Revisiting Waiting Times in DNA evolution

Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron consider a random sequence of length $n$ that does not contain a given $k$-mer or word of size $k$. Under an evolution model of the DNA, they compute the probability $\mathfrak{p}_n$ that this $k$-mer appears after a unit time of 20 years. They prove that the waiting time for the first apparition of the $k$-mer is well approximated by $T_n=1/\mathfrak{p}_n$. Their work relies on the simplifying assumption that the $k$-mer is not self-overlapping. They observe in particular that the waiting time is mostly driven by the initial distribution of letters. Behrens et al. use an approach by automata that relaxes the assumption related to words overlaps. Their numerical evaluations confirms the validity of Behrens and Vingron approach for non self-overlapping words, but provides up to 44% corrections for highly self-overlapping words such as $\mathtt{AAAAA}$. We devised an approach of the problem by clump analysis and generating functions; this approach leads to prove a quasi-linear behaviour of $\mathfrak{p}_n$ for a large range of values of $n$, an important result for DNA evolution. We present here this clump analysis, first by language decomposition, and next by an automaton construction; finally, we describe an equivalent approach by construction of Markov automata.Comment: 19 pages, 3 Figures, 2 Table

Trumpism and being in worlds that fall between worlds

In response to Kyle McGee’s Heathen Earth, this paper says something about the place of toxic legacies in the rise and sustenance of ‘Trumpism’. It takes an interest in rusting factories, melting ice, etc., but as assemblages that are tricky because they concern a build up of externalities and relational factors for which there is a deficit of known co-ordinates. The term ‘sludge’ is sometimes affixed to these unexplained accumulations, which attend the (productive) neglect of externalities in overlapping schemas of relationality. The paper relates this ‘sludge’ to the emergence of a void, somewhere below the legal thresholds of accountability, into which words and actions can be thrown ‘at will’. This void is muddy, and makes politics unbearable to watch; and, yet, we are caught in a loop of reproducing the void through our own charting and supervision of action and, then, being shocked by the filth that comes out. The comment ends with a brief reflection on attending to the situation of forgotten existences and living with the ruins of past and present worlds

Japanese Saving Rate

Japanese and U.S. saving rates have been significantly different over the last forty years. Can a standard growth model explain this difference? The answer is yes. Our results indicate that both an infinite horizon, complete markets setup and an overlapping generations model with incomplete markets are about equally able to generate saving rates that are remarkably similar to the data during 1961-1998. Our quantitative findings identify changes in the growth rate of total factor productivity and the low initial capital stock as the main factors generating the time series behavior of the net national saving rate in Japan. We show that if the Japanese had faced the U.S. TFP and initial conditions, their saving rate would have looked very similar to that of the U.S. households. In other words, it seems that there is nothing peculiar about the Japanese saving behavior.Neoclassical Growth Model, Saving Behavior, Total Factor Productivity

Between the Eurasian and European subsystems: migration and migration policy in the CIS and Baltic Countries in the 1990s - 2020s

The article analyses migration from border countries (the so-called overlapping area) of two migration subsystems - Eurasian (centred in the Russian Federation) and European (the European Union) from 1991 to 2021 (before the recent events in Ukraine). A step-by-step analysis of the migration situation in the countries of the former USSR - Belarus, Latvia, Lithuania, Moldova, Ukraine and Estonia was conducted. The article examines bilateral and multilateral migration processes, analyses the main factors influencing their development and explores migration policy measures and their impact on the regulation of migration processes in the countries of the overlapping area. These countries, located between the two centres of major migration subsystems in Eurasia (Eurasian and European, or, in other words, between the Russian Federation and the core of the EU), are subject to their strong influence and 'competitive gravitation'. The strength of this gravitation depends not only on pull and push factors but also on the attractiveness and non-attractiveness of the migration policies prevailing in these migration subsystems at a given point in time

PREFIX UNITS WITHIN THE MENTAL LEXICON

International audienceThree masked priming experiments associated with the lexical decision task were carried out in order to examine the cognitive processing of prefixed words in French. To this end we systematically compared the effects of the prior presentation of prefixed words (e.g., prénom), prefixed nonwords (e.g., dénom) or orthographic nonwords (e.g., danom) on the recognition latencies of their root (e.g., nom) or of another related prefixed word (e.g., surnom). When compared to unrelated primes, both prefixed words and nonwords facilitated target recognition (Experiments 1 & 2) and this was not an effect arising from the frequency ratio between roots and prefixed derivations. However, when morphological priming effects were measured against orthographic nonword controls, that where combinations of existing roots with nonexisting prefixes, morphological effects did not differ significantly from orthographic effects (Experiment 3). This finding suggests that morphological priming effects do not totally depend on the decomposition of the prime in two distinct morphemes, as suggested by Rastle & Davis (2008) but tend to be sensitive to formal factors (more precisely overlapping roots), even though they cannot be reduced to simple orthographic priming. Taken together, the present data moderate the full decomposition approach of morphological processing. A new model is proposed, integrating both sublexical units corresponding to "morphomes" (Aronoff, 1994) and supralexical units assimilated to "base-lexemes"

When the words are not everything: the use of laughter, fillers, back-channel, silence, and overlapping speech in phone calls

This article presents an observational study on how some common conversational cues – laughter, fillers, back-channel, silence, and overlapping speech – are used during mobile phone conversations. The observations are performed over the SSPNet Mobile Corpus, a collection of 60 calls between pairs of unacquainted individuals (120 subjects for roughly 12 h of material in total). The results show that the temporal distribution of the social signals above is not uniform, but it rather reflects the social meaning they carry and convey. In particular, the results show significant use differences depending on factors such as gender, role (caller or receiver), topic, mode of interaction (agreement or disagreement), personality traits, and conflict handling style

Coding limits on the number of transcription factors

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms. We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction. The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/ http://www.biomedcentral.com/1471-2164/7/23

Generic properties of subgroups of free groups and finite presentations

Asymptotic properties of finitely generated subgroups of free groups, and of finite group presentations, can be considered in several fashions, depending on the way these objects are represented and on the distribution assumed on these representations: here we assume that they are represented by tuples of reduced words (generators of a subgroup) or of cyclically reduced words (relators). Classical models consider fixed size tuples of words (e.g. the few-generator model) or exponential size tuples (e.g. Gromov's density model), and they usually consider that equal length words are equally likely. We generalize both the few-generator and the density models with probabilistic schemes that also allow variability in the size of tuples and non-uniform distributions on words of a given length.Our first results rely on a relatively mild prefix-heaviness hypothesis on the distributions, which states essentially that the probability of a word decreases exponentially fast as its length grows. Under this hypothesis, we generalize several classical results: exponentially generically a randomly chosen tuple is a basis of the subgroup it generates, this subgroup is malnormal and the tuple satisfies a small cancellation property, even for exponential size tuples. In the special case of the uniform distribution on words of a given length, we give a phase transition theorem for the central tree property, a combinatorial property closely linked to the fact that a tuple freely generates a subgroup. We then further refine our results when the distribution is specified by a Markovian scheme, and in particular we give a phase transition theorem which generalizes the classical results on the densities up to which a tuple of cyclically reduced words chosen uniformly at random exponentially generically satisfies a small cancellation property, and beyond which it presents a trivial group

Languages invariant under more symmetries: overlapping factors versus palindromic richness

Factor complexity $\mathcal{C}$ and palindromic complexity $\mathcal{P}$ of infinite words with language closed under reversal are known to be related by the inequality $\mathcal{P}(n) + \mathcal{P}(n+1) \leq 2 + \mathcal{C}(n+1)-\mathcal{C}(n)$ for any $n\in \mathbb{N}$\,. Word for which the equality is attained for any $n$ is usually called rich in palindromes. In this article we study words whose languages are invariant under a finite group $G$ of symmetries. For such words we prove a stronger version of the above inequality. We introduce notion of $G$-palindromic richness and give several examples of $G$-rich words, including the Thue-Morse sequence as well.Comment: 22 pages, 1 figur

Primitive Vassiliev Invariants and Factorization in Chern-Simons Perturbation Theory

The general structure of the perturbative expansion of the vacuum expectation value of a Wilson line operator in Chern-Simons gauge field theory is analyzed. The expansion is organized according to the independent group structures that appear at each order. It is shown that the analysis is greatly simplified if the group factors are chosen in a certain way that we call canonical. This enables us to show that the logarithm of a polinomial knot invariant can be written in terms of primitive Vassiliev invariants only.Comment: 15 pages, latex, 2 figure