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A multi-protease, multi-dissociation, bottom-up-to-top-down proteomic view of the Loxosceles intermedia venom

Scientific Data 2017年第1期4卷 170090-170096页

作者： Trevisan-Silva, Dilza Bednaski, Aline V. Fischer, Juliana S.G. Veiga, Silvio S. Bandeira, Nuno Guthals, Adrian Marchini, Fabricio K. Leprevost, Felipe V. Barbosa, Valmir C. Senff-Ribeiro, Andrea Carvalho, Paulo C. Department of Cell Biology Federal University of Paraná Curitiba 81531-980 Brazil Computational Mass Spectrometry and Proteomics Group Carlos Chagas Institute Fiocruz Curitiba 81.350-010 Brazil Center for Computational Mass Spectrometry University of California San Diego 92093-0404 United States Functional Genomics Laboratory Carlos Chagas Institute Fiocruz Curitiba 81.350-010 Brazil Mass Spectrometry Facility RPT02H Carlos Chagas Institute Fiocruz Curitiba 81.350-010 Brazil Systems Engineering and Computer Science Program COPPE Federal University of Rio de Janeiro Rio de Janeiro 21941-914 Brazil Laboratory of Toxinology Fiocruz Rio de Janeiro 21040-900 Brazil

Venoms are a rich source for the discovery of molecules with biotechnological applications, but their analysis is challenging even for state-of-the-art proteomics. Here we report on a large-scale proteomic assessment of the venom of Loxosceles intermedia, the so-called brown spider. Venom was extracted from 200 spiders and fractioned into two aliquots relative to a 10 kDa cutoff mass. Each of these was further fractioned and digested with trypsin (4 h), trypsin (18 h), pepsin (18 h), and chymotrypsin (18 h), then analyzed by MudPIT on an LTQ-Orbitrap XL ETD mass spectrometer fragmenting precursors by CID, HCD, and ETD. Aliquots of undigested samples were also analyzed. Our experimental design allowed us to apply spectral networks, thus enabling us to obtain meta-contig assemblies, and consequently de novo sequencing of practically complete proteins, culminating in a deep proteome assessment of the venom. Data are available via ProteomeXchange, with identifier PXD005523.

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Information Extraction to Improve Link Prediction in Scientific Social Networks

Information Extraction to Improve Link Prediction in Scienti...

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IEEE International Conference on computer Supported Cooperative Work in Design

作者： Victor Stroele Fernanda Campos Crystiam K. Pereira Geraldo Zimbrao Jano M. Souza PGCC - Postgraduate Program in Computer Science UFJF - Federal University of Juiz de Fora COPPE - Systems Engineering and Computer Program UFRJ - Federal University of Rio de Janeiro

ISBN: (纸本)9781509019168

Link Prediction is a classic social networks analysis problem. Knowing in advance future actions in social network can help, for example, agents decision. Link Prediction techniques are based on metrics that have different approaches. In this paper, we model a multi-relational scientific social network to assess the impact of content extraction on topological metrics. Thus, a metric composed of topological and semantic approach is proposed to solve link prediction problem. The results were compared with those presented by Katz metric.

关键词： Information Extraction Link Prediction Scientific Social Network

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Assembling a Network out of Ambiguous Patches

Assembling a Network out of Ambiguous Patches

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Annual Allerton Conference on Communication, Control, and Computing

作者： Lyudmila Yartseva Jefferson Elbert Sim?es Matthias Grossglauser School of Computer and Communication Sciences école Polytechnique Fédérale de Lausanne (EPFL) Switzerland Systems Engineering and Computer Science Program COPPE Federal University of Rio de Janeiro Brazil

ISBN: (纸本)9781509045518

Many graph mining and network analysis problems rely on the availability of the full network over a set of nodes. But inferring a full network is sometimes non-trivial if the raw data is in the form of many small patches or subgraphs, of the true network, and if there are ambiguities in the identities of nodes or edges in these patches. This may happen because of noise or because of the nature of data;for instance, in social networks, names are typically not unique. Graph assembly refers to the problem of reconstructing a graph from these many, possibly noisy, partial observations. Prior work suggests that graph assembly is essentially impossible in regimes of interest when the true graph is Erdos-Rényi. The purpose of the present paper is to show that a modest amount of clustering is sufficient to assemble even very large graphs. We introduce the G(n,p;q) random graph model, which is the random closure over all open triangles of a G(n,p) Erdos-Rényi, and show that this model exhibits higher clustering than an equivalent Erdos-Rényi . We focus on an extreme case of graph assembly: the patches are small (1-hop egonets) and are unlabeled. We show that in realistic regimes, graph assembly is fundamentally feasible, because we can identify, for every edge e, a subgraph induced by its neighbors that is unique and present in every patch containing e. Using this result, we build a practical algorithm that uses canonical labeling to reconstruct the original graph from noiseless patches. We also provide an achievability result for noisy patches, which are obtained by edge-sampling the original egonets.

关键词： mining network analysis

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An information visualization feature model for supporting the selection of software visualizations 22

An information visualization feature model for supporting th...

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22nd International Conference on program Comprehension, ICPC 2014

作者： Vasconcelos, Renan Schots, Marcelo Werner, Cláudia Systems Engineering and Computer Science Program COPPE/UFRJ PO Box 68511 Rio de Janeiro RJCEP21945-970 Brazil

ISBN: (纸本)9781450328791

Software development comprises the execution of a variety of tasks, such as bug discovery, finding reusable assets, dependency analysis etc. A better understanding of the task at hand and its surroundings can improve the development performance in general. Software visualizations can support such understanding by addressing different issues according to the necessity of stakeholders. However, knowing which visualizations better fit a given task in progress is not a trivial skill. In this sense, a feature model, intended for organizing the knowledge of a given domain and allowing the reuse of components, can support the identification, categorization and selection of information visualization elements. This work presents an ongoing domain analysis performed for building an information visualization feature model, whose goal is to support the process of choosing and building proper, suitable software visualizations. Copyright © 2014 ACM.

关键词： Visualization

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Extracting Semantic Information from Patent Claims Using Phrasal Structure Annotations

Extracting Semantic Information from Patent Claims Using Phr...

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Brazilian Conference on Intelligent systems (BRACIS)

作者： Danilo Silva de Carvalho Felipe Maia Galvão França Priscila Machado Vieira Lima Systems Engineering and Computer Science Program-COPPE Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil Instituto Tércio Pacitti (NCE) Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil

The rapid change of trading values from tangible assets to Intelectual Property has put both businesses and academia in a race to acquire and protect the rights to exploit such property. This is mainly accomplished in the form of patent issuing by the governments, being time consuming and complicated due to the vast amount of documents that need to be analyzed in order to assert the novelty or validity of a patent application. Patent information retrieval research is thus growing quickly to support document analysis across multiple domains and information systems. One of the big challenges in patent analysis is the identification of the elements of innovation (concepts, processes, materials) and the relations between them, in the patent text. This paper presents a method for extracting semantic information from patent claims by using semantic annotations on phrasal structures, abstracting domain ontology information and outputting ontology-friendly structures to achieve generalization. An extraction system built upon the method is briefly evaluated on a document sample from INPI, the Brazilian patent office, a challenging information source.

关键词： Semantics Patents Syntactics Data mining Training Ontologies Testing

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Learning context to adapt business processes

Learning context to adapt business processes

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International Conference on computer Supported Cooperative Work in Design

作者： Juliana do E. Santo Carvalho Flavia Maria Santoro Kate Revoredo Vanessa Tavares Nunes Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil COPPE PESC-Systems Engineering and Computer Science Program UFRJ Rio de Janeiro Brazil

ISBN: (纸本)9781467360845

Dynamic adaptation is the customization of a business process to make it applicable to a particular situation at any time of its life cycle. Adapting requires experience, and involves knowledge about various, internal and external, aspects of business. Thus, we argue for the application of adaptation rules, considering the context of a particular process instance. Furthermore, we state that a context-based adaptation environment should go beyond, and learn from decisions, as well as continuously identify new unforeseen situations (context definitions). The aim of this paper is to present a computational engine that infers the need to update situations and adaptation rules, suggesting changes to them. An application scenario is presented to discuss the usage of the proposal.

关键词： Context Itemsets Proposals Adaptation models Aircraft Runtime

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A reconfigurable ray-tracing Multi-Processor SoC with hardware replication-aware instruction set extension

A reconfigurable ray-tracing Multi-Processor SoC with hardwa...

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13th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2013

作者： Nery, Alexandre S. Nedjah, Nadia França, Felipe M.G. Jozwiak, Lech Corporaal, Henk LAM - Computer Architecture and Microeletronics Laboratory Systems Engineering and Computer Science Program COPPE Federal University of Rio de Janeiro Brazil Department of Electronics Engineering and Telecommunications Faculty of Engineering State University of Rio de Janeiro Brazil Department of Electrical Engineering - Electronic Systems Eindhoven University of Technology Netherlands

ISBN: (纸本)9783319038582

Application code and processor parallelization, together with instruction set customization, are the most common and effective ways to enhance the performance and efficiency of application-specific processors (ASIPs). Both the effective code parallelization and data/task parallelism exploitation, as well as effective instruction set customization, enable an ASIP to achieve a significant performance improvement using limited extra hardware resources. However, a naive parallelization or instruction set customization may not result in the required performance improvement, leading to a waste of computing and energy resources. Therefore, when performing parallelization or custom instruction selection, complex tradeoffs between processing speed, circuit area and power consumption must be closely observed. In this paper, we propose and discuss an efficient ASIP-based Multi-Processor System-on-a-Chip (MPSoC) design for ray-tracing, exploiting application parallelism and hardware replication-aware instruction set customization. Without hardware sharing among the custom instructions units, the proposed parallel ray-tracer MPSoC design with custom instructions achieves 77% speed up in comparison to a single microprocessor design with the default instruction set. However, with the replication-aware instruction set customization, the speed up increases to 81%. © Springer International Publishing Switzerland 2013.

关键词： Integrated circuit design

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Introducing software process tailoring to BPMN: BPMNt

Introducing software process tailoring to BPMN: BPMNt

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2012 International Conference on Software and System Process, ICSSP 2012

作者： Pillat, Raquel M. Oliveira, Toacy C. Fonseca, Fabio L. Systems Engineering and Computer Science Program - PESC / COPPE Federal University of Rio de Janeiro - UFRJ Rio de Janeiro Brazil

ISBN: (纸本)9781467323529

BPMN 2.0 is a widely used notation to model business process that has associated tools and techniques to facilitate process management, execution and monitoring. As a result using BPMN to model Software Development Process (SDP) can leverage on the BPMN's infrastructure to improve SDP quality. Nevertheless, when using BPMN to model Software Processes one can observe the lack of an important feature: means to represent process tailoring. This article introduces the BPMNt, a conservative extension to BPMN that aims at aggregating a tailoring representation mechanism as the one found at SPEM 2.0. BPMNt uses the extensibility classes already present in the BPMN meta-model. Our work also presents an example to illustrate the approach. © 2012 IEEE.

关键词： Software design

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Formalizing the situation of a business process activity

Formalizing the situation of a business process activity

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2012 IEEE 16th International Conference on computer Supported Cooperative Work in Design, CSCWD 2012

作者： Mattos, Talita Da Cunha Santoro, Flávia Maria Revoredo, Kate Nunes, Vanessa Tavares Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil COPPE/PESC - Systems Engineering and Computer Science Program UFRJ Rio de Janeiro Brazil

ISBN: (纸本)9781467312127

Business processes are dynamic and constantly evolving. Contextual elements that had not yet been identified and represented can arise and influence the execution of each process instance in diverse manners. In this scenario, the identification of these elements is considered of great importance. This paper proposes a formalism for context associated with business processes that intends to identify the situation of an activity in order to subsidize decisions to be taken within the execution of a process. © 2012 IEEE.

关键词： Business Process Context

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Mediating process adaptation through a goal-oriented context-aware approach

Mediating process adaptation through a goal-oriented context...

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2012 IEEE 16th International Conference on computer Supported Cooperative Work in Design, CSCWD 2012

作者： Nunes, Vanessa Tavares Werner, Cláudia M. Lima Santoro, Flávia Maria COPPE/PESC - Systems Engineering and Computer Science Program UFRJ PO Box 68511 21945-970 Rio de Janeiro Brazil NP2Tec and Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil

ISBN: (纸本)9781467312127

Complexity and dynamism of day-to-day activities in organizations are inextricably linked, one impacting the other, increasing the challenges for constant adaptation on the way to organize work to address emerging demands. Market is demanding systems that are aware of organizations processes and able to evolve and adapt to new situations in everyday working activities. We argue that flexibility in processes could be managed in real time, by PAIS (Process-aware Information systems), using context information collected in the work environment. This paper proposes CGAdapt, a context management architecture approach that aims to improve and automate dynamic process adaptation. We explain how process adaptation may occur in real time through an existent scenario using this proposal and discuss the value of context-awareness to reason about process alternative adaptations in a goal oriented approach. © 2012 IEEE.

关键词： Real time systems

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