Modularizing and Specifying Protocols among Threads

We identify three problems with current techniques for implementing protocols among threads, which complicate and impair the scalability of multicore software development: implementing synchronization, implementing coordination, and modularizing protocols. To mend these deficiencies, we argue for the use of domain-specific languages (DSL) based on existing models of concurrency. To demonstrate the feasibility of this proposal, we explain how to use the model of concurrency Reo as a high-level protocol DSL, which offers appropriate abstractions and a natural separation of protocols and computations. We describe a Reo-to-Java compiler and illustrate its use through examples.Comment: In Proceedings PLACES 2012, arXiv:1302.579

Toward Sequentializing Overparallelized Protocol Code

In our ongoing work, we use constraint automata to compile protocol specifications expressed as Reo connectors into efficient executable code, e.g., in C. We have by now studied this automata based compilation approach rather well, and have devised effective solutions to some of its problems. Because our approach is based on constraint automata, the approach, its problems, and our solutions are in fact useful and relevant well beyond the specific case of compiling Reo. In this short paper, we identify and analyze two such rather unexpected problems.Comment: In Proceedings ICE 2014, arXiv:1410.701

Data optimizations for constraint automata

Constraint automata (CA) constitute a coordination model based on finite automata on infinite words. Originally introduced for modeling of coordinators, an interesting new application of CAs is implementing coordinators (i.e., compiling CAs into executable code). Such an approach guarantees correctness-by-construction and can even yield code that outperforms hand-crafted code. The extent to which these two potential advantages materialize depends on the smartness of CA-compilers and the existence of proofs of their correctness. Every transition in a CA is labeled by a "data constraint" that specifies an atomic data-flow between coordinated processes as a first-order formula. At run-time, compiler-generated code must handle data constraints as efficiently as possible. In this paper, we present, and prove the correctness of two optimization techniques for CA-compilers related to handling of data constraints: a reduction to eliminate redundant variables and a translation from (declarative) data constraints to (imperative) data commands expressed in a small sequential language. Through experiments, we show that these optimization techniques can have a positive impact on performance of generated executable code

Partially distributed coordination with Reo and constraint automata

Algorithms and the Foundations of Software technolog

A Reo model of Software Defined Networks

Reo is a compositional coordination language for component connectors with a formal semantics based on automata. In this paper, we propose a formal model of software defined networks (SDNs) based on Reo where declarative constructs comprising of basic Reo primitives compose to specify descriptive models of both data and control planes of SDNs. We first describe the model of an SDN switch which can be compactly represented as a single state constraint automaton with a memory storing its flow table. A full network can then be compositionally constructed by composing the switches with basic communication channels. The reactive and proactive behaviour of the controllers in the control plane of an SDN can also be modelled by Reo connectors, which can compose the connectors representing data plane. The resulting model is suitable for testing, simulation, visualization, verification, and ultimately compilation into SDN switch code using the standard tools already available for Reo

PMG: Multi-core metabolite identification

Distributed computing has been considered for decades as a promising way of speeding up software execution, resulting in a valuable collection of safe and efficient concurrent algorithms. With the pervasion of multi-core processors, parallelization has moved to the center of attention with new challenges, especially regarding scalability to tens or even hundreds of parallel cores. In this paper, we present a scalable multi-core tool for the metabolomics community. This tool addresses the problem of metabolite identification which is currently a bottleneck in metabolomics pipeline.Analytical BioScience

The Study of Education Effect on Knowledge of, and Attitudes Toward Electroconvulsive Therapy Among Iranian Nurses and Patients’ Relatives in a Psychiatric Hospital, 2009-2010

AbstractElectroconvulsive therapy (ECT) is a cost effective method in the treatment of some psychiatric disorders. Although, service users such as health providers and nurses, also patients and their relatives may refuse ECT when indicated, due to the myths and little or lack of knowledge about the procedure. The knowledge of and attitudes toward ECT among nurses, may reflect on patients and influence treatment choice. For doing this procedure relatives informed consent is necessary, so their knowledge of and attitude toward ECT is important for getting informed consent and following treatment sessions. Objective: This research was conducted as a quasi-experimental study to measure knowledge of and attitudes toward ECT in 2 groups: relatives and nursing. Also, to study the effect of education on knowledge of and attitudes toward ECT in 2 groups. Methods: In this research the pre and post test self – administered questionnaires were completed by 46 relatives and 46 nurses before and after education about ECT. Results: Nurses in this research received a mean score of X=34.97 knowledge before education and X=39.78 after education (t=2.02, p<0.05), and a mean score of X=33.41 attitude before education and, X=42.82 after education (t=-14.25, p<0.001). Relatives received a mean score of X=23.41 knowledge before education and X=30.15 after education (t=-12.44, p<0.001), and a mean score of X=33.39 attitude before education and, X=41.13 after education (t=-9.10, p<0.001). The differences between the 2 means among two groups were found to be statistically significant. Conclusion: Education given to nurses and relatives about ECT increased their knowledge of, and improved their attitudes toward ECT. For this reason it is recommended that continuing education about ECT process should be planned and given at regular intervals

Recommendations on Surveillance for Differentiated Thyroid Carcinoma in Children with PTEN Hamartoma Tumor Syndrome

BACKGROUND: PTEN hamartoma tumor syndrome (PHTS) represents a group of syndromes caused by a mutation in the PTEN gene. Children with a germline PTEN mutation have an increased risk of developing differentiated thyroid carcinoma (DTC). Several guidelines have focused on thyroid surveillance in these children, but studies substantiating these recommendations are lacking. OBJECTIVE: The present study intends to provide the available evidence for a thyroid carcinoma surveillance program in children with PHTS. METHODS: An extensive literature search was performed to identify all studies on DTC in pediatric PHTS patients. Two pediatric cases are presented to illustrate the pros and cons of thyroid carcinoma surveillance. Recommendations for other patient groups at risk for DTC were evaluated. Consensus within the study team on recommendations for children with PHTS was reached by balancing the incidence and behavior of DTC with the pros and cons of thyroid surveillance, and the different surveillance methods. RESULTS: In 5 cohort studies the incidence of DTC in childhood ranged from 4 to 12%. In total 57 cases of DTC and/or benign nodular disease in pediatric PHTS patients were identified, of which 27 had proven DTC, with a median age of 12 years (range 4-17). Follicular thyroid carcinoma (FTC) was diagnosed in 52% of the pediatric DTC patients. No evidence was found for a different clinical behavior of DTC in PHTS patients compared to sporadic DTC. CONCLUSIONS: Children with PHTS are at increased risk for developing DTC, with 4 years being the youngest age reported at presentation and FTC being overrepresented. DTC in pediatric PHTS patients does not seem to be more aggressive than sporadic DTC. RECOMMENDATIONS: Surveillance for DTC in pediatric PHTS patients seems justified, as early diagnosis may decrease morbidity. Consensus within the study team was reached to recommend surveillance from the age of 10 years onwards, since at that age the incidence of DTC seems to reach 5%. Surveillance for DTC should consist of yearly neck palpation and triennial thyroid ultrasound. Surveillance in children with PHTS should be performed in a center of excellence for pediatric thyroid disease or PHTS