86,427 research outputs found
Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem
This paper builds upon the fundamental work of Niwa et al. [34], which
provides the unique possibility to analyze the relative aggregation/folding
propensity of the elements of the entire Escherichia coli (E. coli) proteome in
a cell-free standardized microenvironment. The hardness of the problem comes
from the superposition between the driving forces of intra- and inter-molecule
interactions and it is mirrored by the evidences of shift from folding to
aggregation phenotypes by single-point mutations [10]. Here we apply several
state-of-the-art classification methods coming from the field of structural
pattern recognition, with the aim to compare different representations of the
same proteins gathered from the Niwa et al. data base; such representations
include sequences and labeled (contact) graphs enriched with chemico-physical
attributes. By this comparison, we are able to identify also some interesting
general properties of proteins. Notably, (i) we suggest a threshold around 250
residues discriminating "easily foldable" from "hardly foldable" molecules
consistent with other independent experiments, and (ii) we highlight the
relevance of contact graph spectra for folding behavior discrimination and
characterization of the E. coli solubility data. The soundness of the
experimental results presented in this paper is proved by the statistically
relevant relationships discovered among the chemico-physical description of
proteins and the developed cost matrix of substitution used in the various
discrimination systems.Comment: 17 pages, 3 figures, 46 reference
Sparse Modeling for Image and Vision Processing
In recent years, a large amount of multi-disciplinary research has been
conducted on sparse models and their applications. In statistics and machine
learning, the sparsity principle is used to perform model selection---that is,
automatically selecting a simple model among a large collection of them. In
signal processing, sparse coding consists of representing data with linear
combinations of a few dictionary elements. Subsequently, the corresponding
tools have been widely adopted by several scientific communities such as
neuroscience, bioinformatics, or computer vision. The goal of this monograph is
to offer a self-contained view of sparse modeling for visual recognition and
image processing. More specifically, we focus on applications where the
dictionary is learned and adapted to data, yielding a compact representation
that has been successful in various contexts.Comment: 205 pages, to appear in Foundations and Trends in Computer Graphics
and Visio
The Grid Dependence of Well Inflow Performance in Reservoir Simulation
Imperial Users onl
The p_T Spectrum in Heavy-Flavour Photoproduction
We consider the transverse-momentum distribution of heavy flavours in
photon-hadron collisions. We present a formalism in which large
transverse-momentum logarithms are resummed to the next-to-leading level, and
mass effects are included exactly up to order alpha_em alpha_s^2, so as to
retain predictivity at both small and large transverse momenta.
Phenomenological applications relevant to charm photoproduction at HERA are
given.Comment: 26 pages, Latex, epsfig, 15 figures. Submitted to JHE
- …