Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs

Author(s):  
Tero Harju ◽  
Ion Petre ◽  
Grzegorz Rozenberg
2009 ◽  
Vol 20 (02) ◽  
pp. 271-291 ◽  
Author(s):  
ROBERT BRIJDER ◽  
HENDRIK JAN HOOGEBOOM ◽  
GRZEGORZ ROZENBERG

Ciliates are unicellular organisms having two types of functionally different nuclei: micronucleus and macronucleus. Gene assembly transforms a micronucleus into a macronucleus, thereby transforming each gene from its micronuclear form to its macronuclear form. Within a formal intramolecular model of gene assembly based on strings, the notion of reduction graph represents the macronuclear form of a gene, including byproducts, given only a description of the micronuclear form of that gene. For a more abstract model of gene assembly based on graphs, one cannot, in general, define the notion of reduction graphs. We show that if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature), then the notion of reduction graph can be defined in a manner equivalent to the string model. This allows one to carry over from the string model to the graph model several results that rely on the notion of reduction graph.


2018 ◽  
Author(s):  
Lauren Marie Ackerman

Until now, there has been little experimental work investigating the processing and formal properties of the singular they suite of pronouns. As scientific and popular attention to singular they increases, it will be critical for research to acknowledge theoretical and ethical issues regarding discussion of this phenomenon. This commentary uses the recent paper by Doherty & Conklin (2017) as a starting point to discuss issues surrounding work on the various forms of singular they. It concludes that there is sufficient theoretical and empirical evidence to claim they has a grammatically singular form (at least in colloquial English). It also recommends care be taken in academic discussions of the grammaticality and acceptability of terms which are associated with marginalised communities.


2011 ◽  
Vol 12 (3) ◽  
pp. 279-288
Author(s):  
Shuang WANG ◽  
Guoqing CHAI ◽  
Changsong HU

1981 ◽  
Vol 4 (1) ◽  
pp. 19-34
Author(s):  
Ryszard Danecki

Closure properties of binary ETOL-languages are investigated by means of multiple tree automata. Decidability of the equivalence problem of deterministic binary ETOL-systems is proved.


2011 ◽  
Vol 52 (5) ◽  
pp. 053509 ◽  
Author(s):  
Caroline M. Cochran ◽  
Raymond G. McLenaghan ◽  
Roman G. Smirnov
Keyword(s):  

2006 ◽  
Vol 49 (2) ◽  
pp. 170-184
Author(s):  
Richard Atkins

AbstractThis paper investigates the relationship between a system of differential equations and the underlying geometry associated with it. The geometry of a surface determines shortest paths, or geodesics connecting nearby points, which are defined as the solutions to a pair of second-order differential equations: the Euler–Lagrange equations of the metric. We ask when the converse holds, that is, when solutions to a system of differential equations reveals an underlying geometry. Specifically, when may the solutions to a given pair of second order ordinary differential equations d2y1/dt2 = f (y, ẏ, t) and d2y2/dt2 = g(y, ẏ, t) be reparameterized by t → T(y, t) so as to give locally the geodesics of a Euclidean space? Our approach is based upon Cartan's method of equivalence. In the second part of the paper, the equivalence problem is solved for a generic pair of second order ordinary differential equations of the above form revealing the existence of 24 invariant functions.


1992 ◽  
Vol 17 (1-2) ◽  
pp. 157-173
Author(s):  
Grigori Schwarz

We propose a new variant of autoepistemic logic which, intuitively, corresponds to understanding a belief operator L as “is known”, in contrast to the interpretation of L as “is believed” in Moore’s autoepistemic logic. Formal properties of the new logic and relationship to Moore’s logic are studied in detail.


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