3,759 research outputs found
Ngugi’s retrospective gaze: The shape of history in A grain of wheat
Ngugi Wa Thiong’o’s engagement with history in A Grain of Wheat has been commented upon by critics differently. G.D. Killam (201) and Andrew Gurr (92) view it within the post-colonial frame in which ‘received history is tampered with, rewritten, and realigned from the point of view of the victims of its destructive process’ (Ashcroft et al 34). In their view, Ngugi’s first three novels — Weep Not, Child, The River Between, and A Grain of Wheat — provide his version of Kenya’s history from the 1920s to the time of its independence. Ime Ikiddeh too considers Ngugi a novelist-historian, who focuses on key phases in the history of Kenya covered in the novels, but reads A Grain of Wheat mostly as a story of heroism and betrayal, of human relationships in a chosen situation (76–77)
Predicting B Cell Receptor Substitution Profiles Using Public Repertoire Data
B cells develop high affinity receptors during the course of affinity
maturation, a cyclic process of mutation and selection. At the end of affinity
maturation, a number of cells sharing the same ancestor (i.e. in the same
"clonal family") are released from the germinal center, their amino acid
frequency profile reflects the allowed and disallowed substitutions at each
position. These clonal-family-specific frequency profiles, called "substitution
profiles", are useful for studying the course of affinity maturation as well as
for antibody engineering purposes. However, most often only a single sequence
is recovered from each clonal family in a sequencing experiment, making it
impossible to construct a clonal-family-specific substitution profile. Given
the public release of many high-quality large B cell receptor datasets, one may
ask whether it is possible to use such data in a prediction model for
clonal-family-specific substitution profiles. In this paper, we present the
method "Substitution Profiles Using Related Families" (SPURF), a penalized
tensor regression framework that integrates information from a rich assemblage
of datasets to predict the clonal-family-specific substitution profile for any
single input sequence. Using this framework, we show that substitution profiles
from similar clonal families can be leveraged together with simulated
substitution profiles and germline gene sequence information to improve
prediction. We fit this model on a large public dataset and validate the
robustness of our approach on an external dataset. Furthermore, we provide a
command-line tool in an open-source software package
(https://github.com/krdav/SPURF) implementing these ideas and providing easy
prediction using our pre-fit models.Comment: 23 page
Exact extremal statistics in the classical Coulomb gas
We consider a one-dimensional classical Coulomb gas of like-charges in a
harmonic potential -- also known as the one-dimensional one-component plasma
(1dOCP). We compute analytically the probability distribution of the position
of the rightmost charge in the limit of large . We show that the
typical fluctuations of around its mean are described by a
non-trivial scaling function, with asymmetric tails. This distribution is
different from the Tracy-Widom distribution of for the Dyson's
log-gas. We also compute the large deviation functions of explicitly
and show that the system exhibits a third-order phase transition, as in the
log-gas. Our theoretical predictions are verified numerically.Comment: 5 pages + 5 pages of supplementary material, 4 figure
Run-and-tumble particle in one-dimensional confining potential: Steady state, relaxation and first passage properties
We study the dynamics of a one-dimensional run and tumble particle subjected
to confining potentials of the type , with . The
noise that drives the particle dynamics is telegraphic and alternates between
values. We show that the stationary probability density has a
rich behavior in the -plane. For , the distribution has a
finite support in and there is a critical line that
separates an active-like phase for where diverges
at , from a passive-like phase for where
vanishes at . For , the stationary density collapses to a
delta function at the origin, . In the marginal case ,
we show that, for , the stationary density is a
symmetric exponential, while for , it again is a delta
function . For the special cases and , we obtain
exactly the full time-dependent distribution , that allows us to study
how the system relaxes to its stationary state. In addition, in these two
cases, we also study analytically the full distribution of the first-passage
time to the origin. Numerical simulations are in complete agreement with our
analytical predictions.Comment: 17 pages, 12 figure
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.
The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling
Electron impact ionization of metastable 2P-state hydrogen atoms in the coplanar geometry
AbstractTriple differential cross sections (TDCS) for the ionization of metastable 2P-state hydrogen atoms by electrons are calculated for various kinematic conditions in the asymmetric coplanar geometry. In this calculation, the final state is described by a multiple-scattering theory for ionization of hydrogen atoms by electrons. Results show qualitative agreement with the available experimental data and those of other theoretical computational results for ionization of hydrogen atoms from ground state, and our first Born results. There is no available other theoretical results and experimental data for ionization of hydrogen atoms from the 2P state. The present study offers a wide scope for the experimental study for ionization of hydrogen atoms from the metastable 2P state
Percolation Systems away from the Critical Point
This article reviews some effects of disorder in percolation systems even
away from the critical density p_c. For densities below p_c, the statistics of
large clusters defines the animals problem. Its relation to the directed
animals problem and the Lee-Yang edge singularity problem is described. Rare
compact clusters give rise to Griffiths singuraties in the free energy of
diluted ferromagnets, and lead to a very slow relaxation of magnetization. In
biassed diffusion on percolation clusters, trapping in dead-end branches leads
to asymptotic drift velocity becoming zero for strong bias, and very slow
relaxation of velocity near the critical bias field.Comment: Minor typos fixed. Submitted to Praman
Algebraic Aspects of Abelian Sandpile Models
The abelian sandpile models feature a finite abelian group G generated by the
operators corresponding to particle addition at various sites. We study the
canonical decomposition of G as a product of cyclic groups G = Z_{d_1} X
Z_{d_2} X Z_{d_3}...X Z_{d_g}, where g is the least number of generators of G,
and d_i is a multiple of d_{i+1}. The structure of G is determined in terms of
toppling matrix. We construct scalar functions, linear in height variables of
the pile, that are invariant toppling at any site. These invariants provide
convenient coordinates to label the recurrent configurations of the sandpile.
For an L X L square lattice, we show that g = L. In this case, we observe that
the system has nontrivial symmetries coming from the action of the cyclotomic
Galois group of the (2L+2)th roots of unity which operates on the set of
eigenvalues of the toppling matrix. These eigenvalues are algebraic integers,
whose product is the order |G|. With the help of this Galois group, we obtain
an explicit factorizaration of |G|. We also use it to define other simpler,
though under-complete, sets of toppling invariants.Comment: 39 pages, TIFR/TH/94-3
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