The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

<p>Abstract</p> <p>Background</p> <p>Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data.</p> <p>Results</p> <p>The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks.</p> <p>Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents.</p> <p>We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe <it>Halobacterium salinarum NRC-1 </it>in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved.</p> <p>Conclusion</p> <p>The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.</p

Moving Frontiers in Transition Metal Catalysis: Synthesis, Characterization and Modeling

Nanosized transition metal particles are important materials in catalysis with a key role not only in academic research but also in many processes with industrial and societal relevance. Although small improvements in catalytic properties can lead to significant economic and environmental impacts, it is only now that knowledge-based design of such materials is emerging, partly because the understanding of catalytic mechanisms on nanoparticle surfaces is increasingly improving. A knowledge-based design requires bottom-up synthesis of well-defined model catalysts, an understanding of the catalytic nanomaterials “at work” (operando), and both a detailed understanding and a prediction by theoretical methods. This article reports on progress in colloidal synthesis of transition metal nanoparticles for preparation of model catalysts to close the materials gap between the discoveries of fundamental surface science and industrial application. The transition metal particles, however, often undergo extensive transformations when applied to the catalytic process and much progress has recently been achieved operando characterization techniques under relevant reaction conditions. They allow better understanding of size/structure–activity correlations in these systems. Moreover, the growth of computing power and the improvement of theoretical methods uncover mechanisms on nanoparticles and have recently predicted highly active particles for CO/CO₂ hydrogenation or direct H₂O₂ synthesis

Dynamics of fermions coupling to a U(1) gauge field in the limit e2→∞e^2\to\infty

We study in this paper the properties of a gas of fermions coupling to a U(1) gauge field at wavevectors $q<\Lambda<<k_F$ at dimensions larger than one, where $\Lambda<<k_F$ is a high momentum cutoff and $k_F$ is the fermi wave vector. In particular, we shall consider the $e^2\to\infty$ limit where charge and current fluctuations at wave vectors $q<\Lambda$ are forbidden. Within a bosonization approximation, effective actions describing the low energy physics of the system are constructed, where we show that the system can be described as a fermion liquid formed by chargeless quasi-particles which has vanishing wavefunction overlap with the bare fermions in the system.Comment: 25 page

Sub-surface Oxygen and Surface Oxide Formation at Ag(111): A Density-functional Theory Investigation

To help provide insight into the remarkable catalytic behavior of the oxygen/silver system for heterogeneous oxidation reactions, purely sub-surface oxygen, and structures involving both on-surface and sub-surface oxygen, as well as oxide-like structures at the Ag(111) surface have been studied for a wide range of coverages and adsorption sites using density-functional theory. Adsorption on the surface in fcc sites is energetically favorable for low coverages, while for higher coverage a thin surface-oxide structure is energetically favorable. This structure has been proposed to correspond to the experimentally observed (4x4) phase. With increasing O concentrations, thicker oxide-like structures resembling compressed Ag2O(111) surfaces are energetically favored. Due to the relatively low thermal stability of these structures, and the very low sticking probability of O2 at Ag(111), their formation and observation may require the use of atomic oxygen (or ozone, O3) and low temperatures. We also investigate diffusion of O into the sub-surface region at low coverage (0.11 ML), and the effect of surface Ag vacancies in the adsorption of atomic oxygen and ozone-like species. The present studies, together with our earlier investigations of on-surface and surface-substitutional adsorption, provide a comprehensive picture of the behavior and chemical nature of the interaction of oxygen and Ag(111), as well as of the initial stages of oxide formation.Comment: 17 pages including 14 figures, Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Prevalence of transcription promoters within archaeal operons and coding sequences

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ∼64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein–DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3′ ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes—events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements

Astrometry and geodesy with radio interferometry: experiments, models, results

Summarizes current status of radio interferometry at radio frequencies between Earth-based receivers, for astrometric and geodetic applications. Emphasizes theoretical models of VLBI observables that are required to extract results at the present accuracy levels of 1 cm and 1 nanoradian. Highlights the achievements of VLBI during the past two decades in reference frames, Earth orientation, atmospheric effects on microwave propagation, and relativity.Comment: 83 pages, 19 Postscript figures. To be published in Rev. Mod. Phys., Vol. 70, Oct. 199

Insights into the function of silver as an oxidation catalyst by ab initio, atomistic thermodynamics

To help understand the high activity of silver as an oxidation catalyst, e.g., for the oxidation of ethylene to epoxide and the dehydrogenation of methanol to formaldehyde, the interaction and stability of oxygen species at the Ag(111) surface has been studied for a wide range of coverages. Through calculation of the free energy, as obtained from density-functional theory and taking into account the temperature and pressure via the oxygen chemical potential, we obtain the phase diagram of O/Ag(111). Our results reveal that a thin surface-oxide structure is most stable for the temperature and pressure range of ethylene epoxidation and we propose it (and possibly other similar structures) contains the species actuating the catalysis. For higher temperatures, low coverages of chemisorbed oxygen are most stable, which could also play a role in oxidation reactions. For temperatures greater than about 775 K there are no stable oxygen species, except for the possibility of O atoms adsorbed at under-coordinated surface sites Our calculations rule out thicker oxide-like structures, as well as bulk dissolved oxygen and molecular ozone-like species, as playing a role in the oxidation reactions.Comment: 15 pages including 9 figures, Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Potent Activity of the HIV-1 Maturation Inhibitor Bevirimat in SCID-hu Thy/Liv Mice

The HIV-1 maturation inhibitor, 3-O-(3',3'-dimethylsuccinyl) betulinic acid (bevirimat, PA-457) is a promising drug candidate with 10 nM in vitro antiviral activity against multiple wild-type (WT) and drug-resistant HIV-1 isolates. Bevirimat has a novel mechanism of action, specifically inhibiting cleavage of spacer peptide 1 (SP1) from the C-terminus of capsid which results in defective core condensation.Oral administration of bevirimat to HIV-1-infected SCID-hu Thy/Liv mice reduced viral RNA by >2 log(10) and protected immature and mature T cells from virus-mediated depletion. This activity was observed at plasma concentrations that are achievable in humans after oral dosing, and bevirimat was active up to 3 days after inoculation with both WT HIV-1 and an AZT-resistant HIV-1 clinical isolate. Consistent with its mechanism of action, bevirimat caused a dose-dependent inhibition of capsid-SP1 cleavage in HIV-1-infected human thymocytes obtained from these mice. HIV-1 NL4-3 with an alanine-to-valine substitution at the N-terminus of SP1 (SP1/A1V), which is resistant to bevirimat in vitro, was also resistant to bevirimat treatment in the mice, and SP1/AIV had replication and thymocyte kinetics similar to that of WT NL4-3 with no evidence of fitness impairment in in vivo competition assays. Interestingly, protease inhibitor-resistant HIV-1 with impaired capsid-SP1 cleavage was hypersensitive to bevirimat in vitro with a 50% inhibitory concentration 140 times lower than for WT HIV-1.These results support further clinical development of this first-in-class maturation inhibitor and confirm the usefulness of the SCID-hu Thy/Liv model for evaluation of in vivo antiretroviral efficacy, drug resistance, and viral fitness

Techno-Ecological Synergy: A Framework for Sustainable Engineering

Even though the importance of ecosystems in sustaining all human activities is well-known, methods for sustainable engineering fail to fully account for this role of nature. Most methods account for the demand for ecosystem services, but almost none account for the supply. Incomplete accounting of the very foundation of human well-being can result in perverse outcomes from decisions meant to enhance sustainability and lost opportunities for benefiting from the ability of nature to satisfy human needs in an economically and environmentally superior manner. This paper develops a framework for understanding and designing synergies between technological and ecological systems to encourage greater harmony between human activities and nature. This framework considers technological systems ranging from individual processes to supply chains and life cycles, along with corresponding ecological systems at multiple spatial scales ranging from local to global. The demand for specific ecosystem services is determined from information about emissions and resource use, while the supply is obtained from information about the capacity of relevant ecosystems. Metrics calculate the sustainability of individual ecosystem services at multiple spatial scales and help define necessary but not sufficient conditions for local and global sustainability. Efforts to reduce ecological overshoot encourage enhancement of life cycle efficiency, development of industrial symbiosis, innovative designs and policies, and ecological restoration, thus combining the best features of many existing methods. Opportunities for theoretical and applied research to make this framework practical are also discussed