289 research outputs found
A subgraph isomorphism algorithm and its application to biochemical data
BackgroundGraphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph to a target graph. Accomplishing this is inherently difficult (NP-complete) and the efficiency of heuristic algorithms for the problem may depend upon the input graphs. The common aim of existing algorithms is to eliminate unsuccessful mappings as early as and as inexpensively as possible.ResultsWe propose a new subgraph isomorphism algorithm which applies a search strategy to significantly reduce the search space without using any complex pruning rules or domain reduction procedures. We compare our method with the most recent and efficient subgraph isomorphism algorithms (VFlib, LAD, and our C++ implementation of FocusSearch which was originally distributed in Modula2) on synthetic, molecules, and interaction networks data. We show a significant reduction in the running time of our approach compared with these other excellent methods and show that our algorithm scales well as memory demands increase.ConclusionsSubgraph isomorphism algorithms are intensively used by biochemical tools. Our analysis gives a comprehensive comparison of different software approaches to subgraph isomorphism highlighting their weaknesses and strengths. This will help researchers make a rational choice among methods depending on their application. We also distribute an open-source package including our system and our own C++ implementation of FocusSearch together with all the used datasets (http://ferrolab.dmi.unict.it/ri.html). In future work, our findings may be extended to approximate subgraph isomorphism algorithms
A subgraph isomorphism algorithm and its application to biochemical data
BackgroundGraphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph to a target graph. Accomplishing this is inherently difficult (NP-complete) and the efficiency of heuristic algorithms for the problem may depend upon the input graphs. The common aim of existing algorithms is to eliminate unsuccessful mappings as early as and as inexpensively as possible.ResultsWe propose a new subgraph isomorphism algorithm which applies a search strategy to significantly reduce the search space without using any complex pruning rules or domain reduction procedures. We compare our method with the most recent and efficient subgraph isomorphism algorithms (VFlib, LAD, and our C++ implementation of FocusSearch which was originally distributed in Modula2) on synthetic, molecules, and interaction networks data. We show a significant reduction in the running time of our approach compared with these other excellent methods and show that our algorithm scales well as memory demands increase.ConclusionsSubgraph isomorphism algorithms are intensively used by biochemical tools. Our analysis gives a comprehensive comparison of different software approaches to subgraph isomorphism highlighting their weaknesses and strengths. This will help researchers make a rational choice among methods depending on their application. We also distribute an open-source package including our system and our own C++ implementation of FocusSearch together with all the used datasets (http://ferrolab.dmi.unict.it/ri.html). In future work, our findings may be extended to approximate subgraph isomorphism algorithms
Impasse in the management of recurrent basal cell carcinoma of the skull with sagittal sinus erosion1
Abstract Basal cell carcinoma (BCC) is a non melanocytic skin cancer that arises from basal cells, affecting commonly fair-skinned human beings. Although the tumor is well known for local recurrences, extension into the intracranial space is reported. A case of a giant BCC of the scalp invading the middle and posterior third of the superior sagittal sinus (SSS) is reported. A 70-year-old male with a basal cell carcinoma history presented with a massive bleeding from the SSS invaded by the tumor. Since the patient refused surgery the bleeding was managed through direct compression by applying a thrombin-based hemostatic agents and sterile dressings. This procedure was performed daily in order to stimulate the spontaneous thrombosis of the dural sinus and development of collateral circle. BCC invading the SSS is rarely reported. A technical description of this case is provided. This case underscores the importance of early and appropriate treatment for high risk BCC, and whenever surgical procedure is not suitable appropriate conservative treatment may be efficacious
A rare case of extra-intramedullary dorsal tanycitic ependymoma, radically removed with intraoperative neurophysiological monitoring
Introduction: Tanycitic dorsal extra and intramedullary ependymoma is a rare form of tumor. From the histological point of view, these tumors show several aspects that make difficult the differential diagnosis from schwannomas and pilocytic astrocytomas. Tanycytic variant, often occurs in the thoracic tract of the spinal cord, and it is constituted by tanycites, that are typical elongated and bipolar cells that give to the tumor fibrillary aspects. Tanycitic variant has been recently characterized as a variant of ependymoma, since the 2000 World Health Organization (WHO) system. Case presentation: A 57 years old woman presented with intractable back pain often radiating to the left leg. Neurological exam revealed mild weakness in left tight flexion. No sensory or sphincterial disturbances were present. A dorso-lumbar Magnetic Resonance Imaging (MRI)with contrast medium showed a well-demarked T12 intradural extramedullary lesion, suggestive for schwannoma. The tumor was radically removed, with an excellent neurological outcome, and was then characterized as a grade II tanycitic ependymoma. Conclusion: To differentiate the diagnosis between extramedullary ependymomas and schwannomas, meningiomas or astrocytomas is necessary a histopathological examination and a close follow up period is recommended since the tumor could evolve into higher grade. Neurophysiological monitoring is necessary for a satisfactory neurological outcome
13 Mannose binding lectin gene as a modifier of cystic fibrosis phenotype in Argentinian pediatric patients
Delayed chronic intracranial subdural hematoma complicating resection of a tanycytic thoracic ependymoma
Background: To demonstrate that the diagnosis of an intracranial subdural hematoma should be considered for patients presenting with acute or delayed symptoms of intracranial pathology following resection of a spinal tumor. Case Description: We present a case of a 57-year-old woman found to have a chronic subdural hematoma 1 month following resection of a thoracic extramedullary ependymoma. Evacuation of the hematoma through a burr hole relieved the presenting symptoms and signs. Resolution of the hematoma was confirmed with a computed tomography (CT) scan. Conclusion: Headache and other symptoms not referable to spinal pathology should be regarded as a warning sign of an intracranial subdural hematoma, and a CT scan of the head should be obtained. The mechanism of the development of the hematoma may be related to the leakage of cerebrospinal fluid with subsequent intracranial hypotension leading to an expanding subdural space and hemorrhage
A rare case of extra-intramedullary dorsal tanycitic ependymoma, radically removed with intraoperative neurophysiological monitoring
Introduction: Tanycitic dorsal extra and intramedullary ependymoma is a rare form of tumor. From the histological point of view, these tumors show several aspects that make difficult the differential diagnosis from schwannomas and pilocytic astrocytomas. Tanycytic variant, often occurs in the thoracic tract of the spinal cord, and it is constituted by tanycites, that are typical elongated and bipolar cells that give to the tumor fibrillary aspects. Tanycitic variant has been recently characterized as a variant of ependymoma, since the 2000 World Health Organization (WHO) system. Case presentation: A 57 years old woman presented with intractable back pain often radiating to the left leg. Neurological exam revealed mild weakness in left tight flexion. No sensory or sphincterial disturbances were present. A dorso-lumbar Magnetic Resonance Imaging (MRI)with contrast medium showed a well-demarked T12 intradural extramedullary lesion, suggestive for schwannoma. The tumor was radically removed, with an excellent neurological outcome, and was then characterized as a grade II tanycitic ependymoma. Conclusion: To differentiate the diagnosis between extramedullary ependymomas and schwannomas, meningiomas or astrocytomas is necessary a histopathological examination and a close follow up period is recommended since the tumor could evolve into higher grade. Neurophysiological monitoring is necessary for a satisfactory neurological outcome
Tools and collaborative environments for bioinformatics research
Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies
How to tell a gravastar from a black hole
Gravastars have been recently proposed as potential alternatives to explain
the astrophysical phenomenology traditionally associated to black holes,
raising the question of whether the two objects can be distinguished at all.
Leaving aside the debate about the processes that would lead to the formation
of a gravastar and the astronomical evidence in their support, we here address
two basic questions: Is a gravastar stable against generic perturbations? If
stable, can an observer distinguish it from a black hole of the same mass? To
answer these questions we construct a general class of gravastars and determine
the conditions they must satisfy in order to exist as equilibrium solutions of
the Einstein equations. For such models we perform a systematic stability
analysis against axial-perturbations, computing the real and imaginary parts of
the eigenfrequencies. Overall, we find that gravastars are stable to axial
perturbations, but also that their quasi-normal modes differ from those of a
black hole of the same mass and thus can be used to discern, beyond dispute, a
gravastar from a black hole.Comment: 16 pages, 13 figures, minor improvemen
Extracellular circulating viral microRNAs: Current knowledge and perspectives
MicroRNAs (miRNAs) are small non-coding RNAs responsible of post-transcriptional regulation of gene expression through interaction with messenger RNAs (mRNAs). They are involved in important biological processes and are often dysregulated in a variety of diseases, including cancer and infections. Viruses also encode their own sets of miRNAs, which they use to control the expression of either the host's genes and/or their own. In the past few years evidence of the presence of cellular miRNAs in extracellular human body fluids such as serum, plasma, saliva, and urine has accumulated. They have been found either cofractionate with the Argonaute2 protein or in membrane-bound vesicles such as exosomes. Although little is known about the role of circulating miRNAs, it has been demonstrated that miRNAs secreted by virus-infected cells are transferred to and act in uninfected recipient cells. In this work we summarize the current knowledge on viral circulating miRNAs and provide a few examples of computational prediction of their functio
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