42,471 research outputs found
Developing and applying heterogeneous phylogenetic models with XRate
Modeling sequence evolution on phylogenetic trees is a useful technique in
computational biology. Especially powerful are models which take account of the
heterogeneous nature of sequence evolution according to the "grammar" of the
encoded gene features. However, beyond a modest level of model complexity,
manual coding of models becomes prohibitively labor-intensive. We demonstrate,
via a set of case studies, the new built-in model-prototyping capabilities of
XRate (macros and Scheme extensions). These features allow rapid implementation
of phylogenetic models which would have previously been far more
labor-intensive. XRate's new capabilities for lineage-specific models,
ancestral sequence reconstruction, and improved annotation output are also
discussed. XRate's flexible model-specification capabilities and computational
efficiency make it well-suited to developing and prototyping phylogenetic
grammar models. XRate is available as part of the DART software package:
http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog
Calipso: Physics-based Image and Video Editing through CAD Model Proxies
We present Calipso, an interactive method for editing images and videos in a
physically-coherent manner. Our main idea is to realize physics-based
manipulations by running a full physics simulation on proxy geometries given by
non-rigidly aligned CAD models. Running these simulations allows us to apply
new, unseen forces to move or deform selected objects, change physical
parameters such as mass or elasticity, or even add entire new objects that
interact with the rest of the underlying scene. In Calipso, the user makes
edits directly in 3D; these edits are processed by the simulation and then
transfered to the target 2D content using shape-to-image correspondences in a
photo-realistic rendering process. To align the CAD models, we introduce an
efficient CAD-to-image alignment procedure that jointly minimizes for rigid and
non-rigid alignment while preserving the high-level structure of the input
shape. Moreover, the user can choose to exploit image flow to estimate scene
motion, producing coherent physical behavior with ambient dynamics. We
demonstrate Calipso's physics-based editing on a wide range of examples
producing myriad physical behavior while preserving geometric and visual
consistency.Comment: 11 page
Adaptive Sentence Boundary Disambiguation
Labeling of sentence boundaries is a necessary prerequisite for many natural
language processing tasks, including part-of-speech tagging and sentence
alignment. End-of-sentence punctuation marks are ambiguous; to disambiguate
them most systems use brittle, special-purpose regular expression grammars and
exception rules. As an alternative, we have developed an efficient, trainable
algorithm that uses a lexicon with part-of-speech probabilities and a
feed-forward neural network. After training for less than one minute, the
method correctly labels over 98.5\% of sentence boundaries in a corpus of over
27,000 sentence-boundary marks. We show the method to be efficient and easily
adaptable to different text genres, including single-case texts.Comment: This is a Latex version of the previously submitted ps file
(formatted as a uuencoded gz-compressed .tar file created by csh script). The
software from the work described in this paper is available by contacting
[email protected]
A Computational-Experimental Approach Identifies Mutations That Enhance Surface Expression of an Oseltamivir-Resistant Influenza Neuraminidase
The His274 β Tyr (H274Y) oseltamivir (Tamiflu) resistance mutation causes a substantial decrease in the total levels of surface-expressed neuraminidase protein and activity in early isolates of human seasonal H1N1 influenza, and in the swine-origin pandemic H1N1. In seasonal H1N1, H274Y only became widespread after the occurrence of secondary mutations that counteracted this decrease. H274Y is currently rare in pandemic H1N1, and it remains unclear whether secondary mutations exist that might similarly counteract the decreased neuraminidase surface expression associated with this resistance mutation in pandemic H1N1. Here we investigate the possibility of predicting such secondary mutations. We first test the ability of several computational approaches to retrospectively identify the secondary mutations that enhanced levels of surface-expressed neuraminidase protein and activity in seasonal H1N1 shortly before the emergence of oseltamivir resistance. We then use the most successful computational approach to predict a set of candidate secondary mutations to the pandemic H1N1 neuraminidase. We experimentally screen these mutations, and find that several of them do indeed partially counteract the decrease in neuraminidase surface expression caused by H274Y. Two of the secondary mutations together restore surface-expressed neuraminidase activity to wildtype levels, and also eliminate the very slight decrease in viral growth in tissue-culture caused by H274Y. Our work therefore demonstrates a combined computational-experimental approach for identifying mutations that enhance neuraminidase surface expression, and describes several specific mutations with the potential to be of relevance to the spread of oseltamivir resistance in pandemic H1N1
Exact theory of kinkable elastic polymers
The importance of nonlinearities in material constitutive relations has long
been appreciated in the continuum mechanics of macroscopic rods. Although the
moment (torque) response to bending is almost universally linear for small
deflection angles, many rod systems exhibit a high-curvature softening. The
signature behavior of these rod systems is a kinking transition in which the
bending is localized. Recent DNA cyclization experiments by Cloutier and Widom
have offered evidence that the linear-elastic bending theory fails to describe
the high-curvature mechanics of DNA. Motivated by this recent experimental
work, we develop a simple and exact theory of the statistical mechanics of
linear-elastic polymer chains that can undergo a kinking transition. We
characterize the kinking behavior with a single parameter and show that the
resulting theory reproduces both the low-curvature linear-elastic behavior
which is already well described by the Wormlike Chain model, as well as the
high-curvature softening observed in recent cyclization experiments.Comment: Revised for PRE. 40 pages, 12 figure
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