EST-PAC HPC - a web portal for high-throughput EST annotation and protein sequence prediction

Expressed Sequence Tags (ESTs) are short DNA sequences generated by sequencing the transcribed cDNAs coming from a gene expression. They can provide significant functional, structural and evolutionary information and thus are a primary resource for gene discovery. EST annotation basically refers to the analysis of unknown ESTs that can be performed by database similarity search for possible identities and database search for functional prediction of translation products. Such kind of annotation typically consists of a series of repetitive tasks which should be automated, and be customizable and amenable to using distributed computing resources. Furthermore, processing of EST data should be done efficiently using a high performance computing platform. In this paper, we describe an EST annotator, EST-PACHPC, which has been developed for harnessing HPC resources potentially from Grid and Cloud systems for high throughput EST annotations. The performance analysis of EST-PACHPC has shown that it provides substantial performance gain in EST annotation.<br /

An imaging time-of-propagation system for charged particle identification at a super B factory

Super B factories that will further probe the flavor sector of the Standard Model and physics beyond will demand excellent charged particle identification (PID), particularly K/pi separation, for momenta up to 4 GeV/c, as well as the ability to operate under beam backgrounds significantly higher than current B factory experiments. We describe an Imaging Time-of-Propagation (iTOP) detector which shows significant potential to meet these requirements. Photons emitted from charged particle interactions in a Cerenkov radiator bar are internally reflected to the end of the bar, where they are collected on a compact image plane using photodetectors with fine spatial segmentation in two dimensions. Precision measurements of photon arrival time are used to enhance the two dimensional imaging, allowing the system to provide excellent PID capabilities within a reduced detector envelope. Results of the ongoing optimization of the geometric and physical properties of such a detector are presented, as well as simulated PID performance. Validation of simulations is being performed using a prototype in a cosmic ray test stand at the University of Hawaii.Comment: 3 pages, 5 figures, submitted to TIPP09 proceeding

Element release and reaction-induced porosity alteration during shale-hydraulic fracturing fluid interactions

The use of hydraulic fracturing techniques to extract oil and gas from low permeability shale reservoirs has increased significantly in recent years. During hydraulic fracturing, large volumes of water, often acidic and oxic, are injected into shale formations. This drives fluid-rock interaction that can release metal contaminants (e.g., U, Pb) and alter the permeability of the rock, impacting the transport and recovery of water, hydrocarbons, and contaminants. To identify the key geochemical processes that occur upon exposure of shales to hydraulic fracturing fluid, we investigated the chemical interaction of hydraulic fracturing fluids with a variety of shales of different mineralogical texture and composition. Batch reactor experiments revealed that the dissolution of both pyrite and carbonate minerals occurred rapidly, releasing metal contaminants and generating porosity. Oxidation of pyrite and aqueous Fe drove precipitation of Fe(III)-(oxy)hydroxides that attenuated the release of these contaminants via co-precipitation and/or adsorption. The precipitation of these (oxy)hydroxides appeared to limit the extent of pyrite reaction. Enhanced removal of metals and contaminants in reactors with higher fluid pH was inferred to reflect increased Fe-(oxy)hydroxide precipitation associated with more rapid aqueous Fe(II) oxidation. The precipitation of both Al- and Fe-bearing phases revealed the potential for the occlusion of pores and fracture apertures, whereas the selective dissolution of calcite generated porosity. These pore-scale alterations of shale texture and the cycling of contaminants indicate that chemical interactions between shales and hydraulic fracturing fluids may exert an important control on the efficiency of hydraulic fracturing operations and the quality of water recovered at the surface

Atomically Resolved Imaging of Highly Ordered Alternating Fluorinated Graphene

One of the most desirable goals of graphene research is to produce ordered 2D chemical derivatives of suitable quality for monolayer device fabrication. Here we reveal, by focal series exit wave reconstruction, that C2F chair is a stable graphene derivative and demonstrates pristine long-range order limited only by the size of a functionalized domain. Focal series of images of graphene and C2F chair formed by reaction with XeF2 were obtained at 80 kV in an aberration-corrected transmission electron microscope. EWR images reveal that single carbon atoms and carbon-fluorine pairs in C2F chair alternate strictly over domain sizes of at least 150 nm^2 with electron diffraction indicating ordered domains >/= 0.16 square micrometer. Our results also indicate that, within an ordered domain, functionalization occurs on one side only as theory predicts. Additionally we show that electron diffraction provides a quick and easy method for distinguishing between graphene, C2F chair and fully fluorinated stoichiometric CF 2D phases

miRNA_targets : a database for miRNA target predictions in coding and non-coding regions of mRNAs

AbstractMicroRNAs (miRNAs) are small non-coding RNAs that play a role in post-transcriptional regulation of gene expression in most eukaryotes. They help in fine-tuning gene expression by targeting messenger RNAs (mRNA). The interactions of miRNAs and mRNAs are sequence specific and computational tools have been developed to predict miRNA target sites on mRNAs, but miRNA research has been mainly focused on target sites within 3′ untranslated regions (UTRs) of genes. There is a need for an easily accessible repository of genome wide full length mRNA — miRNA target predictions with versatile search capabilities and visualization tools. We have created a web accessible database of miRNA target predictions for human, mouse, cow, chicken, Zebra fish, fruit fly and Caenorhabditis elegans using two different target prediction algorithms, The database has target predictions for miRNA's on 5′ UTRs, coding region and 3′ UTRs of all mRNAs. This database can be freely accessed at http://mamsap.it.deakin.edu.au/mirna_targets/

Broadband Dielectric Spectroscopy on Glass-Forming Propylene Carbonate

Dielectric spectroscopy covering more than 18 decades of frequency has been performed on propylene carbonate in its liquid and supercooled-liquid state. Using quasi-optic submillimeter and far-infrared spectroscopy the dielectric response was investigated up to frequencies well into the microscopic regime. We discuss the alpha-process whose characteristic timescale is observed over 14 decades of frequency and the excess wing showing up at frequencies some three decades above the peak frequency. Special attention is given to the high-frequency response of the dielectric loss in the crossover regime between alpha-peak and boson-peak. Similar to our previous results in other glass forming materials we find evidence for additional processes in the crossover regime. However, significant differences concerning the spectral form at high frequencies are found. We compare our results to the susceptibilities obtained from light scattering and to the predictions of various models of the glass transition.Comment: 13 pages, 9 figures, submitted to Phys. Rev.

Targeted Cyclo[8]pyrrole-Based NIR-II Photoacoustic Tomography Probe for Suppression of Orthotopic Pancreatic Tumor Growth and Intra-abdominal Metastases

Pancreatic cancer is highly lethal. New diagnostic and treatment modalities are desperately needed. We report here that an expanded porphyrin, cyclo[8]pyrrole (CP), with a high extinction coefficient (89.16 L/g·cm) within the second near-infrared window (NIR-II), may be formulated with an αvβ3-specific targeting peptide, cyclic-Arg-Gly-Asp (cRGD), to form cRGD-CP nanoparticles (cRGD-CPNPs) with promising NIR-II photothermal (PT) therapeutic and photoacoustic (PA) imaging properties. Studies with a ring-array PA tomography system, coupled with analysis of control nanoparticles lacking a targeting element (CPNPs), revealed that cRGD conjugation promoted the delivery of the NPs through abnormal vessels around the tumor to the solid tumor core. This proved true in both subcutaneous and orthotopic pancreatic tumor mice models, as confirmed by immunofluorescent studies. In combination with NIR-II laser photoirradiation, the cRGD-CPNPs provided near-baseline tumor growth inhibition through PTT both in vitro and in vivo. Notably, the combination of the present cRGD-CPNPs and photoirradiation was found to inhibit intra-abdominal metastases in an orthotopic pancreatic tumor mouse model. The cRGD-CPNPs also displayed good biosafety profiles, as inferred from PA tomography, blood analyses, and H&amp;E staining. They thus appear promising for use in combined PA imaging and PT therapeutic treatment of pancreatic cancer

Exoplanet phase curves: observations and theory

Phase curves are the best technique to probe the three dimensional structure of exoplanets' atmospheres. In this chapter we first review current exoplanets phase curve observations and the particular challenges they face. We then describe the different physical mechanisms shaping the atmospheric phase curves of highly irradiated tidally locked exoplanets. Finally, we discuss the potential for future missions to further advance our understanding of these new worlds.Comment: Fig.5 has been updated. Table 1 and corresponding figures have been updated with new values for WASP-103b and WASP-18b. Contains a table sumarizing phase curve observation

Air pollution and the microvasculature: A cross-sectional assessment of in vivo retinal images in the population-based multi-ethnic study of atherosclerosis (MESA)

10.1371/journal.pmed.1000372PLoS Medicine711

High-Throughput In Vivo Analysis of Gene Expression in Caenorhabditis elegans

Using DNA sequences 5′ to open reading frames, we have constructed green fluorescent protein (GFP) fusions and generated spatial and temporal tissue expression profiles for 1,886 specific genes in the nematode Caenorhabditis elegans. This effort encompasses about 10% of all genes identified in this organism. GFP-expressing wild-type animals were analyzed at each stage of development from embryo to adult. We have identified 5′ DNA regions regulating expression at all developmental stages and in 38 different cell and tissue types in this organism. Among the regulatory regions identified are sequences that regulate expression in all cells, in specific tissues, in combinations of tissues, and in single cells. Most of the genes we have examined in C. elegans have human orthologs. All the images and expression pattern data generated by this project are available at WormAtlas (http://gfpweb.aecom.yu.edu/index) and through WormBase (http://www.wormbase.org)