Alignments with non-overlapping moves, inversions and tandem duplications in O ( n 4) time

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitutions. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n 3) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n 5) for general scoring schemes, O(n 4log n) for concave scoring schemes and O(n 4) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provide

D-SLATS: Distributed Simultaneous Localization and Time Synchronization

Through the last decade, we have witnessed a surge of Internet of Things (IoT) devices, and with that a greater need to choreograph their actions across both time and space. Although these two problems, namely time synchronization and localization, share many aspects in common, they are traditionally treated separately or combined on centralized approaches that results in an ineffcient use of resources, or in solutions that are not scalable in terms of the number of IoT devices. Therefore, we propose D-SLATS, a framework comprised of three different and independent algorithms to jointly solve time synchronization and localization problems in a distributed fashion. The First two algorithms are based mainly on the distributed Extended Kalman Filter (EKF) whereas the third one uses optimization techniques. No fusion center is required, and the devices only communicate with their neighbors. The proposed methods are evaluated on custom Ultra-Wideband communication Testbed and a quadrotor, representing a network of both static and mobile nodes. Our algorithms achieve up to three microseconds time synchronization accuracy and 30 cm localization error

Computer-controlled in-vitro simulation of multiple dosing regimens

The bactericidal effect of gentarrucin on Pseudomonas aeruginosa ATCC 27853 was investigated in a computer controlled dynamic in-vitro model, which allows the simultaneous simulation of three different dosing regimens for several days. The same total dose reduced cfu-counts of Pseudomonas aeruginosa most effectively, when administered with peak concentrations of 32 mg/l every 32 h, whereas the other dosing regimens with peak concentrations of 16 mg/l every 16 h and 8 mg/l every 8 h were distinctly less effective following the second and subsequent doses. It was shown that the use of a microcomputer facilitates the in-vitro investigation of multiple dosing regimens but counting of cfu cannot be substituted by automatic measurements of turbidity when rapid bactericidal effects occu