3,813 research outputs found
A conditional compression distance that unveils insights of the genomic evolution
We describe a compression-based distance for genomic sequences. Instead of
using the usual conjoint information content, as in the classical Normalized
Compression Distance (NCD), it uses the conditional information content. To
compute this Normalized Conditional Compression Distance (NCCD), we need a
normal conditional compressor, that we built using a mixture of static and
dynamic finite-context models. Using this approach, we measured chromosomal
distances between Hominidae primates and also between Muroidea (rat and mouse),
observing several insights of evolution that so far have not been reported in
the literature.Comment: Full version of DCC 2014 paper "A conditional compression distance
that unveils insights of the genomic evolution
Conservation laws arising in the study of forward-forward Mean-Field Games
We consider forward-forward Mean Field Game (MFG) models that arise in
numerical approximations of stationary MFGs. First, we establish a link between
these models and a class of hyperbolic conservation laws as well as certain
nonlinear wave equations. Second, we investigate existence and long-time
behavior of solutions for such models
A Contribution to the Modal Identification of the Damping Factor based on the Dissipated Energy
ABSTRACT: The identification of the modal parameters from frequency response functions is a subject that is not new. However, the starting point often comes from the equations that govern the dynamic motion. In this paper, a novel approach is shown, resulting from an analysis that starts on the dissipated energy per cycle of vibration. For lightly damped systems with conveniently spaced modes, it produced quite accurate results in comparison to the direct application of the method of the inverse, both in the numerical and in the experimental examples. It also is a simple technique that can be used to produce quick estimates of the modal damping factors. Furthermore, this is also a contribution to further developments on modal analysis and identification methods as, up to today, the developed technique has not yet been proposed.Final Published versio
Information profiles for DNA pattern discovery
Finite-context modeling is a powerful tool for compressing and hence for
representing DNA sequences. We describe an algorithm to detect genomic
regularities, within a blind discovery strategy. The algorithm uses information
profiles built using suitable combinations of finite-context models. We used
the genome of the fission yeast Schizosaccharomyces pombe strain 972 h- for
illustration, unveilling locations of low information content, which are
usually associated with DNA regions of potential biological interest.Comment: Full version of DCC 2014 paper "Information profiles for DNA pattern
discovery
Comparison of musculoskeletal networks of the primate forelimb
Anatomical network analysis is a framework for quantitatively characterizing the topological organization of anatomical structures, thus providing a way to compare structural integration and modularity among species. Here we apply this approach to study the macroevolution of the forelimb in primates, a structure whose proportions and functions vary widely within this group. We analyzed musculoskeletal network models in 22 genera, including members of all major extant primate groups and three outgroup taxa, after an extensive literature survey and dissections. The modules of the proximal limb are largely similar among taxa, but those of the distal limb show substantial variation. Some network parameters are similar within phylogenetic groups (e.g., non-primates, strepsirrhines, New World monkeys, and hominoids). Reorganization of the modules in the hominoid hand compared to other primates may relate to functional changes such as coordination of individual digit movements, increased pronation/supination, and knuckle-walking. Surprisingly, humans are one of the few taxa we studied in which the thumb musculoskeletal structures do not form an independent anatomical module. This difference may be caused by the loss in humans of some intrinsic muscles associated with the digits or the acquisition of additional muscles that integrate the thumb more closely with surrounding structures
Solution of a singular integral equation by a split-interval method
The article is available at http://www.math.ualberta.ca/ijnam/Volume-4-2007/No-1-07/2007-01-05.pdf. This article is not available through the Chester Digital RepositoryThis article discusses a new numerical method for the solution of a singular integral equation of Volterra type that has an infinite class of solutions. The split-interval method is discussed and examples demonstrate its effectiveness
Preventing Atomicity Violations with Contracts
Software developers are expected to protect concurrent accesses to shared
regions of memory with some mutual exclusion primitive that ensures atomicity
properties to a sequence of program statements. This approach prevents data
races but may fail to provide all necessary correctness properties.The
composition of correlated atomic operations without further synchronization may
cause atomicity violations. Atomic violations may be avoided by grouping the
correlated atomic regions in a single larger atomic scope. Concurrent programs
are particularly prone to atomicity violations when they use services provided
by third party packages or modules, since the programmer may fail to identify
which services are correlated. In this paper we propose to use contracts for
concurrency, where the developer of a module writes a set of contract terms
that specify which methods are correlated and must be executed in the same
atomic scope. These contracts are then used to verify the correctness of the
main program with respect to the usage of the module(s). If a contract is well
defined and complete, and the main program respects it, then the program is
safe from atomicity violations with respect to that module. We also propose a
static analysis based methodology to verify contracts for concurrency that we
applied to some real-world software packages. The bug we found in Tomcat 6.0
was immediately acknowledged and corrected by its development team
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