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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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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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Using ontology and data provenance to improve software processes

Using ontology and data provenance to improve software proce...

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Brazilian Seminar on Ontologies, ONTOBRAS 2015

作者： Dalpra, Humberto L. O. Costa, Gabriella C. B. Sirqueira, Tássio F. M. Braga, Regina Werner, Cláudia M. L. Campos, Fernanda David, José Maria N. UFJF - Federal University of Juiz de Fora Department of Computer Science Juiz de Fora - MG Brazil UFRJ - Federal University of Rio de Janeiro COPPE Systems Engineering and Computer Science Department Rio de Janeiro - RJ Brazil

Provenance refers to the origin of a particular object. In computational terms, provenance is a historical record of the derivation of data that can help to understand the current record. In this context, this work presents a proposal for software processes improvement using a provenance data model and an ontology. This improvement can be obtained by process data execution analysis with an approach called PROV-Process, which uses a layer for storing process provenance and an ontology based on PROV-O.

关键词： Ontology

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A practical experience of a software process line creation 18

A practical experience of a software process line creation

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18th Ibero-American Conference on Software engineering, CIBSE 2015

作者： Magdaleno, Andreá M. Araujo, Renata M. Werner, Cláudia M L. Batista, Carlos Freud Alves COPPE - Systems Engineering and Computer Science Department UFRJ - Federal University of Rio de Janeiro P.O. Box 68511 Rio de Janeiro - RJ Brazil UNIRIO Brazil Petrobras - TIC/CPSW/PGOD/PMSW Brazil

ISBN: (纸本)9789972825804

Software process definition is a complex, time consuming and error prone activity. Such activity can be facilitated by a process reuse strategy. This strategy can be implemented through process line and components structures. This work presents a case study of a real process line creation in the context of an oil and gas company in Brazil. The results indicate both practical use and its potential to assess completeness and to identify inconsistencies in the organizational process. Copyright © 2015 by the authors.

关键词： computer software reusability

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A Roadmap for Cloud SECO: EcoData and the New Actors in IoT Era

A Roadmap for Cloud SECO: EcoData and the New Actors in IoT ...

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International Conference on Distributed Computing in Sensor systems (DCOSS)

作者： Marcelo França Rodrigo Santos Claudia Werner IBM - International Business Machines Brazil COPPE/UFRJ - Federal University of Rio de Janeiro Rio de Janeiro Brazil Computer Science and Systems Engineering Department COPPE/UFRJ - Federal University of Rio de Janeiro Rio de Janeiro Brazil

This paper's main goal is to structure an initial research on the Software Ecosystem (SECO) field, regarding the so called CAMSS (Cloud, Analytics, Mobile, Social and Security) and IoT (Internet of Things) technologies. Our main goal is to share our first ideas and some observations we have been conducting in an empirical way. As such, Cloud SECOs bring the ecosystem environment to another level, with new challenges in all three dimensions: technology, social and business. Besides that, we have been observing a possible shift in the center of some SECOs, i.e., Those "things" connected to the Internet have introduced new players - at least in the sense they interact with the environment by providing data. As new software architectures and technologies emerge to support the new scenario being drawn, our research tries to characterize this new ecosystem and identify challenges, providing a roadmap that could help new entrants.

关键词： Companies Cloud computing Ecosystems Mobile communication Security

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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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Monitoring collaboration in software processes using social networks

Monitoring collaboration in software processes using social ...

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20th International Conference on Collaboration and Technology, CRIWG 2014

作者： Costa, Gabriella C. B. Santana, Francisco Magdaleno, Andréa M. Werner, Cláudia M. L. UFRJ - Federal University of Rio de Janeiro COPPE - Systems Engineering and Computer Science Department P.O. Box 68511 21945-970 - Rio de Janeiro - RJ Brazil

ISBN: (纸本)9783319101651

Collaboration monitoring in software process is important to check if the collaboration is indeed happening as planned, but there are few approaches that define how to measure and monitor collaboration. By assessing collaboration during an ongoing process execution, project managers can take corrective actions that might improve the process execution and, consequently, reflect on quality gains of the final product. This research work proposes to evaluate the level of coordination achieved by a running software process through social network analysis metrics. © 2014 Springer International Publishing.

关键词： Social sciences computing

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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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