Sample records for hierarchy additional annotation
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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.)
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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.)
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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
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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.
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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.
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Hierarchy-associated semantic-rule inference framework for classifying indoor scenes
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.
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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
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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
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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
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Evaluating, Comparing, and Interpreting Protein Domain Hierarchies
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
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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.
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Annotation-based feature extraction from sets of SBML models.
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.
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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.
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Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.
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.
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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
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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
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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
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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
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NoGOA: predicting noisy GO annotations using evidences and sparse representation.
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 .
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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
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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
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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.
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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.
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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
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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
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A robust data-driven approach for gene ontology annotation.
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.
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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.
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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.
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Visualising large hierarchies with Flextree
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.
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Neural basis of social status hierarchy across species.
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.
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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
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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
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Pipeline to upgrade the genome annotations
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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.
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q-Deformed KP Hierarchy and q-Deformed Constrained KP Hierarchy
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...
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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
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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.
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The Evolutionary Origins of Hierarchy.
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.
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The Evolutionary Origins of Hierarchy
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
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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.
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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
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On an extended second Painlevé hierarchy
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.
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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
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Semantic annotation of consumer health questions.
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
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Psychophysical "blinding" methods reveal a functional hierarchy of unconscious visual processing.
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.
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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.
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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
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Annotation-based enrichment of Digital Objects using open-source frameworks
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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.
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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.
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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
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Concept annotation in the CRAFT corpus.
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.
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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
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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
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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.
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Can nonstandard interactions jeopardize the hierarchy sensitivity of DUNE?
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.
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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)
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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.
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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)
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BAT: An open-source, web-based audio events annotation tool
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...
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Why and when hierarchy impacts team effectiveness: A meta-analytic integration.
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).
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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.
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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
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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
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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
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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.
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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
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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...
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Integrable Hierarchies and Dispersionless Limit
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...
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Toda hierarchies and their applications
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.
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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
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An Improved Semidefinite Programming Hierarchy for Testing Entanglement
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.
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First generation annotations for the fathead minnow (Pimephales promelas) genome
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...
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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)
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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
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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
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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.)
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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.
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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.))
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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...
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Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.
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.
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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.
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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
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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
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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
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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
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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.
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Use of Annotations for Component and Framework Interoperability
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
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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.
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An annotated corpus with nanomedicine and pharmacokinetic parameters.
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.
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Evolutionary hierarchy of vertebrate-like heterotrimeric G protein families.
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
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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
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Chado controller: advanced annotation management with a community annotation system.
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.
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Creating New Medical Ontologies for Image Annotation A Case Study
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.
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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
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Information slows down hierarchy growth.
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.
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Information slows down hierarchy growth
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.
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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.
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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
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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)
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Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials.
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.
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Global network structure of dominance hierarchy of ant workers.
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.
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On the robustness of Herlihy's hierarchy
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.
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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....
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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)
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Multiview Hessian regularization for image annotation.
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.
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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.)
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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
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A Hierarchy Model of Income Distribution
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...
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Hierarchy is Detrimental for Human Cooperation.
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.
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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.
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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.
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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
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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
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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.
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An open annotation ontology for science on web 3.0.
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
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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.)
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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.
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Evaluating Hierarchical Structure in Music Annotations.
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.
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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.
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Hierarchy is Detrimental for Human Cooperation
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
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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.
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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
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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
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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.
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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
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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)
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Reasoning with Annotations of Texts
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...
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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)
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Multiple Hierarchies and Organizational Control
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)
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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.
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Aspect of Fermion Mass Hierarchy within Flavor Democracy for Yukawa Couplings
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.
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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
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NegGOA: negative GO annotations selection using ontology structure.
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.
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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.
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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...
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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
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Alignment-Annotator web server: rendering and annotating sequence alignments.
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.
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Completing the land resource hierarchy
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...
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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
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Hierarchy, Dominance, and Deliberation: Egalitarian Values Require Mental Effort.
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.
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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
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Hierarchy is Detrimental for Human Cooperation
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...
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Objective-guided image annotation.
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
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On the nesting of Painlevé hierarchies: A Hamiltonian approach
International Nuclear Information System (INIS)
Pickering, A.
2012-01-01
Highlights: ► Explanation of nesting of Painlevé hierarchies in terms of Hamiltonian structures. ► Approach generally phrased and applicable to continuous and discrete systems. ► Importance of related integrable hierarchies in understanding Painlevé hierarchies. - Abstract: We consider the phenomenon whereby two different Painlevé hierarchies, related to the same hierarchy of completely integrable equations, are such that solutions of one member of one of the Painlevé hierarchies are also solutions of a higher-order member of the other Painlevé hierarchy. An explanation is given in terms of the Hamiltonian structures of the related underlying completely integrable hierarchies, and is sufficiently generally formulated so as to be applicable equally to both continuous and discrete Painlevé hierarchies. Special integrals of a further Painlevé hierarchy related by Bäcklund transformation to the other Painlevé hierarchy mentioned above can also be constructed. Examples of the application of this approach to Painlevé hierarchies related to the Korteweg–de Vries, dispersive water wave, Toda and Volterra integrable hierarchies are considered. Our results provide further evidence of the importance of the underlying structures of related completely integrable hierarchies in understanding the properties of Painlevé hierarchies.
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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.
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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...
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Maslow's Hierarchy of Needs Revisited.
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…
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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)
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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....
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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)
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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.
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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.)
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Dominance Hierarchies in Young Children
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…
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Resolution of ranking hierarchies in directed networks
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
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Learning of Alignment Rules between Concept Hierarchies
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.
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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.
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International Nuclear Information System (INIS)
Dong Huanhe; Wang Xiangrong
2008-01-01
The trace identity is extended to the quadratic-form identity. The Hamiltonian structures of the NLS-MKdV hierarchy, and integrable coupling of multi-component Levi hierarchy are obtained by the quadratic-form identity. The method can be used to produce the Hamiltonian structures of the other integrable couplings or multi-component hierarchies
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Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.
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.
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DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.
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.
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Neutrino mass hierarchy and matter effects
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...
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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.
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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.
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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
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Is there a hierarchy of survival reflexes?
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.
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Hierarchy in directed random networks.
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.
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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.
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Semantic annotation in biomedicine: the current landscape.
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.
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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'
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Towards the VWO Annotation Service: a Success Story of the IMAGE RPI Expert Rating System
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
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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.
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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
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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
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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
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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.
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Contributions to In Silico Genome Annotation
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
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Active learning reduces annotation time for clinical concept extraction.
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.
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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...
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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.
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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...
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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.
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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
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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
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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.
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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.
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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.)
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Feeling Expression Using Avatars and Its Consistency for Subjective Annotation
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.
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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
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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.
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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...
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Annotating functional RNAs in genomes using Infernal.
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.
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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)
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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.
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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.
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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)
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Computer systems for annotation of single molecule fragments
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.
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Image annotation under X Windows
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.
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Motion lecture annotation system to learn Naginata performances
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.
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Quantify entanglement by concurrence hierarchy
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.
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BEACON: automated tool for Bacterial GEnome Annotation ComparisON
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/
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BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
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/ .
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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.
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Two New Reformulation Convexification Based Hierarchies for 0-1 MIPs
Directory of Open Access Journals (Sweden)
Hacene Ouzia
2015-01-01
Full Text Available First, we introduce two new reformulation convexification based hierarchies called RTC and RSC for which the rank d continuous relaxations are denoted by P^RTCd and P^RSCd, respectively. These two hierarchies are obtained using two different convexification schemes: term convexification in the case of the RTC hierarchy and standard convexification in the case of the RSC hierarchy. Secondly, we compare the strength of these two hierarchies. We will prove that (i the hierarchy RTC is equivalent to the RLT hierarchy of Sherali-Adams, (ii the hierarchy RTC dominates the hierarchy RSC, and (iii the hierarchy RSC is dominated by the Lift-and-Project hierarchy. Thirdly, for every rank d, we will prove that convTd∩Etd⊆P^RTCd⊆Td and convSd∩Esd⊆P^RSCd⊆Sd where the sets Td and Sd are convex, while Etd and Esd are two nonconvex sets with empty interior (all these sets depend on the convexification step. The first inclusions allow, in some cases, an explicit characterization (in the space of the original variables of the RLT relaxations. Finally, we will discuss weak version of both RTC and RSC hierarchies and we will emphasize some connections between them.
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Annotating temporal information in clinical narratives.
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.
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Assessment of disease named entity recognition on a corpus of annotated sentences.
Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich
2008-04-11
In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to other systems. In addition, we found
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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.
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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
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/
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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
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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.
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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.
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Improving Expression Power in Modeling OLAP Hierarchies
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.
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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.
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Dictionary-driven protein annotation.
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
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Why we live in hierarchies? a quantitative treatise
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...
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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…
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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
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Marsch, Amanda F; Espiritu, Baltazar; Groth, John; Hutchens, Kelli A
2014-06-01
With today's technology, paraffin-embedded, hematoxylin & eosin-stained pathology slides can be scanned to generate high quality virtual slides. Using proprietary software, digital images can also be annotated with arrows, circles and boxes to highlight certain diagnostic features. Previous studies assessing digital microscopy as a teaching tool did not involve the annotation of digital images. The objective of this study was to compare the effectiveness of annotated digital pathology slides versus non-annotated digital pathology slides as a teaching tool during dermatology and pathology residencies. A study group composed of 31 dermatology and pathology residents was asked to complete an online pre-quiz consisting of 20 multiple choice style questions, each associated with a static digital pathology image. After completion, participants were given access to an online tutorial composed of digitally annotated pathology slides and subsequently asked to complete a post-quiz. A control group of 12 residents completed a non-annotated version of the tutorial. Nearly all participants in the study group improved their quiz score, with an average improvement of 17%, versus only 3% (P = 0.005) in the control group. These results support the notion that annotated digital pathology slides are superior to non-annotated slides for the purpose of resident education. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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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....
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Mesotext. Framing and exploring annotations
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
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Inequality matters: classroom status hierarchy and adolescents' bullying.
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.
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Annotating images by mining image search results
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
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Modelling Dominance Hierarchies Under Winner and Loser Effects.
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.
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Principles of synchronous digital hierarchy
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
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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)
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A multi-ontology approach to annotate scientific documents based on a modularization technique.
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.
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H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.
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.
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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.)
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Shakespeare Is Alive and Well in Cyberspace: An Annotated Bibliography.
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)
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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)
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WormBase: Annotating many nematode genomes.
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.
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W-algebra symmetries of generalised Drinfel'd-Sokolov hierarchies
International Nuclear Information System (INIS)
Spence, B.
1992-01-01
Using the zero curvature formulation, it is shown that W-algebra transformations are symmetries of corresponding generalised Drinfel'd-Sokolov hierarchies. This result is illustrated with the examples of the KdV and Boussinesque hierarchies, and the hierarchy associated to the Polyakov-Bershadsky W-algebra. (orig.)
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Teaching and Learning Communities through Online Annotation
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
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Displaying Annotations for Digitised Globes
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.
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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...
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Visual Hierarchy and Mind Motion in Advertising Design
Directory of Open Access Journals (Sweden)
Doaa Farouk Badawy Eldesouky
2013-06-01
Full Text Available Visual hierarchy is a significant concept in the field of advertising, a field that is dominated by effective communication, visual recognition and motion. Designers of advertisements have always been trying to organize the visual hierarchy throughout their advertising designs to aid the eye to recognize information in the desired order, to achieve the ultimate goals of clear perception and effectively delivering the advertising messages. However many assumptions and questions usually rise on how to create effective hierarchy throughout advertising designs and lead the eye and mind of the viewer in the most favorable way. This paper attempts to study visual hierarchy and mind motion in advertising designs and why it is important to develop visual paths when designing an advertisement. It explores the theory behind it, and how the very principles can be used to put these concepts into practice. The paper demonstrates some advertising samples applying visual hierarchy and mind motion in a representation of applying the basics and discussing the results.
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Visual Hierarchy and Mind Motion in Advertising Design
Directory of Open Access Journals (Sweden)
Doaa Farouk Badawy Eldesouky
2013-06-01
Full Text Available Visual hierarchy is a significant concept in the field of advertising, a field that is dominated by effective communication, visual recognition and motion. Designers of advertisements have always been trying to organize the visual hierarchy throughout their advertising designs to aid the eye to recognize information in the desired order, to achieve the ultimate goals of clear perception and effectively delivering the advertising messages. However many assumptions and questions usually rise on how to create effective hierarchy throughout advertising designs and lead the eye and mind of the viewer in the most favorable way. This paper attempts to study visual hierarchy and mind motion in advertising designs and why it is important to develop visual paths when designing an advertisement. It explores the theory behind it, and how the very principles can be used to put these concepts into practice. The paper demonstrates some advertising samples applying visual hierarchy and mind motion in a representation of applying the basics and discussing the results.
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THE DIMENSIONS OF COMPOSITION ANNOTATION.
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…
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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
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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)
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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.
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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
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MimoSA: a system for minimotif annotation
Directory of Open Access Journals (Sweden)
Kundeti Vamsi
2010-06-01
Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to
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Sifrim, Alejandro; Van Houdt, Jeroen Kj; Tranchevent, Leon-Charles; Nowakowska, Beata; Sakai, Ryo; Pavlopoulos, Georgios A; Devriendt, Koen; Vermeesch, Joris R; Moreau, Yves; Aerts, Jan
2012-01-01
The increasing size and complexity of exome/genome sequencing data requires new tools for clinical geneticists to discover disease-causing variants. Bottlenecks in identifying the causative variation include poor cross-sample querying, constantly changing functional annotation and not considering existing knowledge concerning the phenotype. We describe a methodology that facilitates exploration of patient sequencing data towards identification of causal variants under different genetic hypotheses. Annotate-it facilitates handling, analysis and interpretation of high-throughput single nucleotide variant data. We demonstrate our strategy using three case studies. Annotate-it is freely available and test data are accessible to all users at http://www.annotate-it.org.
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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.
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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
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
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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
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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.)
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A new multi-component hierarchy and its integrable expanding model
International Nuclear Information System (INIS)
Dong Huanhe; Liang Xiangqian
2008-01-01
A set of multi-component matrix Lie algebra is constructed, it follows that a type of new loop algebra is presented and multi-component integrable hierarchy is obtained. Furthermore, the loop algebra is expanded into a larger one and a type of integrable coupling system is worked out. As reduction of the hierarchy, some well-known hierarchy such as DNLS, KN, CLL hierarchy are established
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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
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Annotating individual human genomes.
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.
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ANNOTATING INDIVIDUAL HUMAN GENOMES*
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
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Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
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.
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The GATO gene annotation tool for research laboratories
Directory of Open Access Journals (Sweden)
A. Fujita
2005-11-01
Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.
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Stress amplifies memory for social hierarchy.
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.
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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.
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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.
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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.
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A Suggested Modification to Maslow's Need Hierarchy
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)
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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".
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Optimal mesh hierarchies in Multilevel Monte Carlo methods
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.
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Optimal mesh hierarchies in Multilevel Monte Carlo methods
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.
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Solar Tutorial and Annotation Resource (STAR)
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
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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)
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Re-annotation of the genome sequence of Helicobacter pylori 26695
Directory of Open Access Journals (Sweden)
Resende Tiago
2013-12-01
Full Text Available Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.
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Annotating the human genome with Disease Ontology
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
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MIPS bacterial genomes functional annotation benchmark dataset.
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
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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
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Annotating non-coding regions of the genome.
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.
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The Helmholtz Hierarchy: Phase Space Statistics of Cold Dark Matter
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...
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Systems Theory and Communication. Annotated Bibliography.
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)
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The surplus value of semantic annotations
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,
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Seeing the forest for the trees: annotating small RNA producing genes in plants.
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.
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Brane world perspective on the cosmological constant and the hierarchy problems
International Nuclear Information System (INIS)
Flanagan, Eanna; Jones, Nicholas; Stoica, Horace; Tye, S.-H. Henry; Wasserman, Ira
2001-01-01
We elaborate on the recently proposed static brane world scenario, where the effective 4D cosmological constant is exponentially small when parallel 3-branes are far apart. We extend this result to a compactified model with two positive tension branes. In addition to an exponentially small effective 4D cosmological constant, this model incorporates a Randall-Sundrum-like solution to the hierarchy problem. Furthermore, the exponential factors for the hierarchy problem and the cosmological constant problem obey an inequality that is satisfied in nature. This inequality implies that the cosmological constant problem can be explained if the hierarchy problem is understood. The basic idea generalizes to the multibrane world scenario. We discuss models with piecewise adjustable bulk cosmological constants (to be determined by the 5-dimensional Einstein equation), a key element of the scenario. We also discuss the global structure of this scenario and clarify the physical properties of the particle (Rindler) horizons that are present. Finally, we derive a 4D effective theory in which all observers on all branes not separated by particle horizons measure the same Newton's constant and 4D cosmological constant
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Formal language theory: refining the Chomsky hierarchy
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
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Formal language theory: refining the Chomsky hierarchy.
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).
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A computational platform to maintain and migrate manual functional annotations for BioCyc databases.
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.
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The Hierarchy of Proinflammatory Cytokines in Ocular Inflammation.
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.
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SUSY-hierarchy of one-dimensional reflectionless potentials
International Nuclear Information System (INIS)
Maydanyuk, Sergei P.
2005-01-01
A class of one-dimensional reflectionless potentials is studied. It is found that all possible types of the reflectionless potentials can be combined into one SUSY-hierarchy with a constant potential. An approach for determination of a general form of the reflectionless potential on the basis of construction of such a hierarchy by the recurrent method is proposed. A general integral form of interdependence between superpotentials with neighboring numbers of this hierarchy, opening a possibility to find new reflectionless potentials, is found and has a simple analytical view. It is supposed that any possible type of the reflectionless potential can be expressed through finite number of elementary functions (unlike some presentations of the reflectionless potentials, which are constructed on the basis of soliton solutions or are shape invariant in one or many steps with involving scaling of parameters, and are expressed through series). An analysis of absolute transparency existence for the potential which has the inverse power dependence on space coordinate (and here tunneling is possible), i.e., which has the form V (x) = ± α/ vertical bar x-x 0 vertical bar n (where α and x 0 are constants, n is natural number), is fulfilled. It is shown that such a potential can be reflectionless at n = 2 only. A SUSY-hierarchy of the inverse power reflectionless potentials is constructed. Isospectral expansions of this hierarchy are analyzed
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Current and future trends in marine image annotation software
Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.
2016-12-01
Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images
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PANNZER2: a rapid functional annotation web server.
Törönen, Petri; Medlar, Alan; Holm, Liisa
2018-05-08
The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.
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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.
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Virasoro algebra action on integrable hierarchies and Virasoro contraints in matrix models
International Nuclear Information System (INIS)
Semikhatov, A.M.
1991-01-01
The action of the Virasoro algebra on integrable hierarchies of non-linear equations and on related objects ('Schroedinger' differential operators) is investigated. The method consists in pushing forward the Virasoro action to the wave function of a hierarchy, and then reconstructing its action on the dressing and Lax operators. This formulation allows one to observe a number of suggestive similarities between the structures involved in the description of the Virasoro algebra on the hierarchies and the structure of conformal field theory on the world-sheet. This includes, in particular, an 'off-shell' hierarchy version of operator products and of the Cauchy kernel. In relation to matrix models, which have been observed to be effectively described by integrable hierarchies subjected to Virasoro constraints, I propose to define general Virasoro-constrained hierarchies also in terms of dressing operators, by certain equations which carry the information of the hierarchy and the Virasoro algebra simultaneously and which suggest an interpretation as operator versions of recursion/loop equations in topological theories. These same equations provide a relation with integrable hierarchies with quantized spectral parameter introduced recently. The formulation in terms of dressing operators allows a scaling (continuum limit) of discrete (i.e. lattice) hierarchies with the Virasoro constraints into 'continuous' Virasoro-constrained hierarchies. In particular, the KP hierarchy subjected to the Virasoro constraints is recovered as a scaling limit of the Virasoro-constrained Toda hierarchy. The dressing operator method also makes is straightforward to identify the full symmetry algebra of Virasoro-constrained hierarchies, which is related to the family of W ∞ (J) algebras introduced recently. (orig./HS)
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A hierarchy of Ramsey-like cardinals
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.
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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.)
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DFAST and DAGA: web-based integrated genome annotation tools and resources.
Tanizawa, Yasuhiro; Fujisawa, Takatomo; Kaminuma, Eli; Nakamura, Yasukazu; Arita, Masanori
2016-01-01
Quality assurance and correct taxonomic affiliation of data submitted to public sequence databases have been an everlasting problem. The DDBJ Fast Annotation and Submission Tool (DFAST) is a newly developed genome annotation pipeline with quality and taxonomy assessment tools. To enable annotation of ready-to-submit quality, we also constructed curated reference protein databases tailored for lactic acid bacteria. DFAST was developed so that all the procedures required for DDBJ submission could be done seamlessly online. The online workspace would be especially useful for users not familiar with bioinformatics skills. In addition, we have developed a genome repository, DFAST Archive of Genome Annotation (DAGA), which currently includes 1,421 genomes covering 179 species and 18 subspecies of two genera, Lactobacillus and Pediococcus , obtained from both DDBJ/ENA/GenBank and Sequence Read Archive (SRA). All the genomes deposited in DAGA were annotated consistently and assessed using DFAST. To assess the taxonomic position based on genomic sequence information, we used the average nucleotide identity (ANI), which showed high discriminative power to determine whether two given genomes belong to the same species. We corrected mislabeled or misidentified genomes in the public database and deposited the curated information in DAGA. The repository will improve the accessibility and reusability of genome resources for lactic acid bacteria. By exploiting the data deposited in DAGA, we found intraspecific subgroups in Lactobacillus gasseri and Lactobacillus jensenii , whose variation between subgroups is larger than the well-accepted ANI threshold of 95% to differentiate species. DFAST and DAGA are freely accessible at https://dfast.nig.ac.jp.
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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
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International Nuclear Information System (INIS)
Zhang Yufeng
2005-01-01
A set of multi-component matrix Lie algebra is constructed, which is devote to obtaining a new loop algebra A-bar M-1 . It follows that an isospectral problem is established. By making use of Tu scheme, a Liouville integrable multi-component hierarchy of soliton equations is generated, which possesses the bi-Hamiltonian structures. As its reduction cases, the multi-component AKNS hierarchy and the formalism of the multi-component BPT hierarchy are given, respectively
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Objective Bayesian analysis of neutrino masses and hierarchy
Heavens, Alan F.; Sellentin, Elena
2018-04-01
Given the precision of current neutrino data, priors still impact noticeably the constraints on neutrino masses and their hierarchy. To avoid our understanding of neutrinos being driven by prior assumptions, we construct a prior that is mathematically minimally informative. Using the constructed uninformative prior, we find that the normal hierarchy is favoured but with inconclusive posterior odds of 5.1:1. Better data is hence needed before the neutrino masses and their hierarchy can be well constrained. We find that the next decade of cosmological data should provide conclusive evidence if the normal hierarchy with negligible minimum mass is correct, and if the uncertainty in the sum of neutrino masses drops below 0.025 eV. On the other hand, if neutrinos obey the inverted hierarchy, achieving strong evidence will be difficult with the same uncertainties. Our uninformative prior was constructed from principles of the Objective Bayesian approach. The prior is called a reference prior and is minimally informative in the specific sense that the information gain after collection of data is maximised. The prior is computed for the combination of neutrino oscillation data and cosmological data and still applies if the data improve.
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Quark mass hierarchies from the universal seesaw mechanism
International Nuclear Information System (INIS)
Davidson, A.; Michel, L.; Sage, M.L.; Wali, K.C.
1994-01-01
The paper is an extension of the previous work based on the idea of a universal seesaw mechanism to explain the hierarchies in the fermion mass spectrum. A model is proposed within the framework of left-right symmetry with a minimal Higgs system and an axial U(1) symmetry imposed to distinguish the generations. Previous work was confined, for mathematical simplifications, to the case of nonsingular mass matrices. In the present paper, singular matrices are considered. A systematic perturbative technique is developed to display the mass eigenvalues in terms of the vacuum expectation values of the assumed Higgs multiplets. The model successfully correlates the mass hierarchies among the quarks to the assumed hierarchies in the vacuum expectation values without appealing to a hierarchy in the Yukawa-type fermion--Higgs-boson couplings. By considering a general Higgs potential appropriate to the model, we study its minimization and prove that there exists an open subdomain in the parameter space where the orbit of the lowest minima of the potential corresponds to the kind of hierarchy in the vacuum expectation values needed for the success of the model
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Hermitian versus anti-hermitian one-matrix models and their hierarchies
International Nuclear Information System (INIS)
Hollowood, T.; Miramontes, L.; Pasquinucci, A.; Nappi, C.
1992-01-01
Building on a recent work of C. Crnkovic, M. Douglas and G. Moore, a study of multi-critical multi-cut one-matrix models and their associated sl(2, C) integrable hierarchies, is further pursued. The double-scaling limits of hermitian matrix models with different scaling ansaetze, lead to the KdV hierarchy, to the modified KdV hierarchy and part of the non-linear Schroedinger hierarchy. Instead, the anti-hermitian matrix model, in the 2-arc sector, results in the Zakharov-Shabat hierarchy, which contains both KdV and mKdV as reductions. For all the hierarchies it is found that the Virasoro constraints act on the associated τ-functions. Whereas it is known that the ZS and KdV models lead to the Virasoro constraints of an sl(2, C) vacuum, we find that the mKdV model leads to the Virasoro constraints of a highest-weight state with arbitrary conformal dimension. (orig.)
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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.
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On the origins of hierarchy in complex networks
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
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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.
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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.
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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
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Boolean Operations, Joins, and the Extended Low Hierarchy
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...
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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)
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Zhidkov, Ilia; Nagar, Tal; Mishmar, Dan; Rubin, Eitan
2011-11-01
The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming. Copyright © 2011 Elsevier B.V. and Mitochondria Research Society. All rights reserved. All rights reserved.
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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.)
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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%.
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Small molecule annotation for the Protein Data Bank.
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.
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Self-organizing dominance hierarchies in a wild primate population
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...
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Eye Movement Evidence for Hierarchy Effects on Memory Representation of Discourses.
Directory of Open Access Journals (Sweden)
Yingying Wu
Full Text Available In this study, we applied the text-change paradigm to investigate whether and how discourse hierarchy affected the memory representation of a discourse. Three kinds of three-sentence discourses were constructed. In the hierarchy-high condition and the hierarchy-low condition, the three sentences of the discourses were hierarchically organized and the last sentence of each discourse was located at the high level and the low level of the discourse hierarchy, respectively. In the linear condition, the three sentences of the discourses were linearly organized. Critical words were always located at the last sentence of the discourses. These discourses were successively presented twice and the critical words were changed to semantically related words in the second presentation. The results showed that during the early processing stage, the critical words were read for longer times when they were changed in the hierarchy-high and the linear conditions, but not in the hierarchy-low condition. During the late processing stage, the changed-critical words were again found to induce longer reading times only when they were in the hierarchy-high condition. These results suggest that words in a discourse have better memory representation when they are located at the higher rather than at the lower level of the discourse hierarchy. Global discourse hierarchy is established as an important factor in constructing the mental representation of a discourse.
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Eye Movement Evidence for Hierarchy Effects on Memory Representation of Discourses.
Wu, Yingying; Yang, Xiaohong; Yang, Yufang
2016-01-01
In this study, we applied the text-change paradigm to investigate whether and how discourse hierarchy affected the memory representation of a discourse. Three kinds of three-sentence discourses were constructed. In the hierarchy-high condition and the hierarchy-low condition, the three sentences of the discourses were hierarchically organized and the last sentence of each discourse was located at the high level and the low level of the discourse hierarchy, respectively. In the linear condition, the three sentences of the discourses were linearly organized. Critical words were always located at the last sentence of the discourses. These discourses were successively presented twice and the critical words were changed to semantically related words in the second presentation. The results showed that during the early processing stage, the critical words were read for longer times when they were changed in the hierarchy-high and the linear conditions, but not in the hierarchy-low condition. During the late processing stage, the changed-critical words were again found to induce longer reading times only when they were in the hierarchy-high condition. These results suggest that words in a discourse have better memory representation when they are located at the higher rather than at the lower level of the discourse hierarchy. Global discourse hierarchy is established as an important factor in constructing the mental representation of a discourse.
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Hierarchy and social status in Budongo chimpanzees.
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.
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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...
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SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.
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.
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A semi-automatic annotation tool for cooking video
Bianco, Simone; Ciocca, Gianluigi; Napoletano, Paolo; Schettini, Raimondo; Margherita, Roberto; Marini, Gianluca; Gianforme, Giorgio; Pantaleo, Giuseppe
2013-03-01
In order to create a cooking assistant application to guide the users in the preparation of the dishes relevant to their profile diets and food preferences, it is necessary to accurately annotate the video recipes, identifying and tracking the foods of the cook. These videos present particular annotation challenges such as frequent occlusions, food appearance changes, etc. Manually annotate the videos is a time-consuming, tedious and error-prone task. Fully automatic tools that integrate computer vision algorithms to extract and identify the elements of interest are not error free, and false positive and false negative detections need to be corrected in a post-processing stage. We present an interactive, semi-automatic tool for the annotation of cooking videos that integrates computer vision techniques under the supervision of the user. The annotation accuracy is increased with respect to completely automatic tools and the human effort is reduced with respect to completely manual ones. The performance and usability of the proposed tool are evaluated on the basis of the time and effort required to annotate the same video sequences.
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Experiments with crowdsourced re-annotation of a POS tagging data set
DEFF Research Database (Denmark)
Hovy, Dirk; Plank, Barbara; Søgaard, Anders
2014-01-01
Crowdsourcing lets us collect multiple annotations for an item from several annotators. Typically, these are annotations for non-sequential classification tasks. While there has been some work on crowdsourcing named entity annotations, researchers have assumed that syntactic tasks such as part......-of-speech (POS) tagging cannot be crowdsourced. This paper shows that workers can actually annotate sequential data almost as well as experts. Further, we show that the models learned from crowdsourced annotations fare as well as the models learned from expert annotations in downstream tasks....
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MPEG-7 based video annotation and browsing
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.
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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
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Plasticity within stem cell hierarchies in mammalian epithelia.
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.
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Adolescent male chimpanzees do not form a dominance hierarchy with their peers.
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
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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...
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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...
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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...
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Roy, Sharmili; Brown, Michael S; Shih, George L
2014-02-01
This paper introduces a software framework called Visual Interpretation with Three-Dimensional Annotations (VITA) that is able to automatically generate three-dimensional (3D) visual summaries based on radiological annotations made during routine exam reporting. VITA summaries are in the form of rotating 3D volumes where radiological annotations are highlighted to place important clinical observations into a 3D context. The rendered volume is produced as a Digital Imaging and Communications in Medicine (DICOM) object and is automatically added to the study for archival in Picture Archiving and Communication System (PACS). In addition, a video summary (e.g., MPEG4) can be generated for sharing with patients and for situations where DICOM viewers are not readily available to referring physicians. The current version of VITA is compatible with ClearCanvas; however, VITA can work with any PACS workstation that has a structured annotation implementation (e.g., Extendible Markup Language, Health Level 7, Annotation and Image Markup) and is able to seamlessly integrate into the existing reporting workflow. In a survey with referring physicians, the vast majority strongly agreed that 3D visual summaries improve the communication of the radiologists' reports and aid communication with patients.
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Hierarchies of multi-component mKP equations and theirs integrable couplings
International Nuclear Information System (INIS)
Ji Jie; Yao Yuqin; Zhu Fubo; Chen Dengyuan
2008-01-01
First, a new multi-component modified Kadomtsev-Petviashvill (mKP) spectral problem is constructed by k-constraint imposed on a general pseudo-differential operator. Then, two hierarchies of multi-component mKP equations are derived, including positive non-isospectral mKP hierarchy and negative non-isospectral mKP hierarchy. Moreover, new integrable couplings of the resulting mKP soliton hierarchies are constructed by enlarging the associated matrix spectral problem
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Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?
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.
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Random walk hierarchy measure: What is more hierarchical, a chain, a tree or a star?
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
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Hierarchy among Automata on Linear Orderings
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...
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Shrinking population and the urban hierarchy
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 ...
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Propagating annotations of molecular networks using in silico fragmentation.
da Silva, Ricardo R; Wang, Mingxun; Nothias, Louis-Félix; van der Hooft, Justin J J; Caraballo-Rodríguez, Andrés Mauricio; Fox, Evan; Balunas, Marcy J; Klassen, Jonathan L; Lopes, Norberto Peporine; Dorrestein, Pieter C
2018-04-18
The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp.
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Gene calling and bacterial genome annotation with BG7.
Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo
2015-01-01
New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).
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New genes expressed in human brains: implications for annotating evolving genomes.
Zhang, Yong E; Landback, Patrick; Vibranovski, Maria; Long, Manyuan
2012-11-01
New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. Copyright © 2012 WILEY Periodicals, Inc.
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Inequality Matters : Classroom Status Hierarchy and Adolescents' Bullying
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
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Annotation of the Evaluative Language in a Dependency Treebank
Directory of Open Access Journals (Sweden)
Šindlerová Jana
2017-12-01
Full Text Available In the paper, we present our efforts to annotate evaluative language in the Prague Dependency Treebank 2.0. The project is a follow-up of the series of annotations of small plaintext corpora. It uses automatic identification of potentially evaluative nodes through mapping a Czech subjectivity lexicon to syntactically annotated data. These nodes are then manually checked by an annotator and either dismissed as standing in a non-evaluative context, or confirmed as evaluative. In the latter case, information about the polarity orientation, the source and target of evaluation is added by the annotator. The annotations unveiled several advantages and disadvantages of the chosen framework. The advantages involve more structured and easy-to-handle environment for the annotator, visibility of syntactic patterning of the evaluative state, effective solving of discontinuous structures or a new perspective on the influence of good/bad news. The disadvantages include little capability of treating cases with evaluation spread among more syntactically connected nodes at once, little capability of treating metaphorical expressions, or disregarding the effects of negation and intensification in the current scheme.
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Reappraising the functional implications of the primate visual anatomical hierarchy.
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.
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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
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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
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The caBIG annotation and image Markup project.
Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L
2010-04-01
Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.
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Interoperable Multimedia Annotation and Retrieval for the Tourism Sector
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.
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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.
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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
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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
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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.
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Wronskian type solutions for the vector k-constrained KP hierarchy
International Nuclear Information System (INIS)
Zhang Youjin.
1995-07-01
Motivated by a relation of the 1-constrained Kadomtsev-Petviashvili (KP) hierarchy with the 2 component KP hierarchy, the tau-conditions of the vector k-constrained KP hierarchy are constructed by using an analogue of the Baker-Akhiezer (m + 1)-point function. These tau functions are expressed in terms of Wronskian type determinants. (author). 20 refs
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ZHANG, JIAO
2016-01-01
[Abstract]This paper aims to discuss the necessity to advance disclosing fair value by hierarchy in Japan by reviewing the literature about fair value hierarchy information in the U.S. In Japan, ASBJ published the Exposure Draft "Accounting Standards on Fair Value Measurement and Disclosure" in 2010 which specifies that the fair value should be reported by hierarchy. However, it has not published as formal standard until March 2016. Furthermore, some commenters suggested that the hierarchy an...
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A STUDY ON THE HIERARCHY OF MANAGEMENT ELEMENTS
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.
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The Development of Hierarchy of Effects Model in Advertising
Directory of Open Access Journals (Sweden)
Bambang Sukma Wijaya
2012-04-01
Full Text Available This paper aims to review the hierarchy of effects models in advertising, especially the well-known model, AIDA (Attention, Interest, Desire, and Action. Since its introduction by Lewis (1900 and generally attributed in the marketing and advertising literature by Strong (1925, the concept of AIDA’s hierarchy of effects model has been used by many researchers, both academicians and practitioners. The model is used to measure the effect of an advertisement. However, the development of information technology has radically changed the way of how people communicate and socialize; as well as a paradigm shift from product-oriented marketing to consumer-oriented marketing or people-oriented marketing. Therefore, the variables in the hierarchy of effects model needs to be updated in respond to the latest developments in the notice of public power as consumer audience. Based on deep literature review and reflective method, this paper introduces a new developed concept of hierarchy of effects model that was adopted from AIDA’s hierarchy of effects model, namely: AISDALSLove (At-tention, Interest, Search, Desire, Action, Like/dislike, Share, and Love/hate.
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Combined evidence annotation of transposable elements in genome sequences.
Directory of Open Access Journals (Sweden)
Hadi Quesneville
2005-07-01
Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other
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Plann: A command-line application for annotating plastome sequences.
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.
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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)
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Comparing the Hierarchy of Keywords in On-Line News Portals.
Tibély, Gergely; Sousa-Rodrigues, David; Pollner, Péter; Palla, Gergely
2016-01-01
Hierarchical organization is prevalent in networks representing a wide range of systems in nature and society. An important example is given by the tag hierarchies extracted from large on-line data repositories such as scientific publication archives, file sharing portals, blogs, on-line news portals, etc. The tagging of the stored objects with informative keywords in such repositories has become very common, and in most cases the tags on a given item are free words chosen by the authors independently. Therefore, the relations among keywords appearing in an on-line data repository are unknown in general. However, in most cases the topics and concepts described by these keywords are forming a latent hierarchy, with the more general topics and categories at the top, and more specialized ones at the bottom. There are several algorithms available for deducing this hierarchy from the statistical features of the keywords. In the present work we apply a recent, co-occurrence-based tag hierarchy extraction method to sets of keywords obtained from four different on-line news portals. The resulting hierarchies show substantial differences not just in the topics rendered as important (being at the top of the hierarchy) or of less interest (categorized low in the hierarchy), but also in the underlying network structure. This reveals discrepancies between the plausible keyword association frameworks in the studied news portals.
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Comparing the Hierarchy of Keywords in On-Line News Portals.
Directory of Open Access Journals (Sweden)
Gergely Tibély
Full Text Available Hierarchical organization is prevalent in networks representing a wide range of systems in nature and society. An important example is given by the tag hierarchies extracted from large on-line data repositories such as scientific publication archives, file sharing portals, blogs, on-line news portals, etc. The tagging of the stored objects with informative keywords in such repositories has become very common, and in most cases the tags on a given item are free words chosen by the authors independently. Therefore, the relations among keywords appearing in an on-line data repository are unknown in general. However, in most cases the topics and concepts described by these keywords are forming a latent hierarchy, with the more general topics and categories at the top, and more specialized ones at the bottom. There are several algorithms available for deducing this hierarchy from the statistical features of the keywords. In the present work we apply a recent, co-occurrence-based tag hierarchy extraction method to sets of keywords obtained from four different on-line news portals. The resulting hierarchies show substantial differences not just in the topics rendered as important (being at the top of the hierarchy or of less interest (categorized low in the hierarchy, but also in the underlying network structure. This reveals discrepancies between the plausible keyword association frameworks in the studied news portals.
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Semantator: annotating clinical narratives with semantic web ontologies.
Song, Dezhao; Chute, Christopher G; Tao, Cui
2012-01-01
To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator.
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An integrable coupling system of lattice hierarchy and its continuous limits
International Nuclear Information System (INIS)
Yu Fajun; Li Li
2009-01-01
In [E.G. Fan, Phys. Lett. A 372 (2008) 6368], Fan present a lattice hierarchy and its continuous limits. In this Letter, we extend this method, by introducing a complex discrete spectral problem, a coupling lattice hierarchy is derived. It is shown that a new sequence of combinations of complex lattice spectral problem converges to the integrable coupling couplings of soliton equation hierarchy, which has the integrable coupling system of AKNS hierarchy as a continuous limit.
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A generalized Tu formula and Hamiltonian structures of fractional AKNS hierarchy
International Nuclear Information System (INIS)
Wu, Guo-cheng; Zhang, Sheng
2011-01-01
In this Letter, a generalized Tu formula is firstly presented to construct Hamiltonian structures of fractional soliton equations. The obtained results can be reduced to the classical Hamiltonian hierarchy of AKNS in ordinary calculus. -- Highlights: → A generalized Tu formula is first established based on the fractional variational theory for non-differentiable functions. → Hamiltonian structures of fractional AKNS hierarchy are obtained. → The classical AKNS hierarchy is just a special case of the fractional hierarchy.
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A generalized Tu formula and Hamiltonian structures of fractional AKNS hierarchy
Energy Technology Data Exchange (ETDEWEB)
Wu, Guo-cheng, E-mail: wuguocheng2002@yahoo.com.cn [Key Laboratory of Numerical Simulation of Sichuan Province, Neijiang, Sichuan 641112 (China); College of Mathematics and Information Science, Neijiang Normal University, Neijiang, Sichuan 641112 (China); Zhang, Sheng, E-mail: zhshaeng@yahoo.com.cn [School of Mathematical Sciences, Dalian University of Technology, Dalian 116024 (China)
2011-10-03
In this Letter, a generalized Tu formula is firstly presented to construct Hamiltonian structures of fractional soliton equations. The obtained results can be reduced to the classical Hamiltonian hierarchy of AKNS in ordinary calculus. -- Highlights: → A generalized Tu formula is first established based on the fractional variational theory for non-differentiable functions. → Hamiltonian structures of fractional AKNS hierarchy are obtained. → The classical AKNS hierarchy is just a special case of the fractional hierarchy.
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Continuous limits for an integrable coupling system of Toda equation hierarchy
International Nuclear Information System (INIS)
Li Li; Yu Fajun
2009-01-01
In this Letter, we present an integrable coupling system of lattice hierarchy and its continuous limits by using of Lie algebra sl(4). By introducing a complex discrete spectral problem, the integrable coupling system of Toda lattice hierarchy is derived. It is shown that a new complex lattice spectral problem converges to the integrable couplings of discrete soliton equation hierarchy, which has the integrable coupling system of C-KdV hierarchy as a new kind of continuous limit.
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Continuous limits for an integrable coupling system of Toda equation hierarchy
Energy Technology Data Exchange (ETDEWEB)
Li Li [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China); Yu Fajun, E-mail: yfajun@163.co [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China)
2009-09-21
In this Letter, we present an integrable coupling system of lattice hierarchy and its continuous limits by using of Lie algebra sl(4). By introducing a complex discrete spectral problem, the integrable coupling system of Toda lattice hierarchy is derived. It is shown that a new complex lattice spectral problem converges to the integrable couplings of discrete soliton equation hierarchy, which has the integrable coupling system of C-KdV hierarchy as a new kind of continuous limit.
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A generative model for scientific concept hierarchies.
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.
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A generative model for scientific concept hierarchies
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
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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
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Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.
Letunic, Ivica; Bork, Peer
2011-07-01
Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.
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Ontology modularization to improve semantic medical image annotation.
Wennerberg, Pinar; Schulz, Klaus; Buitelaar, Paul
2011-02-01
Searching for medical images and patient reports is a significant challenge in a clinical setting. The contents of such documents are often not described in sufficient detail thus making it difficult to utilize the inherent wealth of information contained within them. Semantic image annotation addresses this problem by describing the contents of images and reports using medical ontologies. Medical images and patient reports are then linked to each other through common annotations. Subsequently, search algorithms can more effectively find related sets of documents on the basis of these semantic descriptions. A prerequisite to realizing such a semantic search engine is that the data contained within should have been previously annotated with concepts from medical ontologies. One major challenge in this regard is the size and complexity of medical ontologies as annotation sources. Manual annotation is particularly time consuming labor intensive in a clinical environment. In this article we propose an approach to reducing the size of clinical ontologies for more efficient manual image and text annotation. More precisely, our goal is to identify smaller fragments of a large anatomy ontology that are relevant for annotating medical images from patients suffering from lymphoma. Our work is in the area of ontology modularization, which is a recent and active field of research. We describe our approach, methods and data set in detail and we discuss our results. Copyright © 2010 Elsevier Inc. All rights reserved.
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Implications of nonzero θ13 for the neutrino mass hierarchy
International Nuclear Information System (INIS)
Ernst, D J; Cogswell, B K; Burroughs, H R; Escamilla-Roa, J; Latimer, D C
2012-01-01
The Daya Bay, RENO, and Double Chooz experiments have discovered a large non-zero value for θ 13 . We present a global analysis that includes these three experiments, Chooz, the Super-K atmospheric data, and the ν μ → ν e T2K and MINOS experiments that are sensitive to the hierarchy and the sign of θ 13 . We report preliminary results in which we fix the mixing parameters other than θ 13 to those from a recent global analysis. Given there is no evidence for a non-zero CP violation, we assume δ = 0. T2K and MINOS lie in a region of L/E where there is a hierarchy degeneracy in the limit of θ 13 → 0 and no matter interaction. For nonzero θ 13 , the symmetry is partially broken, but a degeneracy under the simultaneous exchange of both hierarchy and the sign of θ 13 remains. Matter effects break this symmetry such that the positions of the peaks in the oscillation probabilities maintain the two-fold symmetry, while the magnitude of the oscillations is sensitive to the hierarchy. This renders T2K and NOvA, with different baselines and different matter effects, better able in combination to distinguish the hierarchy and the sign of θ 13 . The present T2K and MINOS data do not distinguish between hierarchies or the sign of θ 13 , but the large value of θ 13 yields effects from atmospheric data that do. We find for normal hierarchy, positive θ 13 , sin 2 2θ 13 = 0.090 ± 0.020 and is 0.2% probable it is the correct combination; for normal hierarchy, negative θ 13 , sin 2 2θ 13 = 0.108 ± 0.023 and is 2.2% probable; for inverse hierarchy, positive θ 13 , sin 2 2θ 13 = 0.110±0.022 and is 7.1% probable; for inverse hierarchy, negative θ 13 , sin 2 2θ 13 = 0.113 ± 0.022 and is 90.5% probable, results that are inconsistent with two similar analyses.
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Two hierarchies of integrable lattice equations associated with a discrete matrix spectral problem
International Nuclear Information System (INIS)
Li Xinyue; Xu Xixiang; Zhao Qiulan
2008-01-01
Two hierarchies of nonlinear integrable positive and negative lattice models are derived from a discrete spectral problem. The two lattice hierarchies are proved to have discrete zero curvature representations associated with a discrete spectral problem, which also shows that the positive and negative hierarchies correspond to positive and negative power expansions of Lax operators with respect to the spectral parameter, respectively. Moreover, the integrable lattice models in the positive hierarchy are of polynomial type, and the integrable lattice models in the negative hierarchy are of rational type. Further, we construct infinite conservation laws of the positive hierarchy, then, the integrable coupling systems of the positive hierarchy are derived from enlarging Lax pair
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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 ...
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Hierarchy Measure for Complex Networks
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
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[Prescription annotations in Welfare Pharmacy].
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.
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A framework for annotating human genome in disease context.
Xu, Wei; Wang, Huisong; Cheng, Wenqing; Fu, Dong; Xia, Tian; Kibbe, Warren A; Lin, Simon M
2012-01-01
Identification of gene-disease association is crucial to understanding disease mechanism. A rapid increase in biomedical literatures, led by advances of genome-scale technologies, poses challenge for manually-curated-based annotation databases to characterize gene-disease associations effectively and timely. We propose an automatic method-The Disease Ontology Annotation Framework (DOAF) to provide a comprehensive annotation of the human genome using the computable Disease Ontology (DO), the NCBO Annotator service and NCBI Gene Reference Into Function (GeneRIF). DOAF can keep the resulting knowledgebase current by periodically executing automatic pipeline to re-annotate the human genome using the latest DO and GeneRIF releases at any frequency such as daily or monthly. Further, DOAF provides a computable and programmable environment which enables large-scale and integrative analysis by working with external analytic software or online service platforms. A user-friendly web interface (doa.nubic.northwestern.edu) is implemented to allow users to efficiently query, download, and view disease annotations and the underlying evidences.
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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
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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. .
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Annotating abstract pronominal anaphora in the DAD project
DEFF Research Database (Denmark)
Navarretta, Costanza; Olsen, Sussi Anni
2008-01-01
n this paper we present an extension of the MATE/GNOME annotation scheme for anaphora (Poesio 2004) which accounts for abstract anaphora in Danish and Italian. By abstract anaphora it is here meant pronouns whose linguistic antecedents are verbal phrases, clauses and discourse segments. The exten......n this paper we present an extension of the MATE/GNOME annotation scheme for anaphora (Poesio 2004) which accounts for abstract anaphora in Danish and Italian. By abstract anaphora it is here meant pronouns whose linguistic antecedents are verbal phrases, clauses and discourse segments....... The extended scheme, which we call the DAD annotation scheme, allows to annotate information about abstract anaphora which is important to investigate their use, see Webber (1988), Gundel et al. (2003), Navarretta (2004) and which can influence their automatic treatment. Intercoder agreement scores obtained...... by applying the DAD annotation scheme on texts and dialogues in the two languages are given and show that th information proposed in the scheme can be recognised in a reliable way....
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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
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Supporting Keyword Search for Image Retrieval with Integration of Probabilistic Annotation
Directory of Open Access Journals (Sweden)
Tie Hua Zhou
2015-05-01
Full Text Available The ever-increasing quantities of digital photo resources are annotated with enriching vocabularies to form semantic annotations. Photo-sharing social networks have boosted the need for efficient and intuitive querying to respond to user requirements in large-scale image collections. In order to help users formulate efficient and effective image retrieval, we present a novel integration of a probabilistic model based on keyword query architecture that models the probability distribution of image annotations: allowing users to obtain satisfactory results from image retrieval via the integration of multiple annotations. We focus on the annotation integration step in order to specify the meaning of each image annotation, thus leading to the most representative annotations of the intent of a keyword search. For this demonstration, we show how a probabilistic model has been integrated to semantic annotations to allow users to intuitively define explicit and precise keyword queries in order to retrieve satisfactory image results distributed in heterogeneous large data sources. Our experiments on SBU (collected by Stony Brook University database show that (i our integrated annotation contains higher quality representatives and semantic matches; and (ii the results indicating annotation integration can indeed improve image search result quality.
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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
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Gauge theories, duality relations and the tensor hierarchy
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
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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...
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A Bayesian Sampler for Optimization of Protein Domain Hierarchies
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
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Lahiani, Amal; Klaiman, Eldad; Grimm, Oliver
2018-01-01
Medical diagnosis and clinical decisions rely heavily on the histopathological evaluation of tissue samples, especially in oncology. Historically, classical histopathology has been the gold standard for tissue evaluation and assessment by pathologists. The most widely and commonly used dyes in histopathology are hematoxylin and eosin (H&E) as most malignancies diagnosis is largely based on this protocol. H&E staining has been used for more than a century to identify tissue characteristics and structures morphologies that are needed for tumor diagnosis. In many cases, as tissue is scarce in clinical studies, fluorescence imaging is necessary to allow staining of the same specimen with multiple biomarkers simultaneously. Since fluorescence imaging is a relatively new technology in the pathology landscape, histopathologists are not used to or trained in annotating or interpreting these images. To allow pathologists to annotate these images without the need for additional training, we designed an algorithm for the conversion of fluorescence images to brightfield H&E images. In this algorithm, we use fluorescent nuclei staining to reproduce the hematoxylin information and natural tissue autofluorescence to reproduce the eosin information avoiding the necessity to specifically stain the proteins or intracellular structures with an additional fluorescence stain. Our method is based on optimizing a transform function from fluorescence to H&E images using least mean square optimization. It results in high quality virtual H&E digital images that can easily and efficiently be analyzed by pathologists. We validated our results with pathologists by making them annotate tumor in real and virtual H&E whole slide images and we obtained promising results. Hence, we provide a solution that enables pathologists to assess tissue and annotate specific structures based on multiplexed fluorescence images.
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Directory of Open Access Journals (Sweden)
Amal Lahiani
2018-01-01
Full Text Available Context: Medical diagnosis and clinical decisions rely heavily on the histopathological evaluation of tissue samples, especially in oncology. Historically, classical histopathology has been the gold standard for tissue evaluation and assessment by pathologists. The most widely and commonly used dyes in histopathology are hematoxylin and eosin (H&E as most malignancies diagnosis is largely based on this protocol. H&E staining has been used for more than a century to identify tissue characteristics and structures morphologies that are needed for tumor diagnosis. In many cases, as tissue is scarce in clinical studies, fluorescence imaging is necessary to allow staining of the same specimen with multiple biomarkers simultaneously. Since fluorescence imaging is a relatively new technology in the pathology landscape, histopathologists are not used to or trained in annotating or interpreting these images. Aims, Settings and Design: To allow pathologists to annotate these images without the need for additional training, we designed an algorithm for the conversion of fluorescence images to brightfield H&E images. Subjects and Methods: In this algorithm, we use fluorescent nuclei staining to reproduce the hematoxylin information and natural tissue autofluorescence to reproduce the eosin information avoiding the necessity to specifically stain the proteins or intracellular structures with an additional fluorescence stain. Statistical Analysis Used: Our method is based on optimizing a transform function from fluorescence to H&E images using least mean square optimization. Results: It results in high quality virtual H&E digital images that can easily and efficiently be analyzed by pathologists. We validated our results with pathologists by making them annotate tumor in real and virtual H&E whole slide images and we obtained promising results. Conclusions: Hence, we provide a solution that enables pathologists to assess tissue and annotate specific structures
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Supplementary Material for: BEACON: automated tool for Bacterial GEnome Annotation ComparisON
Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.
2015-01-01
Abstract 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 BEACONâ 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 27Â %, 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/ .
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The Development of Hierarchy of Effects Model in Advertising
Directory of Open Access Journals (Sweden)
Bambang Sukma Wijaya
2012-04-01
Full Text Available This paper aims to review the hierarchy of effects models in adverti-sing, especially the well-known model, AIDA (Attention, Interest, De-sire, and Action. Since its introduction by Lewis (1900 and generally attributed in the marketing and advertising literature by Strong (1925, the concept of AIDA’s hierarchy of effects model has been used by many researchers, both academicians and practitioners. The model is used to measure the effect of an advertisement. However, the deve-lopment of information technology has radically changed the way of how people communicate and socialize; as well as a paradigm shift from product-oriented marketing to consumer-oriented marketing or people-oriented marketing. Therefore, the variables in the hierarchy of effects model needs to be updated in respond to the latest develop-ments in the notice of public power as consumer audience. Based on deep literature review and reflective method, this paper introduces a new developed concept of hierarchy of effects model that was adop-ted from AIDA’s hierarchy of effects model, namely: AISDALSLove (At-tention, Interest, Search, Desire, Action, Like/dislike, Share, and Love/hate.
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International Nuclear Information System (INIS)
Li Xinyue; Zhao Qiulan
2009-01-01
Two hierarchies of nonlinear integrable positive and negative lattice equations are derived from a discrete spectral problem. The two lattice hierarchies are proved to have discrete zero curvature representations associated with a discrete spectral problem, which also shows that the positive and negative hierarchies correspond to positive and negative power expansions of Lax operators with respect to the spectral parameter, respectively. Moreover, the integrable lattice models in the positive hierarchy are of polynomial type, and the integrable lattice models in the negative hierarchy are of rational type. Further, we construct infinite conservation laws about the positive hierarchy.
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A Global Mitigation Hierarchy for Nature Conservation
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
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Flexible scheme to truncate the hierarchy of pure 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.
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Flexible scheme to truncate the hierarchy of pure 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.
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Extending eScience Provenance with User-Submitted Semantic Annotations
Michaelis, J.; Zednik, S.; West, P.; Fox, P. A.; McGuinness, D. L.
2010-12-01
eScience based systems generate provenance of their data products, related to such things as: data processing, data collection conditions, expert evaluation, and data product quality. Recent advances in web-based technology offer users the possibility of making annotations to both data products and steps in accompanying provenance traces, thereby expanding the utility of such provenance for others. These contributing users may have varying backgrounds, ranging from system experts to outside domain experts to citizen scientists. Furthermore, such users may wish to make varying types of annotations - ranging from documenting the purpose of a provenance step to raising concerns about the quality of data dependencies. Semantic Web technologies allow for such kinds of rich annotations to be made to provenance through the use of ontology vocabularies for (i) organizing provenance, and (ii) organizing user/annotation classifications. Furthermore, through Linked Data practices, Semantic linkages may be made from provenance steps to external data of interest. A desire for Semantically-annotated provenance has been motivated by data management issues in the Mauna Loa Solar Observatory’s (MLSO) Advanced Coronal Observing System (ACOS). In ACOS, photomoeter-based readings are taken of solar activity and subsequently processed into final data products consumable by end users. At intermediate stages of ACOS processing, factors such as evaluations by human experts and weather conditions are logged, which could impact data product quality. If such factors are linked via user-submitted annotations to provenance, it could be significantly beneficial for other users. Likewise, the background of a user could impact the credibility of their annotations. For example, an annotation made by a citizen scientist describing the purpose of a provenance step may not be as reliable as a similar annotation made by an ACOS project member. For this work, we have developed a software package that
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Harnessing Collaborative Annotations on Online Formative Assessments
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…
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Symmetries of integrable hierarchies and matrix model constraints
International Nuclear Information System (INIS)
Vos, K. de
1992-01-01
The orbit construction associates a soliton hierarchy to every level-one vertex realization of a simply laced affine Kac-Moody algebra g. We show that the τ-function of such a hierarchy has the (truncated) Virasoro algebra as an algebra of infinitesimal symmetry transformations. To prove this we use an appropriate bilinear form of these hierarchies together with the coset construction of conformal field theory. For A 1 (1) the orbit construction gives either the Toda or the KdV hierarchy. These both occur in the one-matrix model of two-dimensional quantum gravity, before and after the double scaling limit respectively. The truncated Virasoro symmetry algebra is exactly the algebra of constraints of the one-matrix model. The partition function of the one-matrix model is therefore an invariant τ-function. We also consider the case of A 1 (1) with l>1. Surprisingly, the symmetry algebra in that case is not simply a truncated Casimir algebra. It appears that again only the Virasoro symmetry survives. We speculate on the relation with multi-matrix models. (orig.)
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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...
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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.
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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.
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Directory of Open Access Journals (Sweden)
Christie-Oleza Joseph A
2012-02-01
Full Text Available Abstract Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera, we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase
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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)
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CAUSAL INFERENCE WITH A GRAPHICAL HIERARCHY OF INTERVENTIONS.
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.
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Friesen, Justin P; Kay, Aaron C; Eibach, Richard P; Galinsky, Adam D
2014-04-01
Hierarchies are a ubiquitous form of human social organization. We hypothesized that 1 reason for the prevalence of hierarchies is that they offer structure and therefore satisfy the core motivational needs for order and control relative to less structured forms of social organization. This hypothesis is rooted in compensatory control theory, which posits that (a) individuals have a basic need to perceive the world as orderly and structured, and (b) personal and external sources of control are capable of satisfying this need because both serve the comforting belief that the world operates in an orderly fashion. Our first 2 studies confirmed that hierarchies were perceived as more structured and orderly relative to egalitarian arrangements (Study 1) and that working in a hierarchical workplace promotes a feeling of self-efficacy (Study 2). We threatened participants' sense of personal control and measured perceptions of and preferences for hierarchy in 5 subsequent experiments. Participants who lacked control perceived more hierarchy occurring in ambiguous social situations (Study 3) and preferred hierarchy more strongly in workplace contexts (Studies 4-5). We also provide evidence that hierarchies are indeed appealing because of their structure: Preference for hierarchy was higher among individuals high in Personal Need for Structure and a control threat increased preference for hierarchy even among participants low in Personal Need for Structure (Study 5). Framing a hierarchy as unstructured reversed the effect of control threat on hierarchy (Study 6). Finally, hierarchy-enhancing jobs were more appealing after control threat, even when they were low in power and status (Study 7). (PsycINFO Database Record (c) 2014 APA, all rights reserved).
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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...
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Towards Interactive Construction of Topical Hierarchy: A Recursive Tensor Decomposition Approach.
Wang, Chi; Liu, Xueqing; Song, Yanglei; Han, Jiawei
2015-08-01
Automatic construction of user-desired topical hierarchies over large volumes of text data is a highly desirable but challenging task. This study proposes to give users freedom to construct topical hierarchies via interactive operations such as expanding a branch and merging several branches. Existing hierarchical topic modeling techniques are inadequate for this purpose because (1) they cannot consistently preserve the topics when the hierarchy structure is modified; and (2) the slow inference prevents swift response to user requests. In this study, we propose a novel method, called STROD, that allows efficient and consistent modification of topic hierarchies, based on a recursive generative model and a scalable tensor decomposition inference algorithm with theoretical performance guarantee. Empirical evaluation shows that STROD reduces the runtime of construction by several orders of magnitude, while generating consistent and quality hierarchies.
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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.
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Materials with structural hierarchy
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.
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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
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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.
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A hierarchy of time-scales and the brain.
Kiebel, Stefan J; Daunizeau, Jean; Friston, Karl J
2008-11-01
In this paper, we suggest that cortical anatomy recapitulates the temporal hierarchy that is inherent in the dynamics of environmental states. Many aspects of brain function can be understood in terms of a hierarchy of temporal scales at which representations of the environment evolve. The lowest level of this hierarchy corresponds to fast fluctuations associated with sensory processing, whereas the highest levels encode slow contextual changes in the environment, under which faster representations unfold. First, we describe a mathematical model that exploits the temporal structure of fast sensory input to track the slower trajectories of their underlying causes. This model of sensory encoding or perceptual inference establishes a proof of concept that slowly changing neuronal states can encode the paths or trajectories of faster sensory states. We then review empirical evidence that suggests that a temporal hierarchy is recapitulated in the macroscopic organization of the cortex. This anatomic-temporal hierarchy provides a comprehensive framework for understanding cortical function: the specific time-scale that engages a cortical area can be inferred by its location along a rostro-caudal gradient, which reflects the anatomical distance from primary sensory areas. This is most evident in the prefrontal cortex, where complex functions can be explained as operations on representations of the environment that change slowly. The framework provides predictions about, and principled constraints on, cortical structure-function relationships, which can be tested by manipulating the time-scales of sensory input.
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A hierarchy of time-scales and the brain.
Directory of Open Access Journals (Sweden)
Stefan J Kiebel
2008-11-01
Full Text Available In this paper, we suggest that cortical anatomy recapitulates the temporal hierarchy that is inherent in the dynamics of environmental states. Many aspects of brain function can be understood in terms of a hierarchy of temporal scales at which representations of the environment evolve. The lowest level of this hierarchy corresponds to fast fluctuations associated with sensory processing, whereas the highest levels encode slow contextual changes in the environment, under which faster representations unfold. First, we describe a mathematical model that exploits the temporal structure of fast sensory input to track the slower trajectories of their underlying causes. This model of sensory encoding or perceptual inference establishes a proof of concept that slowly changing neuronal states can encode the paths or trajectories of faster sensory states. We then review empirical evidence that suggests that a temporal hierarchy is recapitulated in the macroscopic organization of the cortex. This anatomic-temporal hierarchy provides a comprehensive framework for understanding cortical function: the specific time-scale that engages a cortical area can be inferred by its location along a rostro-caudal gradient, which reflects the anatomical distance from primary sensory areas. This is most evident in the prefrontal cortex, where complex functions can be explained as operations on representations of the environment that change slowly. The framework provides predictions about, and principled constraints on, cortical structure-function relationships, which can be tested by manipulating the time-scales of sensory input.
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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.)
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The Theory of Ratio Scale Estimation: Saaty's Analytic Hierarchy Process
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...
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Towards Lax Formulation of Integrable Hierarchies of Topological Type
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
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Towards Lax Formulation of Integrable Hierarchies of Topological Type
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
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Optimal City Hierarchy: A Dynamic Programming Approach to Central Place Theory
Wen-Tai Hsu; Thomas J. Holmes
2009-01-01
It is an empirically plausible description of cities and is route to explain empirical regularities in city size distribution and industrial locations. This paper formalizes central place hierarchy by providing a rationale for it via a social planner's problem. The optimal city hierarchy is then compared with the equilibrium city hierarchy in Hsu (2008).
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Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes
Energy Technology Data Exchange (ETDEWEB)
Kuo, Alan; Grigoriev, Igor
2009-04-17
Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.
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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.
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Darboux transformation and soliton solutions for the Boiti-Pempinelli-Tu (BPT) hierarchy
International Nuclear Information System (INIS)
Wang Jiong
2005-01-01
Starting from a spectral problem, we derive the well-known Boiti-Pempinelli-Tu (BPT) hierarchy. An explicit and universal Darboux transformation for the whole hierarchy is constructed. The soliton solutions for the BPT hierarchy are obtained by applying the Darboux transformation
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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....
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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...
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Supersymmetric KP hierarchy in N=1 superspace and its N=2 reductions
International Nuclear Information System (INIS)
Lechtenfeld, O.; Sorin, A.
2000-01-01
A wide class of N=2 reductions of the supersymmetric KP hierarchy in N=1 superspace is described. This class includes a new N=2 supersymmetric generalization of the Toda chain hierarchy. The Lax pair representations of the bosonic and fermionic flows, local and non-local Hamiltonians, finite and infinite discrete symmetries, first two Hamiltonian structures and the recursion operator of this hierarchy are constructed. Its secondary reduction to new N=2 supersymmetric modified KdV hierarchy is discussed
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Supersymmetric KP hierarchy in N=1 superspace and its N=2 reductions
International Nuclear Information System (INIS)
Lechtenfeld, O.; Sorin, A.
1999-01-01
A wide class of N=2 reductions of the supersymmetric KP hierarchy in N=1 superspace is described. This class includes a new N=2 supersymmetric generalization of the Toda chain hierarchy. The Lax pair representations of the bosonic and fermionic flows, local and nonlocal Hamiltonians, finite and infinite discrete symmetries, first two Hamiltonian structures and the recursion operator of this hierarchy are constructed. Its secondary reduction to new N=2 supersymmetric modified KdV hierarchy is discussed
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Neutrino mass hierarchy determination via atmospheric neutrinos with future detectors
International Nuclear Information System (INIS)
Gandhi, Raj; Ghoshal, Pomita; Goswami, Srubabati; Mehta, Poonam; Sankar, S Uma; Shalgar, Shashank
2008-01-01
The issue of determining the neutrino mass hierarchy is one of the outstanding questions in neutrino physics. We consider the potential of hierarchy determination using atmospheric neutrinos as the source in three different proposed future detectors: A large Iron Calorimeter detector, a megaton Water Cerenkov detector and a large-mass Liquid Argon detector. If the mixing angle θ 13 is about 10 deg. (close to CHOOZ upper bound), the hierarchy sensitivity is essentially determined by resonant matter effects. To maximize the potential of these effects in atmospheric neutrinos, charge discrimination capability in the detector is desirable. Hence, detectors with this capability have an advantage in hierarchy determination. We compare and contrast the performance of the above three detectors in this respect. We perform a realistic analysis of the above future detectors for atmospheric neutrinos and show that it is possible to achieve a significant hierarchy sensitivity if the detector characteristics are favourable. Note: The abstract has been modified from its original form to incorporate suggestions received during the conference. The poster is being submitted in its original form.
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Matrix integral solutions to the discrete KP hierarchy and its Pfaffianized version
International Nuclear Information System (INIS)
Lafortune, Stéphane; Li, Chun-Xia
2016-01-01
Matrix integrals used in random matrix theory for the study of eigenvalues of Hermitian ensembles have been shown to provide τ -functions for several hierarchies of integrable equations. In this article, we extend this relation by showing that such integrals can also provide τ -functions for the discrete KP hierarchy and a coupled version of the same hierarchy obtained through the process of Pfaffianization. To do so, we consider the first equation of the discrete KP hierarchy, the Hirota–Miwa equation. We write the Wronskian determinant solutions to the Hirota–Miwa equation and consider a particular form of matrix integrals, which we show is an example of those Wronskian solutions. The argument is then generalized to the whole hierarchy. A similar strategy is used for the Pfaffianized version of the hierarchy except that in that case, the solutions are written in terms of Pfaffians rather than determinants. (paper)
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Humans mimicking animals: A cortical hierarchy for human vocal communication sounds
Talkington, William J.; Rapuano, Kristina M.; Hitt, Laura; Frum, Chris A.; Lewis, James W.
2012-01-01
Numerous species possess cortical regions that are most sensitive to vocalizations produced by their own kind (conspecifics). In humans, the superior temporal sulci (STS) putatively represent homologous voice-sensitive areas of cortex. However, STS regions have recently been reported to represent auditory experience or “expertise” in general rather than showing exclusive sensitivity to human vocalizations per se. Using functional magnetic resonance imaging and a unique non-stereotypical category of complex human non-verbal vocalizations – human-mimicked versions of animal vocalizations – we found a cortical hierarchy in humans optimized for processing meaningful conspecific utterances. This left-lateralized hierarchy originated near primary auditory cortices and progressed into traditional speech-sensitive areas. These results suggest that the cortical regions supporting vocalization perception are initially organized by sensitivity to the human vocal tract in stages prior to the STS. Additionally, these findings have implications for the developmental time course of conspecific vocalization processing in humans as well as its evolutionary origins. PMID:22674283
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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.
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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.
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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
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Model and Interoperability using Meta Data Annotations
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
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Black English Annotations for Elementary Reading Programs.
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…
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Special Issue: Annotated Bibliography for Volumes XIX-XXXII.
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)
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MetaStorm: A Public Resource for Customizable Metagenomics Annotation.
Directory of Open Access Journals (Sweden)
Gustavo Arango-Argoty
Full Text Available Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/, which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.
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MetaStorm: A Public Resource for Customizable Metagenomics Annotation.
Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing
2016-01-01
Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution.
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MIPS: analysis and annotation of genome information in 2007.
Mewes, H W; Dietmann, S; Frishman, D; Gregory, R; Mannhaupt, G; Mayer, K F X; Münsterkötter, M; Ruepp, A; Spannagl, M; Stümpflen, V; Rattei, T
2008-01-01
The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).
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MetaStorm: A Public Resource for Customizable Metagenomics Annotation
Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing
2016-01-01
Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579
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Improving Microbial Genome Annotations in an Integrated Database Context
Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.
2013-01-01
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620
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Improving microbial genome annotations in an integrated database context.
Directory of Open Access Journals (Sweden)
I-Min A Chen
Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.
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SUSY-hierarchy of one-dimensional reflectionless potentials
Maydanyuk, Sergei P
2004-01-01
A class of one-dimensional reflectionless potentials, an absolute transparency of which is concerned with their belonging to one SUSY-hierarchy with a constant potential, is studied. An approach for determination of a general form of the reflectionless potential on the basis of construction of such a hierarchy by the recurrent method is proposed. A general form of interdependence between superpotentials with neighboring numbers of this hierarchy, opening a possibility to find new reflectionless potentials, have a simple analytical view and are expressed through finite number of elementary functions (unlike some reflectionless potentials, which are constructed on the basis of soliton solutions or are shape invariant in one or many steps with involving scaling of parameters, and are expressed through series), is obtained. An analysis of absolute transparency existence for the potential which has the inverse power dependence on space coordinate (and here tunneling is possible), i.e. which has the form $V(x) = \\p...
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The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
Profiti, Giuseppe; Martelli, Pier Luigi; Casadio, Rita
2017-07-03
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints. BAR 3.0 includes 28 869 663 sequences in 1 361 773 clusters, of which 22.2% (22 241 661 sequences) and 47.4% (24 555 055 sequences) have at least one validated GO term and one PFAM domain, respectively. 1.4% of the clusters (36% of all sequences) include PDB structures and the cluster is associated to a hidden Markov model that allows building template-target alignment suitable for structural modeling. Some other 3 399 026 sequences are singletons. BAR 3.0 offers an improved search interface, allowing queries by UniProtKB-accession, Fasta sequence, GO-term, PFAM-domain, organism, PDB and ligand/s. When evaluated on the CAFA2 targets, BAR 3.0 largely outperforms our previous version and scores among state-of-the-art methods. BAR 3.0 is publicly available and accessible at http://bar.biocomp.unibo.it/bar3. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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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.
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Annotating images by mining image search results.
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.
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Collaborative Paper-Based Annotation of Lecture Slides
Steimle, Jurgen; Brdiczka, Oliver; Muhlhauser, Max
2009-01-01
In a study of notetaking in university courses, we found that the large majority of students prefer paper to computer-based media like Tablet PCs for taking notes and making annotations. Based on this finding, we developed CoScribe, a concept and system which supports students in making collaborative handwritten annotations on printed lecture…
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Music journals in South Africa 1854-2010: an annotated bibliography
African Journals Online (AJOL)
Music journals in South Africa 1854-2010: an annotated bibliography. ... The article focuses on presenting an annotated bibliography of music journalism in South Africa from as early as 1854 until 2010. Most of ... Key words: annotated bibliography, electronic journals, music journals, periodicals, South African music history ...
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Behavior-aware cache hierarchy optimization for low-power multi-core embedded systems
Zhao, Huatao; Luo, Xiao; Zhu, Chen; Watanabe, Takahiro; Zhu, Tianbo
2017-07-01
In modern embedded systems, the increasing number of cores requires efficient cache hierarchies to ensure data throughput, but such cache hierarchies are restricted by their tumid size and interference accesses which leads to both performance degradation and wasted energy. In this paper, we firstly propose a behavior-aware cache hierarchy (BACH) which can optimally allocate the multi-level cache resources to many cores and highly improved the efficiency of cache hierarchy, resulting in low energy consumption. The BACH takes full advantage of the explored application behaviors and runtime cache resource demands as the cache allocation bases, so that we can optimally configure the cache hierarchy to meet the runtime demand. The BACH was implemented on the GEM5 simulator. The experimental results show that energy consumption of a three-level cache hierarchy can be saved from 5.29% up to 27.94% compared with other key approaches while the performance of the multi-core system even has a slight improvement counting in hardware overhead.
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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
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Plann: A command-line application for annotating plastome sequences1
Huang, Daisie I.; Cronk, Quentin C. B.
2015-01-01
Premise of the study: 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. Methods and Results: 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. Conclusions: 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. PMID:26312193
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Non-Hamiltonian generalizations of the dispersionless 2DTL hierarchy
International Nuclear Information System (INIS)
Bogdanov, L V
2010-01-01
We consider two-component integrable generalizations of the dispersionless two-dimensional Toda lattice (2DTL) hierarchy connected with non-Hamiltonian vector fields, similar to the Manakov-Santini hierarchy generalizing the dKP hierarchy. They form a one-parametric family connected by hodograph-type transformations. Generating equations and Lax-Sato equations are introduced, and a dressing scheme based on the vector nonlinear Riemann problem is formulated. The simplest two-component generalization of the dispersionless 2DTL equation is derived, and its differential reduction analogous to the Dunajski interpolating system is presented. A symmetric two-component generalization of the dispersionless elliptic 2DTL equation is also constructed.
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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...
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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...
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A Second Look at Maslow's Hierarchy of Basic Needs.
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)…
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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.
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Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian
2017-01-01
Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
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Directory of Open Access Journals (Sweden)
Claas-Thido Pfaff
Full Text Available Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
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Yim, Soorin; Yu, Hasun; Jang, Dongjin; Lee, Doheon
2018-04-11
Signaling pathways can be reconstructed by identifying 'effect types' (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of 'directions' (i.e. upstream/downstream) and 'signs' (i.e. positive/negative), thereby requiring directions as well as signs of PPIs to predict signaling events from PPI networks. Here, we propose a computational method for systemically annotating effect types to PPIs using relations between functional information of proteins. We used regulates, positively regulates, and negatively regulates relations in Gene Ontology (GO) to predict directions and signs of PPIs. These relations indicate both directions and signs between GO terms so that we can project directions and signs between relevant GO terms to PPIs. Independent test results showed that our method is effective for predicting both directions and signs of PPIs. Moreover, our method outperformed a previous GO-based method that did not consider the relations between GO terms. We annotated effect types to human PPIs and validated several highly confident effect types against literature. The annotated human PPIs are available in Additional file 2 to aid signaling pathway reconstruction and network biology research. We annotated effect types to PPIs by using regulates, positively regulates, and negatively regulates relations in GO. We demonstrated that those relations are effective for predicting not only signs, but also directions of PPIs. The usefulness of those relations suggests their potential applications to other types of interactions such as protein-DNA interactions.
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A Clifford algebra approach to chiral symmetry breaking and fermion mass hierarchies
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.
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Fear, Justin M; Arbeitman, Michelle N; Salomon, Matthew P; Dalton, Justin E; Tower, John; Nuzhdin, Sergey V; McIntyre, Lauren M
2015-09-04
The Drosophila sex determination hierarchy is a classic example of a transcriptional regulatory hierarchy, with sex-specific isoforms regulating morphology and behavior. We use a structural equation modeling approach, leveraging natural genetic variation from two studies on Drosophila female head tissues--DSPR collection (596 F1-hybrids from crosses between DSPR sub-populations) and CEGS population (75 F1-hybrids from crosses between DGRP/Winters lines to a reference strain w1118)--to expand understanding of the sex hierarchy gene regulatory network (GRN). This approach is completely generalizable to any natural population, including humans. We expanded the sex hierarchy GRN adding novel links among genes, including a link from fruitless (fru) to Sex-lethal (Sxl) identified in both populations. This link is further supported by the presence of fru binding sites in the Sxl locus. 754 candidate genes were added to the pathway, including the splicing factors male-specific lethal 2 and Rm62 as downstream targets of Sxl which are well-supported links in males. Independent studies of doublesex and transformer mutants support many additions, including evidence for a link between the sex hierarchy and metabolism, via Insulin-like receptor. The genes added in the CEGS population were enriched for genes with sex-biased splicing and components of the spliceosome. A common goal of molecular biologists is to expand understanding about regulatory interactions among genes. Using natural alleles we can not only identify novel relationships, but using supervised approaches can order genes into a regulatory hierarchy. Combining these results with independent large effect mutation studies, allows clear candidates for detailed molecular follow-up to emerge.
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A Discrete Spectral Problem and Related Hierarchy of Discrete Hamiltonian Lattice Equations
International Nuclear Information System (INIS)
Xu Xixiang; Cao Weili
2007-01-01
Staring from a discrete matrix spectral problem, a hierarchy of lattice soliton equations is presented though discrete zero curvature representation. The resulting lattice soliton equations possess non-local Lax pairs. The Hamiltonian structures are established for the resulting hierarchy by the discrete trace identity. Liouville integrability of resulting hierarchy is demonstrated.
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Annotating Logical Forms for EHR Questions.
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.
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Managing and Querying Image Annotation and Markup in XML.
Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel
2010-01-01
Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.
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Managing and Querying Image Annotation and Markup in XML
Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel
2010-01-01
Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167
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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
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Feng, Chunliang; Tian, Tengxiang; Feng, Xue; Luo, Yue-Jia
2015-04-01
Recent behavioral and neuroscientific studies have revealed the preferential processing of superior-hierarchy cues. However, it remains poorly understood whether top-down controlled mechanisms modulate temporal dynamics of neurocognitive substrates underlying the preferential processing of these biologically and socially relevant cues. This was investigated in the current study by recording event-related potentials from participants who were presented with superior or inferior social hierarchy. Participants performed a hierarchy-judgment task that required attention to hierarchy cues or a gender-judgment task that withdrew their attention from these cues. Superior-hierarchy cues evoked stronger neural responses than inferior-hierarchy cues at both early (N170/N200) and late (late positive potential, LPP) temporal stages. Notably, the modulations of top-down attention were identified on the LPP component, such that superior-hierarchy cues evoked larger LPP amplitudes than inferior-hierarchy cues only in the attended condition; whereas the modulations of the N170/N200 component by hierarchy cues were evident in both attended and unattended conditions. These findings suggest that the preferential perception of superior-hierarchy cues involves both relatively automatic attentional bias at the early temporal stage as well as flexible and voluntary cognitive evaluation at the late temporal stage. Finally, these hierarchy-related effects were absent when participants were shown the same stimuli which, however, were not associated with social-hierarchy information in a non-hierarchy task (Experiment 2), suggesting that effects of social hierarchy at early and late temporal stages could not be accounted for by differences in physical attributes between these social cues. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images
Directory of Open Access Journals (Sweden)
Jianfang Cao
2015-01-01
Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.
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New Integrable Couplings of Generalized Kaup-Newell Hierarchy and Its Hamiltonian Structures
International Nuclear Information System (INIS)
Xia Tiecheng; Zhang Gailian; Fan Engui
2011-01-01
A new isospectral problem is firstly presented, then we derive integrable system of soliton hierarchy. Also we obtain new integrable couplings of the generalized Kaup-Newell soliton equations hierarchy and its Hamiltonian structures by using Tu scheme and the quadratic-form identity. The method can be generalized to other soliton hierarchy. (general)
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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.
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Ten steps to get started in Genome Assembly and Annotation
Dominguez Del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella-Gutierrez, Salvadors; Notredame, Cederic; Vinnere Pettersson, Olga; Amselem, Joelle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-Francois; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchal, Mahesh; Lantz, Henrik
2018-01-01
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR). PMID:29568489
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Sharing Map Annotations in Small Groups: X Marks the Spot
Congleton, Ben; Cerretani, Jacqueline; Newman, Mark W.; Ackerman, Mark S.
Advances in location-sensing technology, coupled with an increasingly pervasive wireless Internet, have made it possible (and increasingly easy) to access and share information with context of one’s geospatial location. We conducted a four-phase study, with 27 students, to explore the practices surrounding the creation, interpretation and sharing of map annotations in specific social contexts. We found that annotation authors consider multiple factors when deciding how to annotate maps, including the perceived utility to the audience and how their contributions will reflect on the image they project to others. Consumers of annotations value the novelty of information, but must be convinced of the author’s credibility. In this paper we describe our study, present the results, and discuss implications for the design of software for sharing map annotations.
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Strong Bayesian evidence for the normal neutrino hierarchy
Energy Technology Data Exchange (ETDEWEB)
Simpson, Fergus; Jimenez, Raul; Verde, Licia [ICCUB, University of Barcelona (UB-IEEC), Marti i Franques 1, Barcelona, 08028 (Spain); Pena-Garay, Carlos, E-mail: fergus2@gmail.com, E-mail: raul.jimenez@icc.ub.edu, E-mail: penagaray@gmail.com, E-mail: liciaverde@icc.ub.edu [I2SysBio, CSIC-UVEG, P.O. 22085, Valencia, 46071 (Spain)
2017-06-01
The configuration of the three neutrino masses can take two forms, known as the normal and inverted hierarchies. We compute the Bayesian evidence associated with these two hierarchies. Previous studies found a mild preference for the normal hierarchy, and this was driven by the asymmetric manner in which cosmological data has confined the available parameter space. Here we identify the presence of a second asymmetry, which is imposed by data from neutrino oscillations. By combining constraints on the squared-mass splittings [1] with the limit on the sum of neutrino masses of Σ m {sub ν} < 0.13 eV [2], and using a minimally informative prior on the masses, we infer odds of 42:1 in favour of the normal hierarchy, which is classified as 'strong' in the Jeffreys' scale. We explore how these odds may evolve in light of higher precision cosmological data, and discuss the implications of this finding with regards to the nature of neutrinos. Finally the individual masses are inferred to be m {sub 1}=3.80{sup +26.2}{sub -3.73}meV; m {sub 2}=8.8{sup +18}{sub -1.2}meV; m {sub 3}=50.4{sup +5.8}{sub -1.2}meV (95% credible intervals).
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Nehrlich, Andreas D; Gebauer, Jochen E; Sedikides, Constantine; Abele, Andrea E
2018-03-25
The self has three parts: individual, relational, and collective. Typically, people personally value their individual self most, their relational self less, and their collective self least. This self-hierarchy is consequential, but underlying processes have remained unknown. Here, we propose two process accounts. The content account draws upon selves' agentic-communal content, explaining why the individual self is preferred most. The teleology account draws upon selves' instrumentality for becoming one's personal ideal, explaining why the collective self is preferred least. In Study 1 (N = 200, 45% female, M age = 32.9 years, 79% Caucasian), participants listed characteristics of their three selves (individual, relational, collective) and evaluated those characteristics in seven preference tasks. Additionally, we analyzed the characteristics' agentic-communal content, and participants rated their characteristics' teleological instrumentality. Study 2 (N = 396, 55% female, M age = 34.5 years, 76% Caucasian) used identical methodology and featured an additional condition, where participants evaluated the selves of a friend. Study 1 reconfirmed the self-hierarchy and supported both process accounts. Study 2 replicated and extended findings. As hypothesized, when people evaluate others' selves, a different self-hierarchy emerges (relational > individual > collective). This research pioneers process-driven explanations for the self-hierarchy, establishing why people prefer different self-parts in themselves than in others. © 2018 Wiley Periodicals, Inc.
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Extended N=2 supersymmetric matrix (1, s)-KdV hierarchies
International Nuclear Information System (INIS)
Krivonos, S.O.; Sorin, A.S.
1997-01-01
We propose the Lax operators for N=2 supersymmetric matrix generalization of the bosonic (1, s)-KdV hierarchies. The simplest examples - the N=2 supersymmetric a=4 KdV and a=5/2 Boussinesq hierarchies - are discussed in detail
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The socio-matrix reloaded: from hierarchy to dominance profile in wild lemurs.
Norscia, Ivan; Palagi, Elisabetta
2015-01-01
Dominance hierarchy influences the life quality of social animals, and its definition should in principle be based on the outcome of agonistic interactions. However, defining and comparing the dominance profile of social groups is difficult due to the different dominance measures used and because no one measure explains it all. We applied different analytical methods to winner-loser sociomatrices to determine the dominance profile of five groups of wild lemurs (species: Lemur catta, Propithecus verreauxi, and Eulemur rufus x collaris) from the Berenty forest (Madagascar). They are an excellent study model because they share the same habitat and an apparently similar dominance profile: linear hierarchy and female dominance. Data were collected over more than 1200 h of observation. Our approach included four steps: (1) by applying the binary dyadic dominance relationship method (I&SI) on either aggressions or supplant sociomatrices we verified whether hierarchy was aggression or submission based; (2) by calculating normalized David's scores and measuring steepness from aggression sociomatrices we evaluated whether hierarchy was shallow or steep; (3) by comparing the ranking orders obtained with methods 1 and 2 we assessed whether hierarchy was consistent or not; and (4) by assessing triangle transitivity and comparing it with the linearity index and the level of group cohesion we determined if hierarchy was more or less cohesive. Our results show that L. catta groups have got a steep, consistent, highly transitive and cohesive hierarchy. P. verreauxi groups are characterized by a moderately steep and consistent hierarchy, with variable levels of triangle transitivity and cohesion. E. rufus x collaris group possesses a shallow and inconsistent hierarchy, with lower (but not lowest) levels of transitivity and cohesion. A multiple analytical approach on winner-loser sociomatrices other than leading to an in-depth description of the dominance profile, allows intergroup
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The socio-matrix reloaded: from hierarchy to dominance profile in wild lemurs
Directory of Open Access Journals (Sweden)
Ivan Norscia
2015-01-01
Full Text Available Dominance hierarchy influences the life quality of social animals, and its definition should in principle be based on the outcome of agonistic interactions. However, defining and comparing the dominance profile of social groups is difficult due to the different dominance measures used and because no one measure explains it all. We applied different analytical methods to winner-loser sociomatrices to determine the dominance profile of five groups of wild lemurs (species: Lemur catta, Propithecus verreauxi, and Eulemur rufus x collaris from the Berenty forest (Madagascar. They are an excellent study model because they share the same habitat and an apparently similar dominance profile: linear hierarchy and female dominance. Data were collected over more than 1200 h of observation. Our approach included four steps: (1 by applying the binary dyadic dominance relationship method (I&SI on either aggressions or supplant sociomatrices we verified whether hierarchy was aggression or submission based; (2 by calculating normalized David’s scores and measuring steepness from aggression sociomatrices we evaluated whether hierarchy was shallow or steep; (3 by comparing the ranking orders obtained with methods 1 and 2 we assessed whether hierarchy was consistent or not; and (4 by assessing triangle transitivity and comparing it with the linearity index and the level of group cohesion we determined if hierarchy was more or less cohesive. Our results show that L. catta groups have got a steep, consistent, highly transitive and cohesive hierarchy. P. verreauxi groups are characterized by a moderately steep and consistent hierarchy, with variable levels of triangle transitivity and cohesion. E. rufus x collaris group possesses a shallow and inconsistent hierarchy, with lower (but not lowest levels of transitivity and cohesion. A multiple analytical approach on winner-loser sociomatrices other than leading to an in-depth description of the dominance profile
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Roadmap for annotating transposable elements in eukaryote genomes.
Permal, Emmanuelle; Flutre, Timothée; Quesneville, Hadi
2012-01-01
Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using both de novo and knowledge-based methods to detect TEs, are likely to produce reasonably comprehensive and sensitive results. This chapter provides a roadmap for researchers involved in genome projects to address this issue. At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, we outline the tools and good practices to be used.
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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
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Directory of Open Access Journals (Sweden)
Qiongshi Lu
2017-07-01
Full Text Available Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer's disease (LOAD. Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson's disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available at http://genocanyon.med.yale.edu/GenoSkyline.
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Lu, Qiongshi; Powles, Ryan L; Abdallah, Sarah; Ou, Derek; Wang, Qian; Hu, Yiming; Lu, Yisi; Liu, Wei; Li, Boyang; Mukherjee, Shubhabrata; Crane, Paul K; Zhao, Hongyu
2017-07-01
Continuing efforts from large international consortia have made genome-wide epigenomic and transcriptomic annotation data publicly available for a variety of cell and tissue types. However, synthesis of these datasets into effective summary metrics to characterize the functional non-coding genome remains a challenge. Here, we present GenoSkyline-Plus, an extension of our previous work through integration of an expanded set of epigenomic and transcriptomic annotations to produce high-resolution, single tissue annotations. After validating our annotations with a catalog of tissue-specific non-coding elements previously identified in the literature, we apply our method using data from 127 different cell and tissue types to present an atlas of heritability enrichment across 45 different GWAS traits. We show that broader organ system categories (e.g. immune system) increase statistical power in identifying biologically relevant tissue types for complex diseases while annotations of individual cell types (e.g. monocytes or B-cells) provide deeper insights into disease etiology. Additionally, we use our GenoSkyline-Plus annotations in an in-depth case study of late-onset Alzheimer's disease (LOAD). Our analyses suggest a strong connection between LOAD heritability and genetic variants contained in regions of the genome functional in monocytes. Furthermore, we show that LOAD shares a similar localization of SNPs to monocyte-functional regions with Parkinson's disease. Overall, we demonstrate that integrated genome annotations at the single tissue level provide a valuable tool for understanding the etiology of complex human diseases. Our GenoSkyline-Plus annotations are freely available at http://genocanyon.med.yale.edu/GenoSkyline.
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A Validation Study of Maslow's Hierarchy of Needs Theory.
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…
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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.)
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The super-classical-Boussinesq hierarchy and its super-Hamiltonian structure
International Nuclear Information System (INIS)
Si-Xing, Tao; Tie-Cheng, Xia
2010-01-01
Based on the constructed Lie superalgebra, the super-classical-Boussinesq hierarchy is obtained. Then, its super-Hamiltonian structure is obtained by making use of super-trace identity. Furthermore, the super-classical-Boussinesq hierarchy is also integrable in the sense of Liouville. (general)
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VLSI top-down design based on the separation of hierarchies
Spaanenburg, L.; Broekema, A.; Leenstra, J.; Huys, C.
1986-01-01
Despite the presence of structure, interactions between the three views on VLSI design still lead to lengthy iterations. By separating the hierarchies for the respective views, the interactions are reduced. This separated hierarchy allows top-down design with functional abstractions as exemplified
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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.
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Characterizing and annotating the genome using RNA-seq data.
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.
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The Effects of Multimedia Annotations on Iranian EFL Learners’ L2 Vocabulary Learning
Directory of Open Access Journals (Sweden)
Saeideh Ahangari
2010-05-01
Full Text Available In our modern technological world, Computer-Assisted Language learning (CALL is a new realm towards learning a language in general, and learning L2 vocabulary in particular. It is assumed that the use of multimedia annotations promotes language learners’ vocabulary acquisition. Therefore, this study set out to investigate the effects of different multimedia annotations (still picture annotations, dynamic picture annotations, and written annotations on L2 vocabulary learning. To fulfill this objective, the researchers selected sixty four EFL learners as the participants of this study. The participants were randomly assigned to one of the four groups: a control group that received no annotations and three experimental groups that received: still picture annotations, dynamic picture annotations, and written annotations. Each participant was required to take a pre-test. A vocabulary post- test was also designed and administered to the participants in order to assess the efficacy of each annotation. First for each group a paired t-test was conducted between their pre and post test scores in order to observe their improvement; then through an ANCOVA test the performance of four groups was compared. The results showed that using multimedia annotations resulted in a significant difference in the participants’ vocabulary learning. Based on the results of the present study, multimedia annotations are suggested as a vocabulary teaching strategy.
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Do Convolutional Neural Networks Learn Class Hierarchy?
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.
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Effective potentials for supersymmetric three-scale hierarchies
International Nuclear Information System (INIS)
Polchinski, J.
1983-01-01
We consider the effective potential in models in which supersymmetry breaks at a scale μ but the Goldstone fermion couples only to fields of mass M>>μ. We show that all large perturbative logarithms are removed by taking the renormalization point to be O(M). This makes it possible to calculate the effective potential at large X in those inverted-hierarchy models where the Goldstone fermion couples only to superheavy fields. A general formula for the one-loop logarithm in these models is given. We illustrate the results with an SU(n) example in which the direction as well as the magnitude of the gauge symmetry breaking is undetermined at the tree level. For this example a large perturbative hierarchy does not form and the unbroken subgroup is always SU(n-1) x U(1). In an appendix we show that O'Raifeartaigh models with just one undetermined scalar field always have a decoupled Goldstone fermion when the undetermined field is large, but that this need not be true in more general inverted-hierarchy models
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Evaluating Functional Annotations of Enzymes Using the Gene Ontology.
Holliday, Gemma L; Davidson, Rebecca; Akiva, Eyal; Babbitt, Patricia C
2017-01-01
The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity. These can range from identification of misannotation or other errors in a predicted function to accurate function prediction for an enzyme of entirely unknown function. Although GO annotation applies to any gene products, we focus here a describing our approach for hierarchical classification of enzymes in the Structure-Function Linkage Database (SFLD) (Akiva et al., Nucleic Acids Res 42(Database issue):D521-530, 2014) as a guide for informed utilisation of annotation transfer based on GO terms.
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A modified Toda spectral problem and its hierarchy of bi-Hamiltonian lattice equations
International Nuclear Information System (INIS)
Ma Wenxiu; Xu Xixiang
2004-01-01
Starting from a modified Toda spectral problem, a hierarchy of generalized Toda lattice equations with two arbitrary constants is constructed through discrete zero curvature equations. It is shown that the hierarchy possesses a bi-Hamiltonian structure and a hereditary recursion operator, which implies that there exist infinitely many common commuting symmetries and infinitely many common commuting conserved functionals. Two cases of the involved constants present two specific integrable sub-hierarchies, one of which is exactly the Toda lattice hierarchy
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Minimal string theories and integrable hierarchies
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
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Gauge and moduli hierarchy in a multiply warped braneworld scenario
International Nuclear Information System (INIS)
Das, Ashmita; SenGupta, Soumitra
2013-01-01
Discovery of Higgs-like boson near the mass scale ∼126 Gev generates renewed interest to the gauge hierarchy problem in the standard model related to the stabilisation of the Higgs mass within Tev scale without any unnatural fine tuning. One of the successful attempts to resolve this problem has been the Randall–Sundrum warped geometry model. Subsequently this 5-dimensional model was extended to a doubly warped 6-dimensional (or higher) model which can offer a geometric explanation of the fermion mass hierarchy in the standard model of elementary particles (D. Choudhury and S. SenGupta, 2007 [1]). In an attempt to address the dark energy issue, we in this work extend such 6-dimensional warped braneworld model to include non-flat 3-branes at the orbifold fixed points such that a small but non-vanishing brane cosmological constant is induced in our observable brane. We show that the requirements of a Planck to Tev scale warping along with a vanishingly small but non-zero cosmological constant on the visible brane with non-hierarchical moduli, each with scale close to Planck length, lead to a scenario where the 3-branes can have energy scales either close to Tev or close to Planck scale. Such a scenario can address both the gauge hierarchy as well as fermion mass hierarchy problem in standard model without introducing hierarchical scales between the two moduli. Thus simultaneous resolutions to the gauge hierarchy problem, fermion mass hierarchy problem and non-hierarchical moduli problem are closely linked with the near flatness condition of our universe.
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Making Sense of the Abstraction Hierarchy in the Power Plant Domain
DEFF Research Database (Denmark)
Lind, Morten
2003-01-01
The paper discusses the abstraction hierarchy proposed by Rasmussen [(1986) Information processing and human-machine interaction, North-Holland] for design of human-machine interfaces for supervisory control. The purpose of the abstraction hierarchy is to represent a work domain by multiple levels...... of means-end and part-whole abstractions. It is argued in the paper that the abstraction hierarchy suffers from both methodological and conceptual problems. A cluster of selected problems are analyzed and illustrated by concrete examples from the power plant domain. It is concluded that the semantics...... in the model-building process. It is also pointed out that attempts to clarify the semantics of the abstraction hierarchy will invariably reduce the range of work domains where it can be applied....
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AutoFACT: An Automatic Functional Annotation and Classification Tool
Directory of Open Access Journals (Sweden)
Lang B Franz
2005-06-01
Full Text Available Abstract Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1 analyzes nucleotide and protein sequence data; (2 determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3 assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4 generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at http://megasun.bch.umontreal.ca/Software/AutoFACT.htm.
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LeARN: a platform for detecting, clustering and annotating non-coding RNAs
Directory of Open Access Journals (Sweden)
Schiex Thomas
2008-01-01
Full Text Available Abstract Background In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules. Results LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation. Conclusion This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN
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Hierarchy of non-glucose sugars in Escherichia coli.
Aidelberg, Guy; Towbin, Benjamin D; Rothschild, Daphna; Dekel, Erez; Bren, Anat; Alon, Uri
2014-12-24
Understanding how cells make decisions, and why they make the decisions they make, is of fundamental interest in systems biology. To address this, we study the decisions made by E. coli on which genes to express when presented with two different sugars. It is well-known that glucose, E. coli's preferred carbon source, represses the uptake of other sugars by means of global and gene-specific mechanisms. However, less is known about the utilization of glucose-free sugar mixtures which are found in the natural environment of E. coli and in biotechnology. Here, we combine experiment and theory to map the choices of E. coli among 6 different non-glucose carbon sources. We used robotic assays and fluorescence reporter strains to make precise measurements of promoter activity and growth rate in all pairs of these sugars. We find that the sugars can be ranked in a hierarchy: in a mixture of a higher and a lower sugar, the lower sugar system shows reduced promoter activity. The hierarchy corresponds to the growth rate supported by each sugar- the faster the growth rate, the higher the sugar on the hierarchy. The hierarchy is 'soft' in the sense that the lower sugar promoters are not completely repressed. Measurement of the activity of the master regulator CRP-cAMP shows that the hierarchy can be quantitatively explained based on differential activation of the promoters by CRP-cAMP. Comparing sugar system activation as a function of time in sugar pair mixtures at sub-saturating concentrations, we find cases of sequential activation, and also cases of simultaneous expression of both systems. Such simultaneous expression is not predicted by simple models of growth rate optimization, which predict only sequential activation. We extend these models by suggesting multi-objective optimization for both growing rapidly now and preparing the cell for future growth on the poorer sugar. We find a defined hierarchy of sugar utilization, which can be quantitatively explained by
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Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian
2017-01-01
Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines. PMID:29023519
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MicroScope: a platform for microbial genome annotation and comparative genomics.
Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C
2009-01-01
The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of
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The Emergence and Representation of Knowledge about Social and Nonsocial Hierarchies
Kumaran, Dharshan; Melo, Hans Ludwig; Duzel, Emrah
2012-01-01
Summary Primates are remarkably adept at ranking each other within social hierarchies, a capacity that is critical to successful group living. Surprisingly little, however, is understood about the neurobiology underlying this quintessential aspect of primate cognition. In our experiment, participants first acquired knowledge about a social and a nonsocial hierarchy and then used this information to guide investment decisions. We found that neural activity in the amygdala tracked the development of knowledge about a social, but not a nonsocial, hierarchy. Further, structural variations in amygdala gray matter volume accounted for interindividual differences in social transitivity performance. Finally, the amygdala expressed a neural signal selectively coding for social rank, whose robustness predicted the influence of rank on participants’ investment decisions. In contrast, we observed that the linear structure of both social and nonsocial hierarchies was represented at a neural level in the hippocampus. Our study implicates the amygdala in the emergence and representation of knowledge about social hierarchies and distinguishes the domain-general contribution of the hippocampus. PMID:23141075
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Hamiltonian structure of the integrable coupling of the Jaulent-Miodek hierarchy
International Nuclear Information System (INIS)
Zhang, Yufeng; Fan, Engui
2006-01-01
A scheme for deducing Hamiltonian structures of the higher-dimensional hierarchies of evolution equations is presented which is devoting to obtaining the Hamiltonian structures of integrable coupling of the Jaulent-Miodek hierarchy
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Language variety, language hierarchy, and language choice in the international university
DEFF Research Database (Denmark)
Haberland, Hartmut; Mortensen, Janus
2012-01-01
Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university......Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university...
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An integrable counterpart of the D-AKNS soliton hierarchy from so(3,R)
International Nuclear Information System (INIS)
Ma, Wen-Xiu
2014-01-01
An integrable counterpart of the D-AKNS soliton hierarchy is generated from a matrix spectral problem associated with so(3,R). Hamiltonian structures of the resulting counterpart soliton hierarchy are furnished by using the trace identity, which yields its Liouville integrability. -- Highlights: •Use the Lie algebra so(3,R) to generate a counterpart of the D-AKNS soliton hierarchy. •Generate Hamiltonian structures depending potentials by the trace identity. •Obtain hierarchies of independent commuting symmetries and conserved densities.
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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
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Ilakkuvan, Vinu; Tacelosky, Michael; Ivey, Keith C; Pearson, Jennifer L; Cantrell, Jennifer; Vallone, Donna M; Abrams, David B; Kirchner, Thomas R
2014-04-09
Photographs are an effective way to collect detailed and objective information about the environment, particularly for public health surveillance. However, accurately and reliably annotating (ie, extracting information from) photographs remains difficult, a critical bottleneck inhibiting the use of photographs for systematic surveillance. The advent of distributed human computation (ie, crowdsourcing) platforms represents a veritable breakthrough, making it possible for the first time to accurately, quickly, and repeatedly annotate photos at relatively low cost. This paper describes a methods protocol, using photographs from point-of-sale surveillance studies in the field of tobacco control to demonstrate the development and testing of custom-built tools that can greatly enhance the quality of crowdsourced annotation. Enhancing the quality of crowdsourced photo annotation requires a number of approaches and tools. The crowdsourced photo annotation process is greatly simplified by decomposing the overall process into smaller tasks, which improves accuracy and speed and enables adaptive processing, in which irrelevant data is filtered out and more difficult targets receive increased scrutiny. Additionally, zoom tools enable users to see details within photographs and crop tools highlight where within an image a specific object of interest is found, generating a set of photographs that answer specific questions. Beyond such tools, optimizing the number of raters (ie, crowd size) for accuracy and reliability is an important facet of crowdsourced photo annotation. This can be determined in a systematic manner based on the difficulty of the task and the desired level of accuracy, using receiver operating characteristic (ROC) analyses. Usability tests of the zoom and crop tool suggest that these tools significantly improve annotation accuracy. The tests asked raters to extract data from photographs, not for the purposes of assessing the quality of that data, but rather to
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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.
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ONEMercury: Towards Automatic Annotation of Earth Science Metadata
Tuarob, S.; Pouchard, L. C.; Noy, N.; Horsburgh, J. S.; Palanisamy, G.
2012-12-01
Earth sciences have become more data-intensive, requiring access to heterogeneous data collected from multiple places, times, and thematic scales. For example, research on climate change may involve exploring and analyzing observational data such as the migration of animals and temperature shifts across the earth, as well as various model-observation inter-comparison studies. Recently, DataONE, a federated data network built to facilitate access to and preservation of environmental and ecological data, has come to exist. ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for discovering and accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple data repositories and makes it searchable via a common search interface built upon cutting edge search engine technology, allowing users to interact with the system, intelligently filter the search results on the fly, and fetch the data from distributed data sources. Linking data from heterogeneous sources always has a cost. A problem that ONEMercury faces is the different levels of annotation in the harvested metadata records. Poorly annotated records tend to be missed during the search process as they lack meaningful keywords. Furthermore, such records would not be compatible with the advanced search functionality offered by ONEMercury as the interface requires a metadata record be semantically annotated. The explosion of the number of metadata records harvested from an increasing number of data repositories makes it impossible to annotate the harvested records manually, urging the need for a tool capable of automatically annotating poorly curated metadata records. In this paper, we propose a topic-model (TM) based approach for automatic metadata annotation. Our approach mines topics in the set of well annotated records and suggests keywords for poorly annotated records based on topic similarity. We utilize the
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Conservation laws and self-consistent sources for a super-CKdV equation hierarchy
International Nuclear Information System (INIS)
Li Li
2011-01-01
From the super-matrix Lie algebras, we consider a super-extension of the CKdV equation hierarchy in the present Letter, and propose the super-CKdV hierarchy with self-consistent sources. Furthermore, we establish the infinitely many conservation laws for the integrable super-CKdV hierarchy.
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Conservation laws and self-consistent sources for a super-CKdV equation 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)
2011-03-14
From the super-matrix Lie algebras, we consider a super-extension of the CKdV equation hierarchy in the present Letter, and propose the super-CKdV hierarchy with self-consistent sources. Furthermore, we establish the infinitely many conservation laws for the integrable super-CKdV hierarchy.
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The Diversity Education Dilemma: Exposing Status Hierarchies without Reinforcing Them
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…
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A role for glucocorticoids in the long-term establishment of a social hierarchy.
Timmer, Marjan; Sandi, Carmen
2010-11-01
Stress can affect the establishment and maintenance of social hierarchies. In the present study, we investigated the role of increasing corticosterone levels before or just after a first social encounter between two rats of a dyad in the establishment and the long-term maintenance of a social hierarchy. We show that pre-social encounter corticosterone treatment does not affect the outcome of the hierarchy during a first encounter, but induces a long-term memory for the hierarchy when the corticosterone-injected rat becomes dominant during the encounter, but not when it becomes subordinate. Post-social encounter corticosterone leads to a long-term maintenance of the hierarchy only when the subordinate rat of the dyad is injected with corticosterone. This corticosterone effect mimics previously reported actions of stress on the same model and, hence, implicates glucocorticoids in the consolidation of the memory for a recently established hierarchy. Copyright © 2010 Elsevier Ltd. All rights reserved.
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A Selected Annotated Bibliography on Work Time Options.
Ivantcho, Barbara
This annotated bibliography is divided into three sections. Section I contains annotations of general publications on work time options. Section II presents resources on flexitime and the compressed work week. In Section III are found resources related to these reduced work time options: permanent part-time employment, job sharing, voluntary…
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Impact of hierarchy upon the values of neutrino mixing parameters
International Nuclear Information System (INIS)
Escamilla-Roa, J.; Ernst, D. J.; Latimer, D. C.
2010-01-01
A neutrino-oscillation analysis is performed of the more finely binned Super-Kamiokande (Super-K) atmospheric, MINOS, and CHOOZ data to examine the effect of neutrino hierarchy in this data set on the value of θ 13 and the deviation of θ 23 from maximal mixing. Exact oscillation probabilities are used, thus incorporating all powers of θ 13 and ε:=θ 23 -π/4. The extracted oscillation parameters are found to be dependent on the hierarchy, particularly for θ 13 . We find, at a 90% confidence level, that these parameters are Δ 32 =2.44 -0.20 +0.26 and 2.48 -0.22 +0.25 x10 -3 eV 2 , ε=θ 23 -π/4=0.06 -0.16 +0.06 and 0.06 -0.17 +0.08 , and θ 13 =-0.07 -0.11 +0.18 and -0.13 -0.16 +0.23 , for the normal and inverted hierarchies, respectively. The inverted hierarchy is preferred at a statistically insignificant level of 0.3σ.
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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.)
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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.)
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Organizing product innovation: hierarchy, market or triple-helix networks?
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.
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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
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A density tensor hierarchy for open system dynamics: retrieving the noise
International Nuclear Information System (INIS)
Adler, Stephen L
2007-01-01
We develop a density tensor hierarchy for open system dynamics that recovers information about fluctuations (or 'noise') lost in passing to the reduced density matrix. For the case of fluctuations arising from a classical probability distribution, the hierarchy is formed from expectations of products of pure state density matrix elements and can be compactly summarized by a simple generating function. For the case of quantum fluctuations arising when a quantum system interacts with a quantum environment in an overall pure state, the corresponding hierarchy is defined as the environmental trace of products of system matrix elements of the full density matrix. Whereas all members of the classical noise hierarchy are system observables, only the lowest member of the quantum noise hierarchy is directly experimentally measurable. The unit trace and idempotence properties of the pure state density matrix imply descent relations for the tensor hierarchies, that relate the order n tensor, under contraction of appropriate pairs of tensor indices, to the order n - 1 tensor. As examples to illustrate the classical probability distribution formalism, we consider a spatially isotropic ensemble of spin-1/2 pure states, a quantum system evolving by an Ito stochastic Schroedinger equation and a quantum system evolving by a jump process Schroedinger equation. As examples to illustrate the corresponding trace formalism in the quantum fluctuation case, we consider the tensor hierarchies for collisional Brownian motion of an infinite mass Brownian particle and for the weak coupling Born-Markov master equation. In different specializations, the latter gives the hierarchies generalizing the quantum optical master equation and the Caldeira-Leggett master equation. As a further application of the density tensor, we contrast stochastic Schroedinger equations that reduce and that do not reduce the state vector, and discuss why a quantum system coupled to a quantum environment behaves like
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Directory of Open Access Journals (Sweden)
Nicholas J Schurch
Full Text Available The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1 gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb; (2 disentangling of gene expression in complex regions; (3 clearer interpretation of small RNA expression and (4 identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.