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 ...
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.
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 patc...
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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.
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 pr...
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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.
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 str...
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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) technol...
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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.
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 ...
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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 c...
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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...
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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.
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...
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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.
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)....
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