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

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

A thoracic vertebral localization of a metastasized cutaneous Merkel cell carcinoma: Case report and review of literature

Background: Merkel cell carcinoma (MCC) is a rare neuroendocrine skin tumor, which may be related to sun exposure. It can metastasize to lungs, liver and bone, leading to severe morbidity and mortality. Vertebral metastases from MCC are rare. The authors report the tenth case in the literature, a 59-year-old patient with MCC, which was primarily localized in the scalp, and later provoked distant metastasis to the thoracic spinal column. Case Description: A 59-year-old woman was admitted at our Unit of Neurosurgery with a 4-month history of progressive and severe dorsal back pain, without neurological signs. The patient had been surgically treated for a recidivated MCC in the occipital region in 2007, 2011, and 2013. (In 2013, the surgical treatment also included lateral cervical lymph node dissection). Chemotherapy and radiotherapy had come after the treatments. Magnetic resonance imaging (MRI) of the dorsal spine showed metastatic vertebral involvement with cord impingement of the T7-T8 levels. A total body CT scan revealed lungs and liver metastases, besides vertebral district. After a multidisciplinary consult a palliative surgery was decided and a posterior dorsal approach was employed: Radiofrequency (RF) thermoablation was followed by the injection of cement of T7 and T8 and transpedicle fixation T5-T9. The postoperative course was uneventful and followed by a further adjuvant therapy Conclusion: Spinal metastases from MCC are described in literature only exceptionally. The clinical course is presented, along with a review of literature