2,271 research outputs found
Hairpin lengthening: algorithmic results.
We consider here a new variant of the hairpin completion, called hairpin lengthening, which seems more appropriate for practical implementation. The variant considered here concerns the lengthening of the word that forms a hairpin structure, such that this structure is preserved, without necessarily completing the hairpin. Although our motivation is based on biological phenomena, the present paper is more about some algorithmic properties of this operation. Finally, we propose an algorithm for computing the hairpin lengthening distance between two words in quadratic time
It Is NL-complete to Decide Whether a Hairpin Completion of Regular Languages Is Regular
The hairpin completion is an operation on formal languages which is inspired
by the hairpin formation in biochemistry. Hairpin formations occur naturally
within DNA-computing. It has been known that the hairpin completion of a
regular language is linear context-free, but not regular, in general. However,
for some time it is was open whether the regularity of the hairpin completion
of a regular language is is decidable. In 2009 this decidability problem has
been solved positively by providing a polynomial time algorithm. In this paper
we improve the complexity bound by showing that the decision problem is
actually NL-complete. This complexity bound holds for both, the one-sided and
the two-sided hairpin completions
Dagstuhl Reports : Volume 1, Issue 2, February 2011
Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn
Close interactions of 3-D vortex tubes
The motivation for studying close vortex interactions is briefly discussed in the light of turbulence and coherent structures. Particular attention is given to the interaction known as reconnection. Two reconnection mechanisms are discussed. One is annihilation of vorticity by cross-diffusion, the other is an inviscid head-tail formation. At intermediate Reynolds numbers both mechanisms are operating
Splice variants of DOMINO control Drosophila circadian behavior and pacemaker neuron maintenance.
Circadian clocks control daily rhythms in behavior and physiology. In Drosophila, the small ventral lateral neurons (sLNvs) expressing PIGMENT DISPERSING FACTOR (PDF) are the master pacemaker neurons generating locomotor rhythms. Despite the importance of sLNvs and PDF in circadian behavior, little is known about factors that control sLNvs maintenance and PDF accumulation. Here, we identify the Drosophila SWI2/SNF2 protein DOMINO (DOM) as a key regulator of circadian behavior. Depletion of DOM in circadian neurons eliminates morning anticipatory activity under light dark cycle and impairs behavioral rhythmicity in constant darkness. Interestingly, the two major splice variants of DOM, DOM-A and DOM-B have distinct circadian functions. DOM-A depletion mainly leads to arrhythmic behavior, while DOM-B knockdown lengthens circadian period without affecting the circadian rhythmicity. Both DOM-A and DOM-B bind to the promoter regions of key pacemaker genes period and timeless, and regulate their protein expression. However, we identify that only DOM-A is required for the maintenance of sLNvs and transcription of pdf. Lastly, constitutive activation of PDF-receptor signaling rescued the arrhythmia and period lengthening of DOM downregulation. Taken together, our findings reveal that two splice variants of DOM play distinct roles in circadian rhythms through regulating abundance of pacemaker proteins and sLNvs maintenance
Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition
EZH2 inhibitors have gained great interest for their use as anti-cancer therapeutics. However, most research has focused on EZH2 mutant cancers and recently adverse effects of EZH2 inactivation have come to light. To determine whether colorectal cancer cells respond to EZH2 inhibition and to explore which factors influence the degree of response, we treated a panel of 20 organoid lines derived from human colon tumors with different concentrations of the EZH2 inhibitor GSK126. The resulting responses were associated with mutation status, gene expression and responses to other drugs. We found that the response to GSK126 treatment greatly varied between organoid lines. Response associated with the mutation status of ATRX and PAX2, and correlated with BIK expression. It also correlated well with response to Nutlin-3a which inhibits MDM2-p53 interaction thereby activating p53 signaling. Sensitivity to EZH2 ablation depended on the presence of wild type p53, as tumor organoids became resistant when p53 was mutated or knocked down. Our exploratory study provides insight into which genetic factors predict sensitivity to EZH2 inhibition. In addition, we show that the response to EZH2 inhibition requires wild type p53. We conclude that a subset of colorectal cancer patients may benefit from EZH2-targeting therapies
Two-Sided Derivatives for Regular Expressions and for Hairpin Expressions
The aim of this paper is to design the polynomial construction of a finite
recognizer for hairpin completions of regular languages. This is achieved by
considering completions as new expression operators and by applying derivation
techniques to the associated extended expressions called hairpin expressions.
More precisely, we extend partial derivation of regular expressions to
two-sided partial derivation of hairpin expressions and we show how to deduce a
recognizer for a hairpin expression from its two-sided derived term automaton,
providing an alternative proof of the fact that hairpin completions of regular
languages are linear context-free.Comment: 28 page
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