6,412 research outputs found
Statistical Time Series Models of Pilot Control with Applications to Instrument Discrimination
A general description of the methodology used in obtaining the transfer function models and verification of model fidelity, frequency domain plots of the modeled transfer functions, numerical results obtained from an analysis of poles and zeroes obtained from z plane to s-plane conversions of the transfer functions, and the results of a study on the sequential introduction of other variables, both exogenous and endogenous into the loop are contained
Pairwise alignment incorporating dipeptide covariation
Motivation: Standard algorithms for pairwise protein sequence alignment make
the simplifying assumption that amino acid substitutions at neighboring sites
are uncorrelated. This assumption allows implementation of fast algorithms for
pairwise sequence alignment, but it ignores information that could conceivably
increase the power of remote homolog detection. We examine the validity of this
assumption by constructing extended substitution matrixes that encapsulate the
observed correlations between neighboring sites, by developing an efficient and
rigorous algorithm for pairwise protein sequence alignment that incorporates
these local substitution correlations, and by assessing the ability of this
algorithm to detect remote homologies. Results: Our analysis indicates that
local correlations between substitutions are not strong on the average.
Furthermore, incorporating local substitution correlations into pairwise
alignment did not lead to a statistically significant improvement in remote
homology detection. Therefore, the standard assumption that individual residues
within protein sequences evolve independently of neighboring positions appears
to be an efficient and appropriate approximation
Correction, improvement and model verification of CARE 3, version 3
An independent verification of the CARE 3 mathematical model and computer code was conducted and reported in NASA Contractor Report 166096, Review and Verification of CARE 3 Mathematical Model and Code: Interim Report. The study uncovered some implementation errors that were corrected and are reported in this document. The corrected CARE 3 program is called version 4. Thus the document, correction. improvement, and model verification of CARE 3, version 3 was written in April 1984. It is being published now as it has been determined to contain a more accurate representation of CARE 3 than the preceding document of April 1983. This edition supercedes NASA-CR-166122 entitled, 'Correction and Improvement of CARE 3,' version 3, April 1983
Genetic Correlations in Mutation Processes
We study the role of phylogenetic trees on correlations in mutation
processes. Generally, correlations decay exponentially with the generation
number. We find that two distinct regimes of behavior exist. For mutation rates
smaller than a critical rate, the underlying tree morphology is almost
irrelevant, while mutation rates higher than this critical rate lead to strong
tree-dependent correlations. We show analytically that identical critical
behavior underlies all multiple point correlations. This behavior generally
characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig
Efficient chaining of seeds in ordered trees
We consider here the problem of chaining seeds in ordered trees. Seeds are
mappings between two trees Q and T and a chain is a subset of non overlapping
seeds that is consistent with respect to postfix order and ancestrality. This
problem is a natural extension of a similar problem for sequences, and has
applications in computational biology, such as mining a database of RNA
secondary structures. For the chaining problem with a set of m constant size
seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2)
in space
Consistency analysis of a nonbirefringent Lorentz-violating planar model
In this work analyze the physical consistency of a nonbirefringent
Lorentz-violating planar model via the analysis of the pole structure of its
Feynman propagators. The nonbirefringent planar model, obtained from the
dimensional reduction of the CPT-even gauge sector of the standard model
extension, is composed of a gauge and a scalar fields, being affected by
Lorentz-violating (LIV) coefficients encoded in the symmetric tensor
. The propagator of the gauge field is explicitly evaluated
and expressed in terms of linear independent symmetric tensors, presenting only
one physical mode. The same holds for the scalar propagator. A consistency
analysis is performed based on the poles of the propagators. The isotropic
parity-even sector is stable, causal and unitary mode for .
On the other hand, the anisotropic sector is stable and unitary but in general
noncausal. Finally, it is shown that this planar model interacting with a
Higgs field supports compactlike vortex configurations.Comment: 11 pages, revtex style, final revised versio
SpBase: the sea urchin genome database and web site
SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided
T and CPT Symmetries in Entangled Neutral Meson Systems
Genuine tests of an asymmetry under T and/or CPT transformations imply the
interchange between in-states and out-states. I explain a methodology to
perform model-indepedent separate measurements of the three CP, T and CPT
symmetry violations for transitions involving the decay of the neutral meson
systems in B- and {\Phi}-factories. It makes use of the quantum-mechanical
entanglement only, for which the individual state of each neutral meson is not
defined before the decay of its orthogonal partner. The final proof of the
independence of the three asymmetries is that no other theoretical ingredient
is involved and that the event sample corresponding to each case is different
from the other two. The experimental analysis for the measurements of these
three asymmetries as function of the time interval {\Delta}t > 0 between the
first and second decays is discussed, as well as the significance of the
expected results. In particular, one may advance a first observation of true,
direct, evidence of Time-Reserval-Violation in B-factories by many standard
deviations from zero, without any reference to, and independent of,
CP-Violation. In some quantum gravity framework the CPT-transformation is
ill-defined, so there is a resulting loss of particle-antiparticle identity.
This mechanism induces a breaking of the EPR correlation in the entanglement
imposed by Bose statistics to the neutral meson system, the so-called
{\omega}-effect. I present results and prospects for the {\omega}-parameter in
the correlated neutral meson-antimeson states.Comment: Proc. DISCRETE 2010, Symposium on Prospects in the Physics of
Discrete Symmetries, December 2010, Rom
Isolation and characterization of the full-length cDNA encoding a member of a novel cytochrome p450 family (CYP320A1) from the tropical freshwater snail, Biomphalaria glabrata, intermediate host for Schistosoma mansoni
Cytochrome p450s (cyp450s) are a family of structurally related proteins, with diverse functions, including steroid synthesis and breakdown of toxins. This paper reports the full-length sequence of a novel cyp450 gene, the first to be isolated from the tropical freshwater snail Biomphalaria glabrata, an important intermediate host of Schistosoma mansoni. The nucleotide sequence is 2291 bp with a predicted amino acid sequence of 584aa. The sequence demonstrates conserved cyp450 structural motifs, but is sufficiently different from previously reported cyp450 sequences to be given a new classification, CYP320A1. Initially identified as down-regulated in partially resistant snails in response to S. mansoni infection, amplification of this gene using RT-PCR in both totally resistant or susceptible snail lines when exposed to infection, and all tissues examined, suggests ubiquitous expression. Characterization of the first cyp450 from B. glabrata is significant in understanding the evolution of these metabolically important proteins
Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks
Prediction of one-dimensional protein structures such as secondary structures
and contact numbers is useful for the three-dimensional structure prediction
and important for the understanding of sequence-structure relationship. Here we
present a new machine-learning method, critical random networks (CRNs), for
predicting one-dimensional structures, and apply it, with position-specific
scoring matrices, to the prediction of secondary structures (SS), contact
numbers (CN), and residue-wise contact orders (RWCO). The present method
achieves, on average, accuracy of 77.8% for SS, correlation coefficients
of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS
prediction is comparable to other state-of-the-art methods, and that of the CN
prediction is a significant improvement over previous methods. We give a
detailed formulation of critical random networks-based prediction scheme, and
examine the context-dependence of prediction accuracies. In order to study the
nonlinear and multi-body effects, we compare the CRNs-based method with a
purely linear method based on position-specific scoring matrices. Although not
superior to the CRNs-based method, the surprisingly good accuracy achieved by
the linear method highlights the difficulty in extracting structural features
of higher order from amino acid sequence beyond that provided by the
position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for
publication in BIOPHYSIC
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