Collaborative systems for enhancing the analysis of social surveys: the grid enabled specialist data environments

This paper describes a group of online services which are designed to support social survey research and the production of statistical results. The 'Grid Enabled Specialist Data Environment' (GESDE) services constitute three related systems which offer facilities to search for, extract and exploit supplementary data and metadata concerned with the measurement and operationalisation of survey variables. The services also offer users the opportunity to deposit and distribute their own supplementary data resources for the benefit of dissemination and replication of the details of their own analysis. The GESDE services focus upon three application areas: specialist data relating to the measurement of occupations; educational qualifications; and ethnicity (including nationality, language, religion, national identity). They identify information resources related to the operationalisation of variables which seek to measure each of these concepts - examples include coding frames, crosswalk and translation files, and standardisation and harmonisation recommendations. These resources constitute important supplementary data which can be usefully exploited in the analysis of survey data. The GESDE services work by collecting together as much of this supplementary data as possible, and making it searchable and retrievable to others. This paper discusses the current features of the GESDE services (which have been designed as part of a wider programme of ‘e-Science’ research in the UK), and considers ongoing challenges in providing effective support for variable-oriented statistical analysis in the social sciences

Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression

BACKGROUND: In the search for generic expression strategies for mammalian protein families several bacterial expression vectors were examined for their ability to promote high yields of soluble protein. Proteins studied included cell surface receptors (Ephrins and Eph receptors, CD44), kinases (EGFR-cytoplasmic domain, CDK2 and 4), proteases (MMP1, CASP2), signal transduction proteins (GRB2, RAF1, HRAS) and transcription factors (GATA2, Fli1, Trp53, Mdm2, JUN, FOS, MAD, MAX). Over 400 experiments were performed where expression of 30 full-length proteins and protein domains were evaluated with 6 different N-terminal and 8 C-terminal fusion partners. Expression of an additional set of 95 mammalian proteins was also performed to test the conclusions of this study. RESULTS: Several protein features correlated with soluble protein expression yield including molecular weight and the number of contiguous hydrophobic residues and low complexity regions. There was no relationship between successful expression and protein pI, grand average of hydropathicity (GRAVY), or sub-cellular location. Only small globular cytoplasmic proteins with an average molecular weight of 23 kDa did not require a solubility enhancing tag for high level soluble expression. Thioredoxin (Trx) and maltose binding protein (MBP) were the best N-terminal protein fusions to promote soluble expression, but MBP was most effective as a C-terminal fusion. 63 of 95 mammalian proteins expressed at soluble levels of greater than 1 mg/l as N-terminal H10-MBP fusions and those that failed possessed, on average, a higher molecular weight and greater number of contiguous hydrophobic amino acids and low complexity regions. CONCLUSIONS: By analysis of the protein features identified here, this study will help predict which mammalian proteins and domains can be successfully expressed in E. coli as soluble product and also which are best targeted for a eukaryotic expression system. In some cases proteins may be truncated to minimise molecular weight and the numbers of contiguous hydrophobic amino acids and low complexity regions to aid soluble expression in E. coli

Impact of yttrium-90 microsphere density, flow dynamics, and administration technique on spatial distribution: analysis using an in vitro model

Purpose: To investigate material density, flow, and viscosity effects on microsphere distribution within an in vitro model designed to simulate hepatic arteries.Materials and Methods: A vascular flow model was used to compare distribution of glass and resin surrogates in a clinically derived flow range (60–120 mL/min). Blood-mimicking fluid (BMF) composed of glycerol and water (20%–50% vol/vol) was used to simulate a range of blood viscosities. Microsphere distribution was quantified gravimetrically, and injectate solution was dyed to enable quantification by UV spectrophotometry. Microsphere injection rate (5–30 mL/min) and the influence of contrast agent dilution of injection solution (0%–60% vol/vol) were also investigated.Results: No significant differences in behavior were observed between the glass and resin surrogate materials under any tested flow conditions (P = .182; n = 144 injections). Microspheres tend to align more consistently with the saline injection solution (r2 = 0.5712; n = 144) compared with total BMF flow distribution (r2 = 0.0104; n = 144). The most predictable injectate distribution (ie, greatest alignment with BMF flow, &lt; 5% variation) was demonstrated with &gt; 10-mL/min injection rates of pure saline solution, although &lt; 20% variation with glass microsphere distribution was observed with injection solution containing as much as 30% contrast medium when injected at &gt; 20 mL/min.Conclusions: Glass and resin yttrium-90 surrogates demonstrated similar distribution in a range of clinically relevant flow conditions, suggesting that microsphere density does not have a significant influence on microsphere distribution. Injection parameters that enhanced the mixing of the spheres with the BMF resulted in the most predictable distribution.<br/

Cost-Effective Icy Bodies Exploration using Small Satellite Missions

It has long been known that Saturn's moon Enceladus is expelling water-rich plumes into space, providing passing spacecraft with a window into what is hidden underneath its frozen crust. Recent discoveries indicate that similar events could also occur on other bodies in the solar system, such as Jupiter's moon Europa and the dwarf planet Ceres in the asteroid belt. These plumes provide a possible giant leap forward in the search for organics and assessing habitability beyond Earth, stepping stones toward the long-term goal of finding extraterrestrial life. The United States Congress recently requested mission designs to Europa, to fit within a cost cap of $1B, much less than previous mission designs' estimates. Here, innovative cost-effective small spacecraft designs for the deep-space exploration of these icy worlds, using new and emerging enabling technologies, and how to explore the outer solar system on a budget below the cost horizon of a flagship mission, are investigated. Science requirements, instruments selection, rendezvous trajectories, and spacecraft designs are some topics detailed. The mission concepts revolve around a comparably small-sized and low-cost Plume Chaser spacecraft, instrumented to characterize the vapor constituents encountered on its trajectory. In the event that a plume is not encountered, an ejecta plume can be artificially created by a companion spacecraft, the Plume Maker, on the target body at a location timed with the passage of the Plume Chaser spacecraft. Especially in the case of Ceres, such a mission could be a great complimentary mission to Dawn, as well as a possible future Europa Clipper mission. The comparably small volume of the spacecraft enables a launch to GTO as a secondary payload, providing multiple launch opportunities per year. Plume Maker's design is nearly identical to the Plume Chaser, and fits within the constraints for a secondary payload launch. The cost-effectiveness of small spacecraft missions enables the exploration of multiple solar system bodies in reasonable timeframes despite budgetary constraints, with only minor adaptations. The work presented here is a summary of concepts targeting icy bodies, such as Europa and Ceres, which have been developed over the last year at NASA Ames Research Center's Mission Design Division. The platforms detailed in this work are also applicable to the cost-effective exploration of many other small icy bodies in the solar system

Identification of soluble protein fragments by gene fragmentation and genetic selection

We describe a new method, which identifies protein fragments for soluble expression in Escherichia coli from a randomly fragmented gene library. Inhibition of E. coli dihydrofolate reductase (DHFR) by trimethoprim (TMP) prevents growth, but this can be relieved by murine DHFR (mDHFR). Bacterial strains expressing mDHFR fusions with the soluble proteins green fluroscent protein (GFP) or EphB2 (SAM domain) displayed markedly increased growth rates with TMP compared to strains expressing insoluble EphB2 (TK domain) or ketosteroid isomerase (KSI). Therefore, mDHFR is affected by the solubility of fusion partners and can act as a reporter of soluble protein expression. Random fragment libraries of the transcription factor Fli1 were generated by deoxyuridine incorporation and endonuclease V cleavage. The fragments were cloned upstream of mDHFR and TMP resistant clones expressing soluble protein were identified. These were found to cluster around the DNA binding ETS domain. A selected Fli1 fragment was expressed independently of mDHFR and was judged to be correctly folded by various biophysical methods including NMR. Soluble fragments of the cell-surface receptor Pecam1 were also identified. This genetic selection method was shown to generate expression clones useful for both structural studies and antibody generation and does not require a priori knowledge of domain architecture

Notch-IGF1 signalling in biliary epithelial cells drives their expansion and inhibits hepatocyte differentiation

[no abstract available

Inhibiting Inducible Nitric Oxide Synthase in Enteric Glia Restores Electrogenic Ion Transport in Mice With Colitis

BACKGROUND & AIMS: Disturbances in the control of ion transport lead to epithelial barrier dysfunction in patients with colitis. Enteric glia regulate intestinal barrier function and colonic ion transport. However, it is not clear whether enteric glia are involved in the epithelial hypo-responsiveness. We investigated enteric glial regulation of ion transport in mice with trinitrobenzene sulphonic acid- or dextran sodium sulfate-induced colitis and in Il10(−/−) mice. METHODS: Electrically-evoked ion transport was measured in full-thickness segments of colon from CD1 and Il10(−/−) mice with or without colitis in Ussing chambers. Nitric oxide (NO) production was assessed using amperometry. Bacterial translocation was investigated in the liver, spleen and blood of mice. RESULTS: Electrical stimulation of the colon evoked a tetrodotoxin-sensitive chloride secretion. In mice with colitis, ion transport almost completely disappeared. Inhibiting inducible NO synthase (NOS2), but not neuronal NOS (NOS1), partially restored the evoked secretory response. Blocking glial function with fluoroacetate, which is not a NOS2 inhibitor, also partially restored ion transport. Combined NOS2 inhibition and fluoroacetate administration fully restored secretion. Epithelial responsiveness to vasoactive intestinal peptide was increased after enteric glial function was blocked in mice with colitis. In colons of mice without colitis, NO was produced in the myenteric plexus almost completely via NOS1. NO production was increased in mice with colitis, compared to mice without colitis; a substantial proportion of NOS2 was blocked by fluoroacetate administration. Inhibition of enteric glial function in vivo reduced the severity of trinitrobenzene sulphonic acid -induced colitis and associated bacterial translocation. CONCLUSIONS: Increased production of NOS2 in enteric glia contributes to the dysregulation of intestinal ion transport in mice with colitis. Blocking enteric glial function in these mice restores epithelial barrier function and reduces bacterial translocation

The INNs and outs of antibody nonproprietary names

An important step in drug development is the assignment of an International Nonproprietary Name (INN) by the World Health Organization (WHO) that provides healthcare professionals with a unique and universally available designated name to identify each pharmaceutical substance. Monoclonal antibody INNs comprise a –mab suffix preceded by a substem indicating the antibody type, e.g., chimeric (-xi-), humanized (-zu-), or human (-u-). The WHO publishes INN definitions that specify how new monoclonal antibody therapeutics are categorized and adapts the definitions to new technologies. However, rapid progress in antibody technologies has blurred the boundaries between existing antibody categories and created a burgeoning array of new antibody formats. Thus, revising the INN system for antibodies is akin to aiming for a rapidly moving target. The WHO recently revised INN definitions for antibodies now to be based on amino acid sequence identity. These new definitions, however, are critically flawed as they are ambiguous and go against decades of scientific literature. A key concern is the imposition of an arbitrary threshold for identity against human germline antibody variable region sequences. This leads to inconsistent classification of somatically mutated human antibodies, humanized antibodies as well as antibodies derived from semi-synthetic/synthetic libraries and transgenic animals. Such sequence-based classification implies clear functional distinction between categories (e.g., immunogenicity). However, there is no scientific evidence to support this. Dialog between the WHO INN Expert Group and key stakeholders is needed to develop a new INN system for antibodies and to avoid confusion and miscommunication between researchers and clinicians prescribing antibodies