2,357 research outputs found

    Counting, generating and sampling tree alignments

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    Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees SS and TT. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201

    Schools and education

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    Children in the North are more likely to live in poverty than those in the rest of England – and increasingly so. Poverty is the lead driver of inequalities between children in the North and their counterparts in the rest of the country, leading to worse physical and mental health outcomes, educational attainment, and lower lifelong economic productivity. The COVID-19 pandemic has made this situation worse. Although the full impact is not yet known, modelling suggests that, without intervention, the outlook is bleak. To address the North-South productivity gap we must tackle the stark inequalities evidenced in this report, put in place a child-first place-based recovery plan, and enable the children of the North to fulfil their potential

    RNA secondary structure formation: a solvable model of heteropolymer folding

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    The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

    Constructing transnational solidarity: the role of campaign governance

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    Our inductive study of two transnational labour solidarity efforts focuses on the role of campaign governance. Specifically, we study contrasting campaign strategies, tactics and coalition structures in campaigns by two global union federations, UNI Global Union and the IUF, contextualized in terms of how these campaigns unfolded in India. Our contribution consists of two arguments. The first is that a degree of internal consistency amongst different campaign elements is important for success, and the second is that a mode of articulation that allows for local concerns in affiliate countries to find voice in global campaigns is more likely to result in concrete gains at the local level

    Addition-Deletion Networks

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    We study structural properties of growing networks where both addition and deletion of nodes are possible. Our model network evolves via two independent processes. With rate r, a node is added to the system and this node links to a randomly selected existing node. With rate 1, a randomly selected node is deleted, and its parent node inherits the links of its immediate descendants. We show that the in-component size distribution decays algebraically, c_k ~ k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with the addition rate r. Structural properties of the network including the height distribution, the diameter of the network, the average distance between two nodes, and the fraction of dangling nodes are also obtained analytically. Interestingly, the deletion process leads to a giant hub, a single node with a macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure

    Modeling long-range memory with stationary Markovian processes

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    In this paper we give explicit examples of power-law correlated stationary Markovian processes y(t) where the stationary pdf shows tails which are gaussian or exponential. These processes are obtained by simply performing a coordinate transformation of a specific power-law correlated additive process x(t), already known in the literature, whose pdf shows power-law tails 1/x^a. We give analytical and numerical evidence that although the new processes (i) are Markovian and (ii) have gaussian or exponential tails their autocorrelation function still shows a power-law decay =1/T^b where b grows with a with a law which is compatible with b=a/2-c, where c is a numerical constant. When a<2(1+c) the process y(t), although Markovian, is long-range correlated. Our results help in clarifying that even in the context of Markovian processes long-range dependencies are not necessarily associated to the occurrence of extreme events. Moreover, our results can be relevant in the modeling of complex systems with long memory. In fact, we provide simple processes associated to Langevin equations thus showing that long-memory effects can be modeled in the context of continuous time stationary Markovian processes.Comment: 5 figure

    Rank Statistics in Biological Evolution

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    We present a statistical analysis of biological evolution processes. Specifically, we study the stochastic replication-mutation-death model where the population of a species may grow or shrink by birth or death, respectively, and additionally, mutations lead to the creation of new species. We rank the various species by the chronological order by which they originate. The average population N_k of the kth species decays algebraically with rank, N_k ~ M^{mu} k^{-mu}, where M is the average total population. The characteristic exponent mu=(alpha-gamma)/(alpha+beta-gamma)$ depends on alpha, beta, and gamma, the replication, mutation, and death rates. Furthermore, the average population P_k of all descendants of the kth species has a universal algebraic behavior, P_k ~ M/k.Comment: 4 pages, 3 figure

    Swelfe: a detector of internal repeats in sequences and structures

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    Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results
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