Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Andrology laboratory review : evaluation of sperm concentration

This article is the result of the work of the andrology task-force of the Association of Applied Animal Andrology, American College of Theriogenologists, European College of Animal Reproduction, Society for Theriogenology, and National Association of Animal Breeders. It is intended to serve as a comprehensive reference on methods to evaluate sperm concentration and to contribute to the adoption of best practices in veterinary andrology laboratories. The information covered in the article includes sample preparation and the use of manual counts, spectrohotometers, computer-assisted semen analysis, NucleoCounter, and flow cytometry. Emphasis is given to the principles of the methods and equipment, performing the evaluation, and common mistakes and/or pitfalls. In addition, the precision and accuracy of the different methods are also discussed

Verification of Source Code Transformations by Program Equivalence Checking

Typically, a combination of manual and automated transformations is applied when algorithms for digital signal processing are adapted for energy and performance-e#cient embedded systems. This poses severe verification problems. Verification becomes easier after converting the code into dynamic single-assignment form (DSA). This paper describes a method to prove equivalence between two programs in DSA where subscripts to array variables and loop bounds are (piecewise) a#ne expressions. For such programs, geometric modeling can be used and it can be shown, for groups of elements at once, that the outputs in both programs are the same function of the inputs