15 research outputs found
Orbital Instabilities in a Triaxial Cusp Potential
This paper constructs an analytic form for a triaxial potential that
describes the dynamics of a wide variety of astrophysical systems, including
the inner portions of dark matter halos, the central regions of galactic
bulges, and young embedded star clusters. Specifically, this potential results
from a density profile of the form , where the radial
coordinate is generalized to triaxial form so that . Using the resulting analytic form of the potential, and the
corresponding force laws, we construct orbit solutions and show that a robust
orbit instability exists in these systems. For orbits initially confined to any
of the three principal planes, the motion in the perpendicular direction can be
unstable. We discuss the range of parameter space for which these orbits are
unstable, find the growth rates and saturation levels of the instability, and
develop a set of analytic model equations that elucidate the essential physics
of the instability mechanism. This orbit instability has a large number of
astrophysical implications and applications, including understanding the
formation of dark matter halos, the structure of galactic bulges, the survival
of tidal streams, and the early evolution of embedded star clusters.Comment: 50 pages, accepted for publication in Ap
Recommended from our members
A new arenavirus in a cluster of fatal transplant-associated diseases
Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points
Recommended from our members
A new arenavirus in a cluster of fatal transplant-associated diseases
Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points
Pegasys: software for executing and integrating analyses of biological sequences
Abstract
Background
We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.
Results
The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries.
Conclusions
The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.Science, Faculty ofReviewedFacult
There are three columns – the name of the parameter, its current value and a check box to indicate if this parameter is enabled
<p><b>Copyright information:</b></p><p>Taken from "Pegasys: software for executing and integrating analyses of biological sequences"</p><p>BMC Bioinformatics 2004;5():40-40.</p><p>Published online 19 Apr 2004</p><p>PMCID:PMC406494.</p><p>Copyright © 2004 Shah et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p> Disabled parameters will be excluded from the DAG XML, and consequently from the actual command that is executed on the server. All default values are set in the ProgramList.xml file that the server reads on startup