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 $N$ 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 $|\phi > |\phi^*>$, 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-H2_2 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$_\ast$/M$_\odot$<10) and low metallicity (0.4< Z/Z$_\odot$<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, $\Delta$MS, are needed to quantify variations in the luminosity ratio; metallicity describes the total dust content available to shield CO from UV radiation, while $\Delta$MS describes the strength of this radiation field. We connect the [CII]/CO luminosity ratio to the CO-to-H$_2$ conversion factor and find a multivariate conversion function $\alpha_{CO}$, which can be used up to z~2.5. This function depends primarily on metallicity, with a second order dependence on $\Delta$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$_\ast$/M$_\odot$<10. While the molecular gas depletion time varies with sSFR, it is mostly independent of mass, indicating that the low L$_{CO}$/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

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

Spitzer Quasar and ULIRG evolution study (QUEST): I. The origin of the far infrared continuum of QSOs

This paper addresses the origin of the far-infrared (FIR) continuum of QSOs, based on the Quasar and ULIRG Evolution Study (QUEST) of nearby QSOs and ULIRGs using observations with the Spitzer Space Telescope. For 27 Palomar-Green QSOs at z <~ 0.3, we derive luminosities of diagnostic lines ([NeII]12.8um, [NeV]14.3um, [OIV]25.9um) and emission features (PAH7.7um emission which is related to star formation), as well as continuum luminosities over a range of mid- to far-infrared wavelengths between 6 and 60um. We detect star-formation related PAH emission in 11/26 QSOs and fine-structure line emission in all of them, often in multiple lines. The detection of PAHs in the average spectrum of sources which lack individual PAH detections provides further evidence for the widespread presence of PAHs in QSOs. Similar PAH/FIR and [NeII]/FIR ratios are found in QSOs and in starburst-dominated ULIRGs and lower luminosity starbursts. We conclude that the typical QSO in our sample has at least 30% but likely most of the far-infrared luminosity (~ 10^(10...12)Lsun) arising from star formation, with a tendency for larger star formation contribution at the largest FIR luminosities. In the QSO sample, we find correlations between most of the quantities studied including combinations of AGN tracers and starburst tracers. The common scaling of AGN and starburst luminosities (and fluxes) is evidence for a starburst-AGN connection in luminous AGN. Strong correlations of far-infrared continuum and starburst related quantities (PAH, low excitation [NeII]) offer additional support for the starburst origin of far-infrared emission.Comment: 39 pages, 8 figures, accepted for publication in Ap