sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Background

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene expression profile. Lamb et al first proposed the Connectivity Map [Lamb et al (2006), Science 313, 1929–1935] to make successful connections among small molecules, genes, and diseases using genomic signatures.

Results

Here we have built on the principles of the Connectivity Map to present a simpler and more robust method for the construction of reference gene-expression profiles and for the connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with two randomly generated gene signatures and three experimentally derived gene signatures (for HDAC inhibitors, estrogens, and immunosuppressive drugs, respectively). Our testing with this method indicates that it achieves a higher level of specificity and sensitivity and so advances the original method.

Conclusion

The method presented here not only offers more principled statistical procedures for testing connections, but more importantly it provides effective safeguard against false connections at the same time achieving increased sensitivity. With its robust performance, the method has potential use in the drug development pipeline for the early recognition of pharmacological and toxicological properties in chemicals and new drug candidates, and also more broadly in other 'omics sciences.

Polarimetric signatures of infrared jets in X-ray binaries

We present near-infrared linear spectropolarimetry of a sample of persistent X-ray binaries, Sco X-1, Cyg X-2 and GRS 1915+105. For Sco X-1 and Cyg X-2, the polarization levels at 2.4 µm are 1.3+/-0.10% and 5.4+/-0.7%, respectively, which is greater than the polarization level at 1.65 µm. This cannot be explained by interstellar polarization or electron scattering in the anisotropic environment of the accretion flow. We propose that the most likely explanation is that this is the polarimetric signature of synchrotron emission arising from close to the base of the jet. For Sco X-1 the position angle of the radio jet on the sky is approximately perpendicular to the near-infrared position angle (electric vector), suggesting that the magnetic field is aligned with the jet. These observations may be a first step towards probing the ordering, alignment, and variability of the outflow magnetic field, in a region closer to the central accreting object than is observed in the radio band.

Use of Digital Manufacturing to Improve Management Learning in Aerospace Assembly

The primary goal of this work is to quantify any bene?ts that the use of digital manufacturing methods can offer when used upstream from production, for manufacturing process design, and tool development. Learning at this stage of product development is referred to as management learning. Animated build simulations have been used to develop build procedures and tooling for a panel assembly for the new Bombardier CRJ1000 (Canadair Regional Jet, 100 seat). When the jig format was developed, its simulated performance was compared to that of current CRJ700/900 panel builds to identify and quantify any improvements in terms of tooling cost and panel build time. When comparing like-for-like functions between existing CRJ700/900 (Canadair Regional Jet, 70/90 seat) and the
CRJ1000 tooling, it was predicted that the digitally assisted improvements had brought about a 4.9% reduction in jig cost. An evaluation of the build process for the CRJ1000 uplock panel predicted a 5.2% reduction in the assembly time. In addition to the improvement of existing tooling functions, new jig functionality was added so that both the drilling and riveting functions could be carried out in a single jig for the new RJ1000 panel.

The Architecture of Seduction: An Analysis on Digital Architectures within Consumer Society

Currently new digital tools used in architecture are often at the service of a conception of architecture as a consumer society’s cultural good. Within this neoliberal cultural frame, architects’ social function is no longer seen as the production of urban facts with sense of duty, but as a part within the symbolic logic that rules the social production of cultural values as it was defined by Veblen and developed by Baudrillard. As a result, the potential given by the new digital tools used in representation has shifted from an instrument used to verify a built project to two different main models: At the one hand the development of pure virtual architectures that are exclusively configured within their symbolic value as artistic “images” easily reproducible. On the other hand the development of all those projects which -even maintaining their attention to architecture as a built fact- base their symbolic value on the author’s image and on virtual aesthetics and logics that prevail over architecture’s materiality. Architects’ sense of duty has definitely reached a turning point.

Spectral induced polarization signatures of abiotic FeS precipitation

In recent years, geophysical methods have been shown to be sensitive to microbial-induced mineralization processes. The spectral induced-polarization (SIP) method appears to be very promising for monitoring mineralization and microbial processes. With this work, we study the links of mineralization and SIP signals, in the absence of microbial activity. We recorded the SIP response during abiotic FeS precipitation. We show that the SIP signals are diagnostic of FeS mineralization and can be differentiated from SIP signals from biomineralization processes. More specifically, the imaginary conductivity shows almost linear dependence on the amount of FeS precipitating out of solution, above the threshold value 0.006 gr under our experimental conditions. This research has direct implications for the use of the SIP method as a monitoring and decision-making tool for sustainable remediation of metals in contaminated soils and groundwater.

Self-potential signatures associated with an injection experiment at an in situ biological permeable reactive barrier

Strategies available to evaluate the performance of in situ permeable reactive barriers are currently not well developed and often rely on fluid and media sampling directly from the permeable reactive barrier (PRB). Here, we investigate the utility of the self-potential (SP) method as a technique to monitor in situ PRB performance. Our field study was conducted at in situ biological PRB in Portadown, Northern Ireland, UK, which was emplaced to assist in the remediation of groundwater contamination (e.g., hydrocarbons, ammonia) that resulted from the operations and waste disposal practices of a former gasworks. Borehole SP measurements were collected during the injection of contaminant groundwater slugs in an attempt to monitor/detect the response of the microbial activity associated with the breakdown of the added contaminants into the PRB. In addition, an uncontaminated groundwater slug was injected into a different portion of the PRB as a ‘control’ and SP measurements were collected for comparison to the SP response of the contaminant slugs. The results of the SP signals due to the contaminant injections show that the magnitude of the response was relatively small (<10 mV) yet showed a consistent decrease during both contaminant injections. The net decrease in SP recorded during the contaminant injections slowly rebounded to near background values through ~44 hours post-injection. The SP response during the uncontaminated injection showed a slight, albeit negligible (within the margin of error), 1 mV increase in the measured SP signals, in contrast to the contaminant injections. The results of the SP signals recorded from the uncontaminated groundwater injection also persisted through a period of ~47 hours after injection but show a net increase in SP relative to pre-injection values. Based on the difference in SP response between the contaminated and uncontaminated injections, we suggest that the responses are likely to be the result of differences in the chemistry of the injection types (contaminated versus uncontaminated) and in situ groundwater. We argue that the SP signals associated with the contaminated injections are dominated by diffusion (electrochemical) potential, possibly enhanced by a microbial effect. While the results of our investigation show a consistent SP response associated with the contaminant injections that is dominated by diffusional effects, further studies are required in order to better understand the effect of microbial activity on SP signals and the potential utility for the SP method to detect/monitor changes that may be indicative of biological PRB performance.