5,799 research outputs found
The Gene Ontology: enhancements for 2011
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources
Continuous monitoring of the lunar or Martian subsurface using on-board pattern recognition and neural processing of Rover geophysical data
The ultimate goal is to create an extraterrestrial unmanned system for subsurface mapping and exploration. Neural networks are to be used to recognize anomalies in the profiles that correspond to potentially exploitable subsurface features. The ground penetrating radar (GPR) techniques are likewise identical. Hence, the preliminary research focus on GPR systems will be directly applicable to seismic systems once such systems can be designed for continuous operation. The original GPR profile may be very complex due to electrical behavior of the background, targets, and antennas, much as the seismic record is made complex by multiple reflections, ghosting, and ringing. Because the format of the GPR data is similar to the format of seismic data, seismic processing software may be applied to GPR data to help enhance the data. A neural network may then be trained to more accurately identify anomalies from the processed record than from the original record
State estimation from pair of conjugate qudits
We show that, for parallel input states, an anti-linear map with respect
to a specific basis is essentially a classical operator. We also consider the
information contained in phase-conjugate pairs , and prove
that there is more information about a quantum state encoded in phase-conjugate
pairs than in parallel pairs.Comment: 4 pages, 1 tabl
The Ratio of Ortho- to Para-H2 in Photodissociation Regions
We discuss the ratio of ortho- to para-H2 in photodissociation regions
(PDRs). We draw attention to an apparent confusion in the literature between
the ortho-to-para ratio of molecules in FUV-pumped vibrationally excited
states, and the H2 ortho-to-para abundance ratio. These ratios are not the same
because the process of FUV-pumping of fluorescent H2 emission in PDRs occurs
via optically thick absorption lines. Thus, gas with an equilibrium ratio of
ortho- to para-H2 equal to 3 will yield FUV-pumped vibrationally excited
ortho-to-para ratios smaller than 3, because the ortho-H2 pumping rates are
preferentially reduced by optical depth effects. Indeed, if the ortho and para
pumping lines are on the ``square root'' part of the curve-of-growth, then the
expected ratio of ortho and para vibrational line strengths is the square root
of 3, ~ 1.7, close to the typically observed value. Thus, contrary to what has
sometimes been stated in the literature, most previous measurements of the
ratio of ortho- to para-H2 in vibrationally excited states are entirely
consistent with a total ortho-to-para ratio of 3, the equilibrium value for
temperatures greater than 200 K. We present an analysis and several detailed
models which illustrate the relationship between the total ratios of ortho- to
para-H2 and the vibrationally excited ortho-to-para ratios in PDRs. Recent
Infrared Space Observatory (ISO) measurements of pure rotational and
vibrational H2 emissions from the PDR in the star-forming region S140 provide
strong observational support for our conclusions.Comment: 23 pages (including 5 figures), LaTeX, uses aaspp4.sty, accepted for
publication in Ap
How to realize Lie algebras by vector fields
An algorithm for embedding finite dimensional Lie algebras into Lie algebras
of vector fields (and Lie superalgebras into Lie superalgebras of vector
fields) is offered in a way applicable over ground fields of any
characteristic. The algorithm is illustrated by reproducing Cartan's
interpretations of the Lie algebra of G(2) as the Lie algebra that preserves
certain non-integrable distributions. Similar algorithm and interpretation are
applicable to other exceptional simple Lie algebras, as well as to all
non-exceptional simple ones and many non-simple ones, and to many Lie
superalgebras.Comment: 17 pages, LaTe
Deriving a multivariate CO-to-H conversion function using the [CII]/CO(1-0) ratio and its application to molecular gas scaling relations
We present Herschel PACS observations of the [CII] 158 micron emission line
in a sample of 24 intermediate mass (9<logM/M<10) and low
metallicity (0.4< Z/Z<1.0) galaxies from the xCOLD GASS survey.
Combining them with IRAM CO(1-0) measurements, we establish scaling relations
between integrated and molecular region [CII]/CO(1-0) luminosity ratios as a
function of integrated galaxy properties. A Bayesian analysis reveals that only
two parameters, metallicity and offset from the star formation main sequence,
MS, are needed to quantify variations in the luminosity ratio;
metallicity describes the total dust content available to shield CO from UV
radiation, while MS describes the strength of this radiation field. We
connect the [CII]/CO luminosity ratio to the CO-to-H conversion factor and
find a multivariate conversion function , which can be used up to
z~2.5. This function depends primarily on metallicity, with a second order
dependence on MS. We apply this to the full xCOLD GASS and PHIBSS1
surveys and investigate molecular gas scaling relations. We find a flattening
of the relation between gas mass fraction and stellar mass at
logM/M<10. While the molecular gas depletion time varies with
sSFR, it is mostly independent of mass, indicating that the low L/SFR
ratios long observed in low mass galaxies are entirely due to photodissociation
of CO, and not to an enhanced star formation efficiency.Comment: Submitted to MNRAS, this version after referee comments. 21 page
Central Nervous System Parasitosis and Neuroinflammation Ameliorated by Systemic IL-10 Administration in Trypanosoma brucei-Infected Mice
Peer reviewedPublisher PD
Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions
During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus
Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1
Background:
The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This nematode-bacterium-insect association represents an emerging tripartite model for research on mutualistic and parasitic symbioses. Elucidation of mechanisms underlying these biological processes may serve as a foundation for improving the biological control potential of the nematode-bacterium complex. This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora.
Results:
A total of 31,485 high quality ESTs were generated from cDNA libraries of the adult H. bacteriophora TTO1 strain. Cluster analysis revealed the presence of 3,051 contigs and 7,835 singletons, representing 10,886 distinct EST sequences. About 72% of the distinct EST sequences had significant matches (E value < 1e-5) to proteins in GenBank's non-redundant (nr) and Wormpep190 databases. We have identified 12 ESTs corresponding to 8 genes potentially involved in RNA interference, 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes, and 51 ESTs corresponding to 27 genes potentially involved in defense and stress responses. Comparison to ESTs and proteins of free-living nematodes led to the identification of 554 parasitic nematode-specific ESTs in H. bacteriophora, among which are those encoding F-box-like/WD-repeat protein theromacin, Bax inhibitor-1-like protein, and PAZ domain containing protein. Gene Ontology terms were assigned to 6,685 of the 10,886 ESTs. A total of 168 microsatellite loci were identified with primers designable for 141 loci.
Conclusion:
A total of 10,886 distinct EST sequences were identified from adult H. bacteriophora cDNA libraries. BLAST searches revealed ESTs potentially involved in parasitism, RNA interference, defense responses, stress responses, and dauer-related processes. The putative microsatellite markers identified in H. bacteriophora ESTs will enable genetic mapping and population genetic studies. These genomic resources provide the material base necessary for genome annotation, microarray development, and in-depth gene functional analysis
Trace formulas for stochastic evolution operators: Smooth conjugation method
The trace formula for the evolution operator associated with nonlinear
stochastic flows with weak additive noise is cast in the path integral
formalism. We integrate over the neighborhood of a given saddlepoint exactly by
means of a smooth conjugacy, a locally analytic nonlinear change of field
variables. The perturbative corrections are transfered to the corresponding
Jacobian, which we expand in terms of the conjugating function, rather than the
action used in defining the path integral. The new perturbative expansion which
follows by a recursive evaluation of derivatives appears more compact than the
standard Feynman diagram perturbation theory. The result is a stochastic analog
of the Gutzwiller trace formula with the ``hbar'' corrections computed an order
higher than what has so far been attainable in stochastic and
quantum-mechanical applications.Comment: 16 pages, 1 figure, New techniques and results for a problem we
considered in chao-dyn/980703
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