Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis

Background: The probe percent bound value, calculated using multi-state equilibrium models of solution hybridization, is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in widespread use on microarrays, but there are few controlled studies of their interactions with mismatched targets compared to 25-mer based platforms. Principal Findings: 50-mer oligonucleotides with centrally placed single, double and triple mismatches were spotted on an array. Over a range of target concentrations it was possible to discriminate binding to perfect matches and mismatches, and the type of mismatch could be predicted accurately in the concentration midrange (100 pM to 200 pM) using solution hybridization modeling methods. These results have implications for microarray design, optimization and analysis methods. Conclusions: Our results highlight the importance of incorporating biophysical factors in both the design and the analysis of microarrays. Use of the probe ‘‘percent bound’ ’ value predicted by equilibrium models of hybridization is confirmed to be important for predicting and interpreting the behavior of long oligonucleotide arrays, as has been shown for shor

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

The incorporation of fixed cost and multilevel capacities into the discrete and continuous single source capacitated facility location problem

In this study we investigate the single source location problem with the presence of several possible capacities and the opening (fixed) cost of a facility that is depended on the capacity used and the area where the facility is located. Mathematical models of the problem for both the discrete and the continuous cases using the Rectilinear and Euclidean distances are produced. Our aim is to find the optimal number of open facilities, their corresponding locations, and their respective capacities alongside the assignment of the customers to the open facilities in order to minimise the total fixed and transportation costs. For relatively large problems, two solution methods are proposed namely an iterative matheuristic approach and VNS-based matheuristic technique. Dataset from the literature is adapted to assess our proposed methods. To assess the performance of the proposed solution methods, the exact method is first applied to small size instances where optimal solutions can be identified or lower and upper bounds can be recorded. Results obtained by the proposed solution methods are also reported for the larger instances