Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Steinert's syndrome presenting as anal incontinence: a case report

<p>Abstract</p> <p>Introduction</p> <p>Myotonic dystrophy (MD) or Steinert's syndrome is a rare cause of chronic diarrhea and anal incontinence. In the presence of chronic diarrhea and fecal incontinence with muscle weakness, neuromuscular disorders such as myotonic dystrophy should be considered in the differential diagnosis.</p> <p>Case Presentation</p> <p>We present the case of a 45-year-old Turkish man with Steinert's syndrome, who was not diagnosed until the age of 45.</p> <p>Conclusions</p> <p>In clinical practice, the persistence of diarrhea and fecal incontinence with muscle weakness should suggest that the physician perform an anal manometric study and electromyography. Neuromuscular disorders such as myotonic dystrophy should be considered in the differential diagnosis.</p

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

Treatment of large persistent tracheoesophageal peristomal fistulas using silicon rings.

Abstract Introduction: Tracheoesophageal peristomal fistulae can often be solved by reducing the size of the fistula or replacing the prosthesis; however, even with conservative techniques, leakage around the fistula may continue in total laryngectomy patients. Also, several techniques have been developed to overcome this problem, including injections around the fistula, fistula closure with local flaps, myofascial flaps, or free flaps and fistula closure using a septal perforation silicon button. Objective: To present the results of the application of silicon ring expanding the voice prosthesis in patients with large and persistent peri-prosthetic fistula. Methods: A voice prosthesis was fitted to 42 patients after total laryngectomy. Leakage was detected around the prosthesis in 18 of these 42 patients. Four patients demonstrated improvement with conservative methods. Eight of 18 patients who couldn't be cured with conservative methods were treated by using primary suture closure and 4 patients were treated with local flaps. As silicon ring was applied as a primary treatment in the 2 remaining patients and also, applied to 2 patients who had recurrence after suture repair and to 2 patients who had recurrence after local flap implementation. Silicon rings were used in a total of 6 patients due to the secondary trachea-esophageal fistula. Patients were treated with provox-1 initially and later with provox-2. At the time of leakage around the fistula, 6 patients had provox-2. Results: Fistulae were treated successfully in 6 patients, and effective speech of patients was preserved. Patients experienced no adaptation problem. Prosthesis changing time was not different between silicon rings expanded and normal prosthesis applied patients. Silicon ring combined voice prosthesis was used 26 times; there was no recurrence in fistula complication during 29 ± 6 months follow up. Conclusion: Silicon rings for modified expanded voice prosthesis seems to be an effective treatment for persistent peri-prosthetic leakage, for both, fistula closure and preserving the patients speech