2,357 research outputs found
Counting, generating and sampling tree alignments
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 and . 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
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
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
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
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
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
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
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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