Parallel Patterns for Agent-based Evolutionary Computing

Computing applications such as metaheuristics-based optimization can greatly benefit from multi-core architectures available on modern supercomputers. In this paper, we describe an easy and efficient way to implement certain population-based algorithms (in the discussed case, multi-agent computing system) on such runtime environments. Our solution is based on an Erlang software library which implements dedicated parallel patterns. We provide technological details on our approach and discuss experimental results

Recurrent mutations of BRCA1, BRCA2 and PALB2 in the population of breast and ovarian cancer patients in Southern Poland

Background Mutations in the BRCA1, BRCA2 and PALB2 genes are well-established risk factors for the development of breast and/or ovarian cancer. The frequency and spectrum of mutations in these genes has not yet been examined in the population of Southern Poland. Methods We examined the entire coding sequences of the BRCA1 and BRCA2 genes and genotyped a recurrent mutation of the PALB2 gene (c.509_510delGA) in 121 women with familial and/or early-onset breast or ovarian cancer from Southern Poland. Results A BRCA1 mutation was identified in 11 of 121 patients (9.1 %) and a BRCA2 mutation was identified in 10 of 121 patients (8.3 %). Two founder mutations of BRCA1 accounted for 91 % of all BRCA1 mutation carriers (c.5266dupC was identified in six patients and c.181 T > G was identified in four patients). Three of the seven different BRCA2 mutations were detected in two patients each (c.9371A > T, c.9403delC and c.1310_1313delAAGA). Three mutations have not been previously reported in the Polish population (BRCA1 c.3531delT, BRCA2 c.1310_1313delAAGA and BRCA2 c.9027delT). The recurrent PALB2 mutation c.509_510delGA was identified in two patients (1.7 %). Conclusions The standard panel of BRCA1 founder mutations is sufficiently sensitive for the identification of BRCA1 mutation carriers in Southern Poland. The BRCA2 mutations c.9371A > T and c.9403delC as well as the PALB2 mutation c.509_510delGA should be included in the testing panel for this population

Enhancing Particle Swarm Optimization with Socio-cognitive Inspirations

Following recently published socio-cognitively inspired ACO concept for global optimization, we try to verify the proposed idea by adapting the PSO in a similar way. The swarm is divided into species and the particles get inspired not only by the global and local optima, but share the knowledge about the optima with neighbourhood agents belonging to other species. After presenting the concept and motivation, the experimental results gathered for common benchmark functions tackled in 100 dimensions are shown and the efficacy of the proposed algorithm is discussed

Recurrent Mutations in <i>BRCA1</i>, <i>BRCA2</i>, <i>RAD51C</i>, <i>PALB2</i> and <i>CHEK2</i> in Polish Patients with Ovarian Cancer

The aim of the study was to analyze the frequency and magnitude of association of 21 recurrent founder germline mutations in BRCA1, BRCA2, PALB2, RAD51C, and CHEK2 genes with ovarian cancer risk among unselected patients in Poland. We genotyped 21 recurrent germline mutations in BRCA1 (9 mutations), BRCA2 (4 mutations), RAD51C (3 mutations), PALB2 (2 mutations), and CHEK2 (3 mutations) among 2270 Polish ovarian cancer patients and 1743 healthy controls, and assessed the odds ratios (OR) for developing ovarian cancer for each gene. Mutations were detected in 369 out of 2095 (17.6%) unselected ovarian cancer cases and 117 out of 1743 (6.7%) unaffected controls. The ovarian cancer risk was associated with mutations in BRCA1 (OR = 40.79, 95% CI: 18.67–114.78; p = 0.29 × 10−15), in BRCA2 (OR = 25.98; 95% CI: 1.55–434.8; p = 0.001), in RAD51C (OR = 6.28; 95% CI 1.77–39.9; p = 0.02), and in PALB2 (OR 3.34; 95% CI: 1.06–14.68; p = 0.06). There was no association found for CHEK2. We found that pathogenic mutations in BRCA1, BRCA2, RAD51C or PALB2 are responsible for 12.5% of unselected cases of ovarian cancer. We recommend that all women with ovarian cancer in Poland and first-degree female relatives should be tested for this panel of 18 mutations