describing the random walk process. In addition, the tests on real world networks provided very intuitive results, e.g., the trophic levels obtained from our approach on a food web were highly consistent with former results from ecology.

  18. Some Evolution Hierarchies Derived from Self-dual Yang-Mills Equations

    International Nuclear Information System (INIS)

    Zhang Yufeng; Hon, Y.C.

    2011-01-01

    We develop in this paper a new method to construct two explicit Lie algebras E and F. By using a loop algebra Ē of the Lie algebra E and the reduced self-dual Yang-Mills equations, we obtain an expanding integrable model of the Giachetti-Johnson (GJ) hierarchy whose Hamiltonian structure can also be derived by using the trace identity. This provides a much simpler construction method in comparing with the tedious variational identity approach. Furthermore, the nonlinear integrable coupling of the GJ hierarchy is readily obtained by introducing the Lie algebra g N . As an application, we apply the loop algebra E-tilde of the Lie algebra E to obtain a kind of expanding integrable model of the Kaup-Newell (KN) hierarchy which, consisting of two arbitrary parameters α and β, can be reduced to two nonlinear evolution equations. In addition, we use a loop algebra F of the Lie algebra F to obtain an expanding integrable model of the BT hierarchy whose Hamiltonian structure is the same as using the trace identity. Finally, we deduce five integrable systems in R 3 based on the self-dual Yang-Mills equations, which include Poisson structures, irregular lines, and the reduced equations. (general)

  19. Model and Interoperability using Meta Data Annotations

    Science.gov (United States)

    David, O.

    2011-12-01

    Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

  20. Biological hierarchies and the nature of extinction.

    Science.gov (United States)

    Congreve, Curtis R; Falk, Amanda R; Lamsdell, James C

    2018-05-01

    Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long-term palaeontological data often show that large-scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short-term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short- and long-term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi-generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population-level dynamics

  1. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.

    Science.gov (United States)

    Tanizawa, Yasuhiro; Fujisawa, Takatomo; Nakamura, Yasukazu

    2018-03-15

    We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future. The software is implemented in Python 3 and runs in both Python 2.7 and 3.4-on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/. yn@nig.ac.jp. Supplementary data are available at Bioinformatics online.

  2. A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

    Science.gov (United States)

    Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

    2014-10-12

    BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

  3. H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.

    Science.gov (United States)

    Kaminuma, Eli; Fujisawa, Takatomo; Tanizawa, Yasuhiro; Sakamoto, Naoko; Kurata, Nori; Shimizu, Tokurou; Nakamura, Yasukazu

    2013-01-01

    H2DB (http://tga.nig.ac.jp/h2db/), an annotation database of genetic heritability estimates for humans and other species, has been developed as a knowledge database to connect trait-associated genomic loci. Heritability estimates have been investigated for individual species, particularly in human twin studies and plant/animal breeding studies. However, there appears to be no comprehensive heritability database for both humans and other species. Here, we introduce an annotation database for genetic heritabilities of various species that was annotated by manually curating online public resources in PUBMED abstracts and journal contents. The proposed heritability database contains attribute information for trait descriptions, experimental conditions, trait-associated genomic loci and broad- and narrow-sense heritability specifications. Annotated trait-associated genomic loci, for which most are single-nucleotide polymorphisms derived from genome-wide association studies, may be valuable resources for experimental scientists. In addition, we assigned phenotype ontologies to the annotated traits for the purposes of discussing heritability distributions based on phenotypic classifications.

  4. Pragmatics Annotated Coloured Petri Nets for Protocol Software Generation and Verification

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    This paper presents the formal definition of Pragmatics Annotated Coloured Petri Nets (PA-CPNs). PA-CPNs represent a class of Coloured Petri Nets (CPNs) that are designed to support automated code genera-tion of protocol software. PA-CPNs restrict the structure of CPN models and allow Petri net...... elements to be annotated with so-called pragmatics, which are exploited for code generation. The approach and tool for gen-erating code is called PetriCode and has been discussed and evaluated in earlier work already. The contribution of this paper is to give a formal def-inition for PA-CPNs; in addition...

  5. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  6. Variable-coefficient nonisospectral Toda lattice hierarchy and its

    Indian Academy of Sciences (India)

    In this paper, a hierarchy of nonisospectral equations with variable coefficients is derived from the compatibility condition of Toda spectral problem and its time evolution. In order to solve the derived Toda lattice hierarchy, the inverse scattering transformation is utilized. As a result, new and more general exact solutions are ...

  7. An alternative approach to KP hierarchy in matrix models

    International Nuclear Information System (INIS)

    Bonora, L.; Xiong, C.S.

    1992-01-01

    We show that there exists an alternative procedure in order to extract differential hierarchies, such as the KdV hierarchy, from one-matrix models, without taking a continuum limit. To prove this we introduce the Toda lattice and reformulate it in operator form. We then consider the reduction to the systems appropriate for a one-matrix model. (orig.)

  8. Nonlinear Super Integrable Couplings of Super Classical-Boussinesq Hierarchy

    Directory of Open Access Journals (Sweden)

    Xiuzhi Xing

    2014-01-01

    Full Text Available Nonlinear integrable couplings of super classical-Boussinesq hierarchy based upon an enlarged matrix Lie super algebra were constructed. Then, its super Hamiltonian structures were established by using super trace identity. As its reduction, nonlinear integrable couplings of the classical integrable hierarchy were obtained.

  9. Inequality Matters : Classroom Status Hierarchy and Adolescents' Bullying

    NARCIS (Netherlands)

    Garandeau, Claire F.; Lee, Ihno A.; Salmivalli, Christina

    2014-01-01

    The natural emergence of status hierarchies in adolescent peer groups has long been assumed to help prevent future intragroup aggression. However, clear evidence of this beneficial influence is lacking. In fact, few studies have examined between-group differences in the degree of status hierarchy

  10. Towards Lax Formulation of Integrable Hierarchies of Topological Type

    NARCIS (Netherlands)

    Carlet, G.; van de Leur, J.; Posthuma, H.; Shadrin, S.

    2014-01-01

    To each partition function of cohomological field theory one can associate an Hamiltonian integrable hierarchy of topological type. The Givental group acts on such partition functions and consequently on the associated integrable hierarchies. We consider the Hirota and Lax formulations of the

  11. Towards Lax Formulation of Integrable Hierarchies of Topological Type

    NARCIS (Netherlands)

    van de Leur, Johannes; Carlet, Guido; Shadrin, Sergey; Posthuma, Hessel

    2014-01-01

    To each partition function of cohomological field theory one can associate an Hamiltonian integrable hierarchy of topological type. The Givental group acts on such partition functions and consequently on the associated integrable hierarchies. We consider theHirota and Lax formulations of the

  12. A Validation Study of Maslow's Hierarchy of Needs Theory.

    Science.gov (United States)

    Clay, Rex J.

    A study was conducted to expand the body of research that tests the validity of Abraham Maslow's hierarchy of needs theory in a work context where it often serves as a guide for the supervisor's relationships with his subordinates. Data was gathered by questionnaire which tested for a hierarchy of needs among instructors at four community colleges…

  13. Gauge theories, duality relations and the tensor hierarchy

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Hartong, Jelle; Hohm, Olaf; Huebscher, Mechthild; Ortin, Tomas; Hübscher, Mechthild

    We compute the complete 3- and 4-dimensional tensor hierarchies, i.e. sets of p-form fields, with 1 We construct gauge-invariant actions that include all the fields in the tensor hierarchies. We elucidate the relation between the gauge transformations of the p-form fields in the action and those of

  14. A Second Look at Maslow's Hierarchy of Basic Needs.

    Science.gov (United States)

    White, Charles M.

    Implications of Maslow's Need Hierarchy are considered in this paper, along with possible qualifications to the suggested structure and potential effects of superimposing relative deprivation theory onto the hierarchy as an approach to adult education. The interfacing of needs and alternative structurings is discussed in terms of two theories: (1)…

  15. The Diversity Education Dilemma: Exposing Status Hierarchies without Reinforcing Them

    Science.gov (United States)

    Amoroso, Lisa M.; Loyd, Denise Lewin; Hoobler, Jenny M.

    2010-01-01

    A "diversity education dilemma" occurs when exposure to information concerning status hierarchies, related to demographic and other socially salient identity groups, reinforces those hierarchies in the classroom. Discussions of diversity-related issues in a variety of management courses (e.g., immigrant issues in labor relations, the composition…

  16. Inverted hierarchy and asymptotic freedom in grand unified supersymmetric theories

    International Nuclear Information System (INIS)

    Aratyn, H.

    1983-01-01

    The interrelation between an inverted hierarchy mechanism and asymptotic freedom in supersymmetric theories is analyzed in two models for which we performed a detailed analysis of the effective potentials and effective couplings. We find it difficult to accommodate an inverted hierarchy together with asymptotic freedom for the matter-Yukawa couplings. (orig.)

  17. A Computational Glimpse at the Leibniz and Frege Hierarchies

    Czech Academy of Sciences Publication Activity Database

    Moraschini, Tommaso

    2018-01-01

    Roč. 169, č. 1 (2018), s. 1-20 ISSN 0168-0072 R&D Projects: GA ČR GA13-14654S Institutional support: RVO:67985807 Keywords : abstract algebraic logic * Leibniz hierarchy * Frege hierarchy Leibniz congruence * decidability * Diophantine equations * relation algebras Subject RIV: BA - General Mathematics Impact factor: 0.647, year: 2016

  18. Women, Islam, and Pakistan: A Selected Annotated Bibliography. Fulbright-Hays Summer Seminar Abroad Project.

    Science.gov (United States)

    Phillips, Brenda

    This bibliography features selected books, book chapters, research projects, and journal articles, published between 1953 and 1994, about the social, legal, economic, educational political, and professional position of Muslim Pakistani women. Sixteen of the references are annotated. An additional 41 bibliographic references to other materials, not…

  19. Seeing the forest for the trees: annotating small RNA producing genes in plants.

    Science.gov (United States)

    Coruh, Ceyda; Shahid, Saima; Axtell, Michael J

    2014-04-01

    A key goal in genomics is the complete annotation of the expressed regions of the genome. In plants, substantial portions of the genome make regulatory small RNAs produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins. These include miRNAs and various types of endogenous siRNAs. Small RNA-seq, enabled by cheap and fast DNA sequencing, has produced an enormous volume of data on plant miRNA and siRNA expression in recent years. In this review, we discuss recent progress in using small RNA-seq data to produce stable and reliable annotations of miRNA and siRNA genes in plants. In addition, we highlight key goals for the future of small RNA gene annotation in plants. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. 'Universality' of the Ablowitz-Ladik hierarchy

    International Nuclear Information System (INIS)

    Vekslerchik, V.E.

    1998-05-01

    The aim of this paper is to summarize some recently obtained relations between the Ablowitz-Ladik hierarchy (ALH) and other integrable equations. It has been shown that solutions of finite subsystems of the ALH can be used to derive a wide range of solutions for, e.g., the 2D Toda lattice, nonlinear Schroedinger, Davey-Stewartson, Kadomtsev-Petviashvili (DP) and some other equations. Similar approach has been used to construct new integrable models: O(3,1) and multi field sigma models. Such 'universality' of the ALH becomes more transparent in the framework of the Hirota's bilinear method. The ALH, which is usually considered as an infinite set of differential-difference equations, has been presented as a finite system of functional-difference equations, which can be viewed as a generalization of the famous bilinear identities for the KP tau-functions. (author)

  1. What's Up with the Storage Hierarchy?

    DEFF Research Database (Denmark)

    Bonnet, Philippe

    2017-01-01

    Ten years ago, Jim Gray observed that flash was about to replace magnetic disks. He also predicted that the need for low latency would make main memory databases commonplace. Most of his predictions have proven accurate. Today, who can make predictions about the future of the storage hierarchy......? Both main memory and storage systems are undergoing profound transformations. First, their design goals are increasingly complex (reconfigurable infrastructure at low latency, high resource utilization and stable energy footprint). Second, the status quo is not an option due to the shortcomings...... of existing solutions (memory bandwidth gap, inefficiency of generic memory/storage controllers). Third, new technologies are emerging (hybrid memories, non-volatile memories still under non-disclosure agreements, near-data processing in memory and storage). The impact of these transformations on the storage...

  2. Scale-independent inflation and hierarchy generation

    Directory of Open Access Journals (Sweden)

    Pedro G. Ferreira

    2016-12-01

    Full Text Available We discuss models involving two scalar fields coupled to classical gravity that satisfy the general criteria: (i the theory has no mass input parameters, (ii classical scale symmetry is broken only through −112ςϕ2R couplings where ς departs from the special conformal value of 1; (iii the Planck mass is dynamically generated by the vacuum expectations values (VEVs of the scalars (iv there is a stage of viable inflation associated with slow roll in the two-scalar potential; (v the final vacuum has a small to vanishing cosmological constant and an hierarchically small ratio of the VEVs and the ratio of the scalar masses to the Planck scale. This assumes the paradigm of classical scale symmetry as a custodial symmetry of large hierarchies.

  3. Structural optimization via a design space hierarchy

    Science.gov (United States)

    Vanderplaats, G. N.

    1976-01-01

    Mathematical programming techniques provide a general approach to automated structural design. An iterative method is proposed in which design is treated as a hierarchy of subproblems, one being locally constrained and the other being locally unconstrained. It is assumed that the design space is locally convex in the case of good initial designs and that the objective and constraint functions are continuous, with continuous first derivatives. A general design algorithm is outlined for finding a move direction which will decrease the value of the objective function while maintaining a feasible design. The case of one-dimensional search in a two-variable design space is discussed. Possible applications are discussed. A major feature of the proposed algorithm is its application to problems which are inherently ill-conditioned, such as design of structures for optimum geometry.

  4. Dancing Twins: Stellar Hierarchies That Formed Sequentially?

    Science.gov (United States)

    Tokovinin, Andrei

    2018-04-01

    This paper draws attention to the class of resolved triple stars with moderate ratios of inner and outer periods (possibly in a mean motion resonance) and nearly circular, mutually aligned orbits. Moreover, stars in the inner pair are twins with almost identical masses, while the mass sum of the inner pair is comparable to the mass of the outer component. Such systems could be formed either sequentially (inside-out) by disk fragmentation with subsequent accretion and migration, or by a cascade hierarchical fragmentation of a rotating cloud. Orbits of the outer and inner subsystems are computed or updated in four such hierarchies: LHS 1070 (GJ 2005, periods 77.6 and 17.25 years), HIP 9497 (80 and 14.4 years), HIP 25240 (1200 and 47.0 years), and HIP 78842 (131 and 10.5 years).

  5. Gauge hierarchy, decoupling, and heavy particle effects

    International Nuclear Information System (INIS)

    Yao, York-Peng

    1981-01-01

    This chapter examines the problems of a large gauge hierarchy and decoupling in theories with spontaneously broken symmetry. Attempts to show, with regard to all orders in the loop expansion, that: once a proper identification is made of the light particles and of the heavy particles at the tree level, then such a division will be maintained order by order in the loop expansion without the necessity of fine tuning; there is a local renormalizable effective Lagrangian, composed of light fields only, which can be used to reproduce all the one light particle irreducible Green's functions; and a set of renormalization group equations can be written down, wherein one stays in the lower energy region to correlate the two sets of parameters in the full and the effective light theories. The appendix gives an algebraic rearrangement method which can be efficiently used to calculate the muon effects on the electron anomalous magnetic moment

  6. Modelling Dominance Hierarchies Under Winner and Loser Effects.

    Science.gov (United States)

    Kura, Klodeta; Broom, Mark; Kandler, Anne

    2015-06-01

    Animals that live in groups commonly form themselves into dominance hierarchies which are used to allocate important resources such as access to mating opportunities and food. In this paper, we develop a model of dominance hierarchy formation based upon the concept of winner and loser effects using a simulation-based model and consider the linearity of our hierarchy using existing and new statistical measures. Two models are analysed: when each individual in a group does not know the real ability of their opponents to win a fight and when they can estimate their opponents' ability every time they fight. This estimation may be accurate or fall within an error bound. For both models, we investigate if we can achieve hierarchy linearity, and if so, when it is established. We are particularly interested in the question of how many fights are necessary to establish a dominance hierarchy.

  7. A study on the hierarchy model of nuclear reactions

    International Nuclear Information System (INIS)

    Kitazoe, Yasuhiro; Sekiya, Tamotsu

    1975-01-01

    The application of the hierarchy model of nuclear reaction is discussed, and the hierarchy model means that the compound nucleus state is formed after several steps, at least, one step of reaction. This model was applied to the analysis of the observed cross sections of 235 U and some other elements. Neglecting exchange scattering effect, the equations for the total neutron cross section of 235 U were obtained. One of these equations describes explicitly the hierarchy of the transition from intermediate reaction state Xm into the compound nucleus state Xs, and another one describes the cross section averaged over an energy interval larger than the average level spacing of compound nucleus eigenvalues. The hierarchy of reaction mechanism was investigated in more detail, and the hierarchy model was applied to the case of unresolved energy region. It was not tried to evaluate the strength function in the mass region (A>140), since the effect of nuclear deformation was neglected in the task. (Iwase, T.)

  8. The Impact of Formal Hierarchies on Enterprise Social Networking Behavior

    DEFF Research Database (Denmark)

    Behrendt, Sebastian; Klier, Julia; Klier, Mathias

    2015-01-01

    With more and more companies using enterprise social networks (ESN) for employee communication and collaboration, the influence of ESN on organizational hierarchies has been subject of countless discussions in practice-oriented media and first academic studies. Conversely, the question whether...... and how formal organizational hierarchies influence ESN usage behavior has not yet been addressed. Drawing on a rich data set comprising 2.5 years of relationship building via direct messages, confirmed contact requests, and group messages, we are able to show that formal hierarchies have an important...... impact on social networking behavior. By applying means of social network analysis and supported by statements from interviews, we illustrate how deeply formal hierarchy impacts the three examined types of relationships. Our results motivate academics to further study the interrelation between hierarchy...

  9. A Hierarchy of Homodesmotic Reactions for Thermochemistry

    Science.gov (United States)

    Schleyer, Paul v. R.

    2009-01-01

    Chemical equations that balance bond types and atom hybridization to different degrees are often used in computational thermochemistry, for example, to increase accuracy when lower levels of theory are employed. We expose the widespread confusion over such classes of equations and demonstrate that the two most widely used definitions of “homodesmotic” reactions are not equivalent. New definitions are introduced and a consistent hierarchy of reaction classes (RC1 – RC5) for hydrocarbons is constructed: isogyric (RC1) ⊇ isodesmic (RC2) ⊇ hypohomodesmotic (RC3) ⊇ homodesmotic (RC4) ⊇ hyperhomodesmotic (RC5). Each of these successively conserves larger molecular fragments. The concept of isodesmic bond separation reactions is generalized to all classes in this hierarchy, providing a unique sectioning of a given molecule for each reaction type. Several ab initio and density functional methods are applied to the bond separation reactions of 38 hydrocarbons containing five or six carbon atoms. RC4 and RC5 reactions provide bond separation enthalpies with errors consistently less than 0.4 kcal mol−1 across a wide range of theoretical levels, performing significantly better than the other reaction types and far superior to atomization routes. Our recommended bond separation reactions were demonstrated by determining the enthalpies of formation (at 298 K) of 1,3,5-hexatriyne (163.7 ± 0.4 kcal mol−1), 1,3,5,7-octatetrayne (217.6 ± 0.6 kcal mol−1), the larger polyynes C10H2 through C26H2, and an infinite acetylenic carbon chain. PMID:19182999

  10. The dynamic nature of social hierarchies : The role of norm violations and hierarchical concerns

    NARCIS (Netherlands)

    Stamkou, E.

    2018-01-01

    Social hierarchy is a fundamental feature of social relations. Hierarchies are appealing psychologically because they facilitate group functioning, which explains why they tend to be reinforced and perpetuated. Hierarchies, however, can also become unstable and eventually undergo change because

  11. Consumer energy research: an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, C.D.; McDougall, G.H.G.

    1980-01-01

    This document is an updated and expanded version of an earlier annotated bibliography by Dr. C. Dennis Anderson and Carman Cullen (A Review and Annotation of Energy Research on Consumers, March 1978). It is the final draft of the major report that will be published in English and French and made publicly available through the Consumer Research and Evaluation Branch of Consumer and Corporate Affairs, Canada. Two agencies granting permission to include some of their energy abstracts are the Rand Corporation and the DOE Technical Information Center. The bibliography consists mainly of empirical studies, including surveys and experiments. It also includes a number of descriptive and econometric studies that utilize secondary data. Many of the studies provide summaries of research is specific areas, and point out directions for future research efforts. 14 tables.

  12. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  13. Status Hierarchy, Attractiveness Hierarchy and Sex Ratio: Three Contextual Factors Explaining the Status-Aggression Link among Adolescents

    Science.gov (United States)

    Zwaan, Michiel; Dijkstra, Jan Kornelis; Veenstra, Rene

    2013-01-01

    The moderating effects of three specific conditions (status hierarchy, attractiveness hierarchy and sex ratio) on the link between status (popularity) and physical and relational aggression were examined in a large sample of adolescent boys ("N" = 1,665) and girls ("N" = 1,637) ("M" age = 13.60). In line with the…

  14. Status hierarchy, attractiveness hierarchy and sex ratio : Three contextual factors explaining the status-aggression link among adolescents

    NARCIS (Netherlands)

    Zwaan, Michiel; Dijkstra, Jan; Veenstra, René

    The moderating effects of three specific conditions (status hierarchy, attractiveness hierarchy and sex ratio) on the link between status (popularity) and physical and relational aggression were examined in a large sample of adolescent boys (N = 1,665) and girls (N = 1,637) (M age = 13.60). In line

  15. Deburring: an annotated bibliography. Volume V

    International Nuclear Information System (INIS)

    Gillespie, L.K.

    1978-01-01

    An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred

  16. Adolescent male chimpanzees do not form a dominance hierarchy with their peers.

    Science.gov (United States)

    Sandel, Aaron A; Reddy, Rachna B; Mitani, John C

    2017-01-01

    Dominance hierarchies are a prominent feature of the lives of many primate species. These hierarchies have important fitness consequences, as high rank is often positively correlated with reproduction. Although adult male chimpanzees strive for status to gain fitness benefits, the development of dominance relationships is not well understood. While two prior studies found that adolescent males do not display dominance relationships with peers, additional research at Ngogo in Kibale National Park, Uganda, indicates that adolescents there form a linear dominance hierarchy. These conflicting findings could reflect different patterns of rank acquisition across sites. An alternate possibility arises from a recent re-evaluation of age estimates at Ngogo and suggests that the report describing decided dominance relationships between adolescent males may have been due to the accidental inclusion of young adult males in the sample. To investigate these issues, we conducted a study of 23 adolescent male chimpanzees of known age during 12 months at Ngogo. Adolescent male chimpanzees exchanged pant grunts, a formal signal of submission, only 21 times. Recipients of pant grunts were late adolescent males, ranging between 14 and 16 years old. In contrast, younger adolescent males never received pant grunts from other males. Aggression between adolescent males was also rare. Analysis of pant grunts and aggressive interactions did not produce a linear dominance hierarchy among adolescent males. These data indicate that adolescent male chimpanzees do not form decided dominance relationships with their peers and are consistent with the hypothesis that the hierarchy described previously at Ngogo resulted from inaccurate age estimates of male chimpanzees. Because dominance relationships develop before adulthood in other primates, our finding that adolescent male chimpanzees do not do so is surprising. We offer possible explanations for why this is the case and suggest future studies

  17. Exploring maintenance policy selection using the Analytic Hierarchy Process; An application for naval ships

    International Nuclear Information System (INIS)

    Goossens, Adriaan J.M.; Basten, Rob J.I.

    2015-01-01

    In this paper we investigate maintenance policy selection (MPS) through the use of the Analytic Hierarchy Process (AHP). A maintenance policy is a policy that dictates which parameter triggers a maintenance action. In practice, selecting the right maintenance policy appears to be a difficult decision. We investigate MPS for naval ships, but our results have wider applicability. For our study we cooperate with the owner and operator of the ships, as well as with a shipbuilder and an original equipment manufacturer of naval ships. We apply a structured five step approach to obtain the relevant criteria that may make one policy preferable over another. The criteria are drawn from both literature and a series of interviews at several navy related companies and are structured into a hierarchy of criteria usable with the AHP. Additionally, we organize three workshops at the three different companies to test the AHP-based MPS approach in practice. We conclude that the AHP is well suited for maintenance policy selection in this broad setting, and that it provides a structured and detailed approach for MPS. Adding to that, it facilitates discussions during and after the sessions, creating a better understanding of the policy selection process. - Highlights: • We use the Analytic Hierarchy Process (AHP) for maintenance policy selection (MPS). • Using both interviews and case studies from the literature, we construct a hierarchy. • In sessions at 3 companies, we find that 1 hierarchy can be used for multiple assets. • The AHP creates a better understanding of the maintenance policy selection process. • Our work is on naval ships, but our approach and findings have wider applicability

  18. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  19. Using Annotated Conceptual Models to Derive Information System Implementations

    Directory of Open Access Journals (Sweden)

    Anthony Berglas

    1994-05-01

    Full Text Available Producing production quality information systems from conceptual descriptions is a time consuming process that employs many of the world's programmers. Although most of this programming is fairly routine, the process has not been amenable to simple automation because conceptual models do not provide sufficient parameters to make all the implementation decisions that are required, and numerous special cases arise in practice. Most commercial CASE tools address these problems by essentially implementing a waterfall model in which the development proceeds from analysis through design, layout and coding phases in a partially automated manner, but the analyst/programmer must heavily edit each intermediate stage. This paper demonstrates that by recognising the nature of information systems, it is possible to specify applications completely using a conceptual model that has een annotated with additional parameters that guide automated implementation. More importantly, it will be argued that a manageable number of annotations are sufficient to implement realistic applications, and techniques will be described that enabled the author's commercial CASE tool, the Intelligent Develope to automated implementation without requiring complex theorem proving technology.

  20. Characterizing and annotating the genome using RNA-seq data.

    Science.gov (United States)

    Chen, Geng; Shi, Tieliu; Shi, Leming

    2017-02-01

    Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

  1. Automatic Function Annotations for Hoare Logic

    Directory of Open Access Journals (Sweden)

    Daniel Matichuk

    2012-11-01

    Full Text Available In systems verification we are often concerned with multiple, inter-dependent properties that a program must satisfy. To prove that a program satisfies a given property, the correctness of intermediate states of the program must be characterized. However, this intermediate reasoning is not always phrased such that it can be easily re-used in the proofs of subsequent properties. We introduce a function annotation logic that extends Hoare logic in two important ways: (1 when proving that a function satisfies a Hoare triple, intermediate reasoning is automatically stored as function annotations, and (2 these function annotations can be exploited in future Hoare logic proofs. This reduces duplication of reasoning between the proofs of different properties, whilst serving as a drop-in replacement for traditional Hoare logic to avoid the costly process of proof refactoring. We explain how this was implemented in Isabelle/HOL and applied to an experimental branch of the seL4 microkernel to significantly reduce the size and complexity of existing proofs.

  2. Jannovar: a java library for exome annotation.

    Science.gov (United States)

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

  3. Annotating breast cancer microarray samples using ontologies

    Science.gov (United States)

    Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

    2008-01-01

    As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

  4. Maslow’s Needs Hierarchy and the Effect of Income on Happiness Levels

    OpenAIRE

    Drakopoulos, Stavros A.; Grimani, Katerina

    2013-01-01

    Abraham Maslow’s theory of hierarchical needs has been employed by a large variety of conceptual frameworks. The theory can also offer additional insights to the research field which investigates the relationship between income and reported happiness levels. The incorporation of needs hierarchy into a happiness framework implies that individuals have a priority approach to happiness. This means that the most important needs must be satisfied first before the secondary needs come into the pict...

  5. Optimization Model for Uncertain Statistics Based on an Analytic Hierarchy Process

    Directory of Open Access Journals (Sweden)

    Yongchao Hou

    2014-01-01

    Full Text Available Uncertain statistics is a methodology for collecting and interpreting the expert’s experimental data by uncertainty theory. In order to estimate uncertainty distributions, an optimization model based on analytic hierarchy process (AHP and interpolation method is proposed in this paper. In addition, the principle of least squares method is presented to estimate uncertainty distributions with known functional form. Finally, the effectiveness of this method is illustrated by an example.

  6. Climate Change Mitigation Through Reduced-Impact Logging and the Hierarchy of Production Forest Management

    Directory of Open Access Journals (Sweden)

    Ben Vickers

    2012-01-01

    Full Text Available The proposed hierarchy of production forest management provides modus operandi for forest concessions to move incrementally towards Sustainable Forest Management (SFM via Reduced-Impact Logging (RIL and forest certification. Financial benefits are sourced in the “Additionality Zone”, financing the rise in the hierarchy and offsetting prohibitive forest and carbon certification costs. RIL carbon registration components consist of developing credible baseline, additionality and leakage arguments around the business-as-usual scenario through the quantification of historical forest inventory and production records, forest infrastructure records and damage to the residual forest. If conventional harvesting is taken as a baseline, research indicates RIL can potentially reduce emissions by approximately 1–7 tCO2e ha−1yr−1. The current market price of USD $7.30 per tCO2e may result in over USD $50 ha−1yr−1 in additional revenue, well above the estimated USD $3–5 ha−1 in carbon transaction costs. Concessions in Sabah Malaysia demonstrate the financial viability of long-term RIL and certification planning. This may act as a basis for future planned forest management activities involving RIL, carbon and forest certification through the hierarchy of production forest management.

  7. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

    Science.gov (United States)

    Sun, Xiaoyong; Zuo, Fenghua; Ru, Yuanbin; Guo, Jiqiang; Yan, Xiaoyan; Sablok, Gaurav

    2015-04-01

    Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Topological hierarchy matters — topological matters with superlattices of defects

    International Nuclear Information System (INIS)

    He Jing; Kou Su-Peng

    2016-01-01

    Topological insulators/superconductors are new states of quantum matter with metallic edge/surface states. In this paper, we review the defects effect in these topological states and study new types of topological matters — topological hierarchy matters. We find that both topological defects (quantized vortices) and non topological defects (vacancies) can induce topological mid-gap states in the topological hierarchy matters after considering the superlattice of defects. These topological mid-gap states have nontrivial topological properties, including the nonzero Chern number and the gapless edge states. Effective tight-binding models are obtained to describe the topological mid-gap states in the topological hierarchy matters. (topical review)

  9. Decomposition of a hierarchy of nonlinear evolution equations

    International Nuclear Information System (INIS)

    Geng Xianguo

    2003-01-01

    The generalized Hamiltonian structures for a hierarchy of nonlinear evolution equations are established with the aid of the trace identity. Using the nonlinearization approach, the hierarchy of nonlinear evolution equations is decomposed into a class of new finite-dimensional Hamiltonian systems. The generating function of integrals and their generator are presented, based on which the finite-dimensional Hamiltonian systems are proved to be completely integrable in the Liouville sense. As an application, solutions for the hierarchy of nonlinear evolution equations are reduced to solving the compatible Hamiltonian systems of ordinary differential equations

  10. Boolean Operations, Joins, and the Extended Low Hierarchy

    OpenAIRE

    Hemaspaandra, Lane A.; Jiang, Zhigen; Rothe, Joerg; Watanabe, Osamu

    1999-01-01

    We prove that the join of two sets may actually fall into a lower level of the extended low hierarchy than either of the sets. In particular, there exist sets that are not in the second level of the extended low hierarchy, EL_2, yet their join is in EL_2. That is, in terms of extended lowness, the join operator can lower complexity. Since in a strong intuitive sense the join does not lower complexity, our result suggests that the extended low hierarchy is unnatural as a complexity measure. We...

  11. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

    Science.gov (United States)

    Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G; Parkhill, Julian; Rajandream, Marie-Adèle

    2008-12-01

    Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/

  12. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

    Science.gov (United States)

    Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G.; Parkhill, Julian; Rajandream, Marie-Adèle

    2008-01-01

    Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18845581

  13. Kinetic mixing and the supersymmetric gauge hierarchy

    International Nuclear Information System (INIS)

    Dienes, K.R.; Kolda, C.; March-Russell, J.

    1997-01-01

    The most general Lagrangian for a model with two U(1) gauge symmetries contains a renormalizable operator which mixes their gauge kinetic terms. Such kinetic mixing can be generated at arbitrarily high scales but will not be suppressed by large masses. In models whose supersymmetry (SUSY)-breaking hidden sectors contain U(1) gauge factors, we show that such terms will generically arise and communicate SUSY breaking to the visible sector through mixing with hypercharge. In the context of the usual supergravity- or gauge-mediated communication scenarios with D-terms of order the fundamental scale of SUSY breaking, this effect can destabilize the gauge hierarchy. Even in models for which kinetic mixing is suppressed or the D-terms are arranged to be small, this effect is a potentially large correction to the soft scalar masses and therefore introduces a new measurable low-energy parameter. We calculate the size of kinetic mixing both in field theory and in string theory, and argue that appreciable kinetic mixing is a generic feature of string models. We conclude that the possibility of kinetic mixing effects cannot be ignored in model building and in phenomenological studies of the low-energy SUSY spectra. (orig.)

  14. Hierarchy Formation and Self-Determination

    Directory of Open Access Journals (Sweden)

    Stefano I. Di Domenico

    2014-12-01

    Full Text Available We examined how self-determination, the subjective experience of one’s behavior as internally initiated and personally endorsed, depends on one’s standing in real-world social hierarchies. We predicted that those with the traits most relevant to status attainment would be those afforded the most opportunities to be self-determining. We examined the trait of physical attractiveness, given its documented association with social status and no known association with self-determination. First-year undergraduates living in same-sex residences rated their housemates’ social status, while an independent set of observers rated the participants’ physical attractiveness. Consistent with prediction, physically attractive individuals attained the highest levels of social status; in turn, those who attained the highest levels of social status experienced the highest levels of self-determination. These findings provide new insights into self-determination as an inherently relational phenomenon and specifically highlight the formative influence of social status on people’s capacities for self-determination.

  15. Metadata Life Cycles, Use Cases and Hierarchies

    Directory of Open Access Journals (Sweden)

    Ted Habermann

    2018-05-01

    Full Text Available The historic view of metadata as “data about data” is expanding to include data about other items that must be created, used, and understood throughout the data and project life cycles. In this context, metadata might better be defined as the structured and standard part of documentation, and the metadata life cycle can be described as the metadata content that is required for documentation in each phase of the project and data life cycles. This incremental approach to metadata creation is similar to the spiral model used in software development. Each phase also has distinct users and specific questions to which they need answers. In many cases, the metadata life cycle involves hierarchies where latter phases have increased numbers of items. The relationships between metadata in different phases can be captured through structure in the metadata standard, or through conventions for identifiers. Metadata creation and management can be streamlined and simplified by re-using metadata across many records. Many of these ideas have been developed to various degrees in several Geoscience disciplines and are being used in metadata for documenting the integrated life cycle of environmental research in the Arctic, including projects, collection sites, and datasets.

  16. Analytic Hierarchy and Economic Analysis of a Plasma Gasification System for Naval Air Station Oceana-Dam Neck

    Science.gov (United States)

    2014-08-30

    disposal at a local landfill . Additionally the base receives its energy requirements from Dominion Virginia Power. In utilizing these services a...Figure 3: Hierarchy Tree for Plasma Gasification Model .............................................. 22 Figure 4: Linear Interpolation...division. Due to a continuing need, variable energy costs and limited land availability for new landfills , the costs associated with these services can

  17. Plann: A command-line application for annotating plastome sequences.

    Science.gov (United States)

    Huang, Daisie I; Cronk, Quentin C B

    2015-08-01

    Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission. Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.

  18. Genome annotation in a community college cell biology lab.

    Science.gov (United States)

    Beagley, C Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

  19. Annotated checklist of Albanian butterflies (Lepidoptera, Papilionoidea and Hesperioidea

    Directory of Open Access Journals (Sweden)

    Rudi Verovnik

    2013-08-01

    Full Text Available The Republic of Albania has a rich diversity of flora and fauna. However, due to its political isolation, it has never been studied in great depth, and consequently, the existing list of butterfly species is outdated and in need of radical amendment. In addition to our personal data, we have studied the available literature, and can report a total of 196 butterfly species recorded from the country. For some of the species in the list we have given explanations for their inclusion and made other annotations. Doubtful records have been removed from the list, and changes in taxonomy have been updated and discussed separately. The purpose of our paper is to remove confusion and conflict regarding published records. However, the revised checklist should not be considered complete: it represents a starting point for further research.

  20. Impingement and entrainment: an updated annotated bibliography. Final report

    International Nuclear Information System (INIS)

    Yost, F.E.; Uziel, M.S.

    1981-05-01

    Presented as an annotated bibliography are 1343 references dealing with entrainment and impingement effects on aquatic organisms passing through the cooling systems of thermal power plants. The references were obtained from open literature and from environmental reports and impact statements prepared by or for the electric utility industry. Two earlier bibliographies contain literature from 1950 through 1976. This update contains additional literature acquired since 1976. Topics covered are site-specific field studies at facilities located on lakes, reservoirs, rivers, or estuaries. The studies include special engineering studies, laboratory studies, studies of biological effects, reviews and methodologies, and studies of the mitigation of effects. References are arranged alphabetically by author, and indexes are provided to personal and corporate authors, and to facility, waterbody, and taxonomic names

  1. Admiration regulates social hierarchy: Antecedents, dispositions, and effects on intergroup behavior.

    Science.gov (United States)

    Sweetman, Joseph; Spears, Russell; Livingstone, Andrew G; Manstead, Antony S R

    2013-05-01

    In four studies, we report evidence that admiration affects intergroup behaviors that regulate social hierarchy. We demonstrate that manipulating the legitimacy of status relations affects admiration for the dominant and that this emotion negatively predicts political action tendencies aimed at social change. In addition, we show that greater warmth and competence lead to greater admiration for an outgroup, which in turn positively predicts deferential behavior and intergroup learning. We also demonstrate that, for those with a disposition to feel admiration, increasing admiration for an outgroup decreases willingness to take political action against that outgroup. Finally, we show that when the object of admiration is a subversive "martyr," admiration positively predicts political action tendencies and behavior aimed at challenging the status quo. These findings provide the first evidence for the important role of admiration in regulating social hierarchy.

  2. A Clifford algebra approach to chiral symmetry breaking and fermion mass hierarchies

    Science.gov (United States)

    Lu, Wei

    2017-09-01

    We propose a Clifford algebra approach to chiral symmetry breaking and fermion mass hierarchies in the context of composite Higgs bosons. Standard model fermions are represented by algebraic spinors of six-dimensional binary Clifford algebra, while ternary Clifford algebra-related flavor projection operators control allowable flavor-mixing interactions. There are three composite electroweak Higgs bosons resulted from top quark, tau neutrino, and tau lepton condensations. Each of the three condensations gives rise to masses of four different fermions. The fermion mass hierarchies within these three groups are determined by four-fermion condensations, which break two global chiral symmetries. The four-fermion condensations induce axion-like pseudo-Nambu-Goldstone bosons and can be dark matter candidates. In addition to the 125 GeV Higgs boson observed at the Large Hadron Collider, we anticipate detection of tau neutrino composite Higgs boson via the charm quark decay channel.

  3. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

    Science.gov (United States)

    Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

    2016-11-01

    usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available. Copyright © 2016 Du et al.

  4. Annotation of mammalian primary microRNAs

    Directory of Open Access Journals (Sweden)

    Enright Anton J

    2008-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately 50% of mammalian miRNAs are expressed from introns of protein-coding genes; the primary transcript (pri-miRNA is therefore assumed to be the host transcript. However, very little is known about the structure of pri-miRNAs expressed from intergenic regions. Here we annotate transcript boundaries of miRNAs in human, mouse and rat genomes using various transcription features. The 5' end of the pri-miRNA is predicted from transcription start sites, CpG islands and 5' CAGE tags mapped in the upstream flanking region surrounding the precursor miRNA (pre-miRNA. The 3' end of the pri-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data. The predicted pri-miRNAs are also analyzed for promoter and insulator-associated regulatory regions. Results We define sets of conserved and non-conserved human, mouse and rat pre-miRNAs using bidirectional BLAST and synteny analysis. Transcription features in their flanking regions are used to demarcate the 5' and 3' boundaries of the pri-miRNAs. The lengths and boundaries of primary transcripts are highly conserved between orthologous miRNAs. A significant fraction of pri-miRNAs have lengths between 1 and 10 kb, with very few introns. We annotate a total of 59 pri-miRNA structures, which include 82 pre-miRNAs. 36 pri-miRNAs are conserved in all 3 species. In total, 18 of the confidently annotated transcripts express more than one pre-miRNA. The upstream regions of 54% of the predicted pri-miRNAs are found to be associated with promoter and insulator regulatory sequences. Conclusion Little is known about the primary transcripts of intergenic miRNAs. Using comparative data, we are able to identify the boundaries of a significant proportion of

  5. Annotated bibliography of Software Engineering Laboratory literature

    Science.gov (United States)

    Morusiewicz, Linda; Valett, Jon D.

    1991-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. All materials have been grouped into eight general subject areas for easy reference: The Software Engineering Laboratory; The Software Engineering Laboratory: Software Development Documents; Software Tools; Software Models; Software Measurement; Technology Evaluations; Ada Technology; and Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

  6. Optimal mesh hierarchies in Multilevel Monte Carlo methods

    KAUST Repository

    Von Schwerin, Erik

    2016-01-08

    I will discuss how to choose optimal mesh hierarchies in Multilevel Monte Carlo (MLMC) simulations when computing the expected value of a quantity of interest depending on the solution of, for example, an Ito stochastic differential equation or a partial differential equation with stochastic data. I will consider numerical schemes based on uniform discretization methods with general approximation orders and computational costs. I will compare optimized geometric and non-geometric hierarchies and discuss how enforcing some domain constraints on parameters of MLMC hierarchies affects the optimality of these hierarchies. I will also discuss the optimal tolerance splitting between the bias and the statistical error contributions and its asymptotic behavior. This talk presents joint work with N.Collier, A.-L.Haji-Ali, F. Nobile, and R. Tempone.

  7. Flexible scheme to truncate the hierarchy of pure states.

    Science.gov (United States)

    Zhang, P-P; Bentley, C D B; Eisfeld, A

    2018-04-07

    The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

  8. Assessing the hierarchy of needs in levels of service

    Science.gov (United States)

    2005-10-01

    The primary focus of this research project was in providing empirical evidence of a Hierarchy of Transportation : Needs. The experimental procedure, methodology, and materials for this project were designed using both : transportation stated preferen...

  9. A generalized AKNS hierarchy and its bi-Hamiltonian structures

    International Nuclear Information System (INIS)

    Xia Tiecheng; You Fucai; Chen Dengyuan

    2005-01-01

    First we construct a new isospectral problem with 8 potentials in the present paper. And then a new Lax pair is presented. By making use of Tu scheme, a class of new soliton hierarchy of equations is derived, which is integrable in the sense of Liouville and possesses bi-Hamiltonian structures. After making some reductions, the well-known AKNS hierarchy and other hierarchies of evolution equations are obtained. Finally, in order to illustrate that soliton hierarchy obtained in the paper possesses bi-Hamiltonian structures exactly, we prove that the linear combination of two-Hamiltonian operators admitted are also a Hamiltonian operator constantly. We point out that two Hamiltonian operators obtained of the system are directly derived from a recurrence relations, not from a recurrence operator

  10. Two-reduction of the super-KP hierarchy

    International Nuclear Information System (INIS)

    McArthur, I.N.

    1994-01-01

    Recursion relations are established for the residues of fractional powers of a two-reduced super-KP operator making use of the Baker-Akhiezer function. These show the integrability of the two-reduced even (or bosonic) flows of the super-KP hierarchy. Similar recursion relations are also proven for the residues of operators associated with the odd (or fermionic) flows of the Mulase-Rabin super-KP hierarchy. Due to the presence of a spectral parameter and itts fermionic partner in the Baker-Akhiezer function, these recursion relations should be relevant to any attempt to prove or disprove a recent proposal that the integrable hierarchy underlying two-dimensional quantum supergravity is the Mulase-Rabin super-KP hierarchy. (orig.)

  11. On natural hierarchy in dynamically broken gauge models

    International Nuclear Information System (INIS)

    Frere, J.M.

    1980-01-01

    A model based on dynamical symmetry breaking provides a naturally large 'mass hierarchy'. Few fermions are needed at intermediate energies, and asymptotic freedom of usual interactions is therefore not imperiled. (orig.)

  12. Neutrino mass hierarchy determination for θ13 = 0

    International Nuclear Information System (INIS)

    Gandhi, Raj; Ghoshal, Pomita; Goswami, Srubabati; Sankar, S. Uma

    2010-01-01

    We examine the possibility of determining the neutrino mass hierarchy in the limit θ 13 = 0 using atmospheric neutrinos as the source. In this limit, θ 13 driven matter effects are absent so independent measurements of Δ 31 and Δ 32 can, in principle, lead to hierarchy determination. Since their difference is Δ 21 , one needs an experimental arrangement where Δ 21 L/E > or approx. 1 can be achieved. This can be satisfied by atmospheric neutrinos which have a large range of L and E. Still, we find that hierarchy determination in the θ 13 = 0 limit with atmospheric neutrinos is not a realistic possibility, even in conjunction with a beam experiment like T2K or NOνA. We discuss why, and also reiterate the general conditions for hierarchy determination if θ 13 = 0.

  13. Variable-coefficient nonisospectral Toda lattice hierarchy and its ...

    Indian Academy of Sciences (India)

    In this paper, a hierarchy of nonisospectral equations with variable coefficients is derived from the ..... from the definitions of Lax integrability and Lax pairs [26] that the variable-coefficient ..... studying which will be the topic for our future study.

  14. Optimal mesh hierarchies in Multilevel Monte Carlo methods

    KAUST Repository

    Von Schwerin, Erik

    2016-01-01

    I will discuss how to choose optimal mesh hierarchies in Multilevel Monte Carlo (MLMC) simulations when computing the expected value of a quantity of interest depending on the solution of, for example, an Ito stochastic differential equation or a partial differential equation with stochastic data. I will consider numerical schemes based on uniform discretization methods with general approximation orders and computational costs. I will compare optimized geometric and non-geometric hierarchies and discuss how enforcing some domain constraints on parameters of MLMC hierarchies affects the optimality of these hierarchies. I will also discuss the optimal tolerance splitting between the bias and the statistical error contributions and its asymptotic behavior. This talk presents joint work with N.Collier, A.-L.Haji-Ali, F. Nobile, and R. Tempone.

  15. On the origins of hierarchy in complex networks

    Science.gov (United States)

    Corominas-Murtra, Bernat; Goñi, Joaquín; Solé, Ricard V.; Rodríguez-Caso, Carlos

    2013-01-01

    Hierarchy seems to pervade complexity in both living and artificial systems. Despite its relevance, no general theory that captures all features of hierarchy and its origins has been proposed yet. Here we present a formal approach resulting from the convergence of theoretical morphology and network theory that allows constructing a 3D morphospace of hierarchies and hence comparing the hierarchical organization of ecological, cellular, technological, and social networks. Embedded within large voids in the morphospace of all possible hierarchies, four major groups are identified. Two of them match the expected from random networks with similar connectivity, thus suggesting that nonadaptive factors are at work. Ecological and gene networks define the other two, indicating that their topological order is the result of functional constraints. These results are consistent with an exploration of the morphospace, using in silico evolved networks. PMID:23898177

  16. Flexible scheme to truncate the hierarchy of pure states

    Science.gov (United States)

    Zhang, P.-P.; Bentley, C. D. B.; Eisfeld, A.

    2018-04-01

    The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a "good" truncation method, where by "good" we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the "n-particle approximation" to HOPS. We also introduce a new approximation, which we call the "n-mode approximation." We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

  17. Plasticity within stem cell hierarchies in mammalian epithelia.

    Science.gov (United States)

    Tetteh, Paul W; Farin, Henner F; Clevers, Hans

    2015-02-01

    Tissue homeostasis and regeneration are fueled by resident stem cells that have the capacity to self-renew, and to generate all the differentiated cell types that characterize a particular tissue. Classical models of such cellular hierarchies propose that commitment and differentiation occur unidirectionally, with the arrows 'pointing away' from the stem cell. Recent studies, all based on genetic lineage tracing, describe various strategies employed by epithelial stem cell hierarchies to replace damaged or lost cells. While transdifferentiation from one tissue type into another ('metaplasia') appears to be generally forbidden in nonpathological contexts, plasticity within an individual tissue stem cell hierarchy may be much more common than previously appreciated. In this review, we discuss recent examples of such plasticity in selected mammalian epithelia, highlighting the different modes of regeneration and their implications for our understanding of cellular hierarchy and tissue self-renewal. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Maslow's Implied Matrix: A Clarification of the Need Hierarchy Theory.

    Science.gov (United States)

    Marsh, Edward

    1978-01-01

    Maslow's need hierarchy theory is restated by means of a matrix arrangement of the constructs within the theory. After consideration of the consequences of this restatement, some significant research is discussed and directions for future research suggested. (Author)

  19. Effects of neutrino oscillation on supernova neutrino. Inverted mass hierarchy

    International Nuclear Information System (INIS)

    Takahashi, Keitaro; Sato, Katsuhiko

    2003-01-01

    We study the effects of neutrino oscillation on supernova neutrinos in the case of the inverted mass hierarchy (m 3 1 2 ) as well as the normal mass hierarchy (m 1 2 3 ). Numerical analysis using realistic supernova and presupernova models allows us to investigate quantitatively the possibility to probe neutrino oscillation parameters. We show that information about the mass hierarchy can be obtained if θ 13 is rather large (sin 2 2θ 13 > 10 -3 ) and that θ 13 can be probed effectively by SuperKamiokande if the neutrino mass hierarchy is inverted. Errors due to the uncertainty in the original neutrino spectra and the Earth effect are also discussed. (author)

  20. The influence of migration on gender hierarchies within the African ...

    African Journals Online (AJOL)

    The influence of migration on gender hierarchies within the African household. ... activities and headship-related roles both within the private and public domains. ... conducted among African women from both formal and informal sectors, this ...

  1. Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

    Science.gov (United States)

    Apweiler, R; Gateau, A; Contrino, S; Martin, M J; Junker, V; O'Donovan, C; Lang, F; Mitaritonna, N; Kappus, S; Bairoch, A

    1997-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

  2. Consultancy services and the urban hierarchy in Western Europe

    OpenAIRE

    P W Daniels; J H J Van Dinteren; M C Monnayer

    1992-01-01

    A cross-national survey of the relationship between the evolving organisation and structure of consultancy service enterprises and the urban hierarchy in Europe has been undertaken. Primate cities in Europe are still the preeminent foci for business services performing strong national and international control. The relationship between markets for consultancy services and the urban hierarchy is complex, but it is possible to suggest a typology of firms on the basis of client characteristics a...

  3. Social Hierarchy and Depression: The Role of Emotion Suppression

    OpenAIRE

    Langner, Carrie A.; Epel, Elissa; Matthews, Karen; Moskowitz, Judith T.; Adler, Nancy

    2012-01-01

    Position in the social hierarchy is a major determinant of health outcomes. We examined the associations between aspects of social hierarchy and depressive symptoms with a specific focus on one potential psychological mechanism: emotion suppression. Suppressing negative emotion has mental health costs, but individuals with low social power and low social status may use these strategies to avoid conflict. Study 1 assessed perceived social power, tendency to suppress negative emotion, and depre...

  4. Quasiclassical deformation in KP hierarchy and Benney's long wave equations

    International Nuclear Information System (INIS)

    Kolokol'tsov, V.N.; Lebedev, D.R.

    1987-01-01

    In the paper by means of the formal variant of Zakharov-Shabat ''dressing'' method various formulas are obtained for the generating functions of the conservation laws of Kadomtsev-Petvias hierarchy which turn into analogous formulas for Benney hierarchy in the quasiclassical limit. The generating fucntion of the conservation laws of Miura type is constructed for higher Benney equations and the simple proof of the related identities is given

  5. Reactions to Crime as a Hierarchy Regulating Strategy:

    DEFF Research Database (Denmark)

    Green, Eva G. T.; Thomsen, Lotte; Sidanius, Jim

    2009-01-01

    Across two studies, we demonstrated that support for group-based hierarchies differentially affects evaluation of ingroup and outgroup criminal offenders and that this effect generalizes to overall evaluations of their respective groups. Drawing on social dominance theory, our results show that d...... of ethnicity or nationality, not education level and employment status, were the important cues for hierarchy-regulating judgments of criminal offenders...

  6. Standard model fermion hierarchies with multiple Higgs doublets

    International Nuclear Information System (INIS)

    Solaguren-Beascoa Negre, Ana

    2016-01-01

    The hierarchies between the Standard Model (SM) fermion masses and mixing angles and the origin of neutrino masses are two of the biggest mysteries in particle physics. We extend the SM with new Higgs doublets to solve these issues. The lightest fermion masses and the mixing angles are generated through radiative effects, correctly reproducing the hierarchy pattern. Neutrino masses are generated in the see-saw mechanism.

  7. Earth Effects and Mass Hierarchy with Supernova Neutrinos

    International Nuclear Information System (INIS)

    Dasgupta, Basudeb

    2009-01-01

    Collective neutrino flavor transformations take place deep inside a supernova if the neutrino mass hierarchy is inverted, even for extremely small values of θ 13 . We show that the presence (or absence) of Earth matter effects in antineutrino signal is directly related to the absence (or presence) of these collective effects, when the mixing angle θ 13 is small. Thus a neutrino signal from a galactic supernova may enable us to distinguish between the hierarchies even for small values of θ 13 .

  8. A Novel Approach to Semantic and Coreference Annotation at LLNL

    Energy Technology Data Exchange (ETDEWEB)

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  9. Review of actinide-sediment reactions with an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Ames, L.L.; Rai, D.; Serne, R.J.

    1976-02-10

    The annotated bibliography is divided into sections on chemistry and geochemistry, migration and accumulation, cultural distributions, natural distributions, and bibliographies and annual reviews. (LK)

  10. Correction of the Caulobacter crescentus NA1000 genome annotation.

    Directory of Open Access Journals (Sweden)

    Bert Ely

    Full Text Available Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%.

  11. Annotating non-coding regions of the genome.

    Science.gov (United States)

    Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

    2010-08-01

    Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

  12. Conformal fields. From Riemann surfaces to integrable hierarchies

    International Nuclear Information System (INIS)

    Semikhatov, A.M.

    1991-01-01

    I discuss the idea of translating ingredients of conformal field theory into the language of hierarchies of integrable differential equations. Primary conformal fields are mapped into (differential or matrix) operators living on the phase space of the hierarchy, whereas operator insertions of, e.g., a current or the energy-momentum tensor, become certain vector fields on the phase space and thus acquire a meaning independent of a given Riemann surface. A number of similarities are observed between the structures arising on the hierarchy and those of the theory on the world-sheet. In particular, there is an analogue of the operator product algebra with the Cauchy kernel replaced by its 'off-shell' hierarchy version. Also, hierarchy analogues of certain operator insertions admit two (equivalent, but distinct) forms, resembling the 'bosonized' and 'fermionized' versions respectively. As an application, I obtain a useful reformulation of the Virasoro constraints of the type that arise in matrix models, as a system of equations on dressing (or Lax) operators (rather than correlation functions, i.e., residues or traces). This also suggests an interpretation in terms of a 2D topological field theory, which might be extended to a correspondence between Virasoro-constrained hierarchies and topological theories. (orig.)

  13. Inequality matters: classroom status hierarchy and adolescents' bullying.

    Science.gov (United States)

    Garandeau, Claire F; Lee, Ihno A; Salmivalli, Christina

    2014-07-01

    The natural emergence of status hierarchies in adolescent peer groups has long been assumed to help prevent future intragroup aggression. However, clear evidence of this beneficial influence is lacking. In fact, few studies have examined between-group differences in the degree of status hierarchy (defined as within-group variation in individual status) and how they are related to bullying, a widespread form of aggression in schools. Data from 11,296 eighth- and ninth-graders (mean age = 14.57, 50.6 % female) from 583 classes in 71 schools were used to determine the direction of the association between classroom degree of status hierarchy and bullying behaviors, and to investigate prospective relationships between these two variables over a 6-month period. Multilevel structural equation modeling analyses showed that higher levels of classroom status hierarchy were concurrently associated with higher levels of bullying at the end of the school year. Higher hierarchy in the middle of the school year predicted higher bullying later in the year. No evidence was found to indicate that initial bullying predicted future hierarchy. These findings highlight the importance of a shared balance of power in the classroom for the prevention of bullying among adolescents.

  14. A Bayesian Sampler for Optimization of Protein Domain Hierarchies

    Science.gov (United States)

    2014-01-01

    Abstract The process of identifying and modeling functionally divergent subgroups for a specific protein domain class and arranging these subgroups hierarchically has, thus far, largely been done via manual curation. How to accomplish this automatically and optimally is an unsolved statistical and algorithmic problem that is addressed here via Markov chain Monte Carlo sampling. Taking as input a (typically very large) multiple-sequence alignment, the sampler creates and optimizes a hierarchy by adding and deleting leaf nodes, by moving nodes and subtrees up and down the hierarchy, by inserting or deleting internal nodes, and by redefining the sequences and conserved patterns associated with each node. All such operations are based on a probability distribution that models the conserved and divergent patterns defining each subgroup. When we view these patterns as sequence determinants of protein function, each node or subtree in such a hierarchy corresponds to a subgroup of sequences with similar biological properties. The sampler can be applied either de novo or to an existing hierarchy. When applied to 60 protein domains from multiple starting points in this way, it converged on similar solutions with nearly identical log-likelihood ratio scores, suggesting that it typically finds the optimal peak in the posterior probability distribution. Similarities and differences between independently generated, nearly optimal hierarchies for a given domain help distinguish robust from statistically uncertain features. Thus, a future application of the sampler is to provide confidence measures for various features of a domain hierarchy. PMID:24494927

  15. Reappraising the functional implications of the primate visual anatomical hierarchy.

    Science.gov (United States)

    Hegdé, Jay; Felleman, Daniel J

    2007-10-01

    The primate visual system has been shown to be organized into an anatomical hierarchy by the application of a few principled criteria. It has been widely assumed that cortical visual processing is also hierarchical, with the anatomical hierarchy providing a defined substrate for clear levels of hierarchical function. A large body of empirical evidence seemed to support this assumption, including the general observations that functional properties of visual neurons grow progressively more complex at progressively higher levels of the anatomical hierarchy. However, a growing body of evidence, including recent direct experimental comparisons of functional properties at two or more levels of the anatomical hierarchy, indicates that visual processing neither is hierarchical nor parallels the anatomical hierarchy. Recent results also indicate that some of the pathways of visual information flow are not hierarchical, so that the anatomical hierarchy cannot be taken as a strict flowchart of visual information either. Thus, while the sustaining strength of the notion of hierarchical processing may be that it is rather simple, its fatal flaw is that it is overly simplistic.

  16. Two hierarchies of multi-component Kaup-Newell equations and theirs integrable couplings

    International Nuclear Information System (INIS)

    Zhu Fubo; Ji Jie; Zhang Jianbin

    2008-01-01

    Two hierarchies of multi-component Kaup-Newell equations are derived from an arbitrary order matrix spectral problem, including positive non-isospectral Kaup-Newell hierarchy and negative non-isospectral Kaup-Newell hierarchy. Moreover, new integrable couplings of the resulting Kaup-Newell soliton hierarchies are constructed by enlarging the associated matrix spectral problem

  17. JUNO. Determination of the neutrino mass hierarchy using reactor neutrinos

    Energy Technology Data Exchange (ETDEWEB)

    Wonsak, Bjoern [Hamburg University, Inst. Exp. Phys., Hamburg (Germany)

    2015-07-01

    The Jiangmen Underground Neutrino Observatory (JUNO) is a medium-baseline reactor neutrino experiment located in China. Its aim is to determine the neutrino mass hierarchy at more than 3 sigma significance after six years of data taking by using a 20kt liquid scintillator detector. To achieve this goal, an energy resolution of less than 3%/√(E) is necessary, creating strict requirements on the detector design and the liquid scintillator. Moreover, JUNO will be the only experiment in the near future able to measure the solar mixing parameters with a precision of better than 1%. This is at the same level as our current knowledge on flavour mixing in the quark sector, marking an important milestone of neutrino physics. In addition, supernova neutrinos, geo-neutrinos, sterile neutrinos as well as solar and atmospheric neutrinos can be studied. JUNO was approved in 2013 and the construction of the underground facility started early this year. In this talk the status of the experiment and its prospects is discussed.

  18. Mirror quintic vacua: hierarchies and inflation

    Energy Technology Data Exchange (ETDEWEB)

    Bizet, Nana Cabo [Mandelstam Institute for Theoretical Physics, School of Physics,and NITheP, University of the Witwatersrand, WITS 2050, Johannesburg (South Africa); Departamento de Física, Universidad de Guanajuato,Loma del Bosque 103, CP 37150, León, Guanajuato (Mexico); Loaiza-Brito, Oscar [Departamento de Física, Universidad de Guanajuato,Loma del Bosque 103, CP 37150, León, Guanajuato (Mexico); Zavala, Ivonne [Department of Physics, Swansea University, Singleton Park,Swansea, SA2 8PP (United Kingdom)

    2016-10-17

    We study the moduli space of type IIB string theory flux compactifications on the mirror of the CY quintic 3-fold in ℙ{sup 4}. We focus on the dynamics of the four dimensional moduli space, defined by the axio-dilaton τ and the complex structure modulus z. The z-plane has critical points, the conifold, the orbifold and the large complex structure with non trivial monodromies. We find the solutions to the Picard-Fuchs equations obeyed by the periods of the CY in the full z-plane as a series expansion in z around the critical points to arbitrary order. This allows us to discard fake vacua, which appear as a result of keeping only the leading order term in the series expansions. Due to monodromies vacua are located at a given sheet in the z-plane. A dS vacuum appears for a set of fluxes. We revisit vacua with hierarchies among the 4D and 6D physical scales close to the conifold point and compare them with those found at leading order in http://dx.doi.org/10.1103/PhysRevD.66.106006, http://dx.doi.org/10.1007/JHEP03(2011)119. We explore slow-roll inflationary directions of the scalar potential by looking at regions where the multi-field slow-roll parameters ϵ and η are smaller than one. The value of ϵ depends strongly on the approximation of the periods and to achieve a stable value, several orders in the expansion are needed. We do not find realizations of single field axion monodromy inflation. Instead, we find that inflationary regions appear along linear combinations of the four real field directions and for certain configurations of fluxes.

  19. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

    2010-05-01

    Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  20. Phenex: ontological annotation of phenotypic diversity.

    Science.gov (United States)

    Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

    2010-05-05

    Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.