Discovering transcriptional modules by Bayesian data integration.

MOTIVATION: We present a method for directly inferring transcriptional modules (TMs) by integrating gene expression and transcription factor binding (ChIP-chip) data. Our model extends a hierarchical Dirichlet process mixture model to allow data fusion on a gene-by-gene basis. This encodes the intuition that co-expression and co-regulation are not necessarily equivalent and hence we do not expect all genes to group similarly in both datasets. In particular, it allows us to identify the subset of genes that share the same structure of transcriptional modules in both datasets. RESULTS: We find that by working on a gene-by-gene basis, our model is able to extract clusters with greater functional coherence than existing methods. By combining gene expression and transcription factor binding (ChIP-chip) data in this way, we are better able to determine the groups of genes that are most likely to represent underlying TMs. AVAILABILITY: If interested in the code for the work presented in this article, please contact the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Fabrication and electrical integration of robust carbon nanotube micropillars by self-directed elastocapillary densification

Vertically aligned carbon nanotube (CNT) 'forest' microstructures fabricated by chemical vapor deposition (CVD) using patterned catalyst films typically have a low CNT density per unit area. As a result, CNT forests have poor bulk properties and are too fragile for integration with microfabrication processing. We introduce a new self-directed capillary densification method where a liquid is controllably condensed onto and evaporated from the CNT forests. Compared to prior approaches, where the substrate with CNTs is immersed in a liquid, our condensation approach gives significantly more uniform structures and enables precise control of the CNT packing density. We present a set of design rules and parametric studies of CNT micropillar densification by self-directed capillary action, and show that self-directed capillary densification enhances Young's modulus and electrical conductivity of CNT micropillars by more than three orders of magnitude. Owing to the outstanding properties of CNTs, this scalable process will be useful for the integration of CNTs as a functional material in microfabricated devices for mechanical, electrical, thermal and biomedical applications. © 2011 IOP Publishing Ltd.

The MHP36 line of murine neural stem cells expresses functional CXCR1 chemokine receptors that initiate chemotaxis in vitro.

Chemokines help to establish cerebral inflammation after ischemia, which comprises a major component of secondary brain injury. The CXCR4 chemokine receptor system induces neural stem cell migration, and hence has been implicated in brain repair. We show that CXCR1 and interleukin-8 also stimulate chemotaxis in murine neural stem cells from the MHP36 cell line. The presence of CXCR1 was confirmed by reverse transcriptase PCR and immunohistochemistry. Interleukin-8 evoked intracellular calcium currents, upregulated doublecortin (a protein expressed by migrating neuroblasts), and elicited positive chemotaxis in vitro. Therefore, effectors of the early innate immune response may also influence brain repair mechanisms.

Network integration for international mergers and Acquisitions

Business activities are increasingly taking place across geographical and ownership boundaries. Post-Merger & Acquisition Integration (PMI) processes are more challenging in network organisations due to the extra complexity and interdependency associated with networks. However, network integration issues are not well addressed in the traditional M&A literature or the network organisation literature. Based on ten in-depth case studies across key industry sectors, this research identifies the essential network integration issues for international M&As with a configuration concept, and demonstrates different network integration patterns according to M&A objectives for growth and efficiency. This paper extends the theoretical understanding of PMI for network organisations. It can also provide practical guidance for managers to assess the feasibility of an M&A transition or to go through the PMI process successfully. Copyright © 2010 Inderscience Enterprises Ltd.

A comparative study of plasma-enhanced chemical vapor gate dielectrics for solution-processed polymer thin-film transistor circuit integration

This paper considers plasma-enhanced chemical vapor deposited (PECVD) silicon nitride (SiNx) and silicon oxide (SiOx) as gate dielectrics for organic thin-film transistors (OTFTs), with solution-processed poly[5, 5′ -bis(3-dodecyl-2-thienyl)-2, 2′ -bithiophene] (PQT-12) as the active semiconductor layer. We examine transistors with SiNx films of varying composition deposited at 300 °C as well as 150 °C for plastic compatibility. The transistors show over 100% (two times) improvement in field-effect mobility as the silicon content in SiNx increases, with mobility (μFE) up to 0.14 cm2 /V s and on/off current ratio (ION / IOFF) of 108. With PECVD SiOx gate dielectric, preliminary devices exhibit a μFE of 0.4 cm2 /V s and ION / IOFF of 108. PQT-12 OTFTs with PECVD SiNx and SiOx gate dielectrics on flexible plastic substrates are also presented. These results demonstrate the viability of using PECVD SiN x and SiOx as gate dielectrics for OTFT circuit integration, where the low temperature and large area deposition capabilities of PECVD films are highly amenable to integration of OTFT circuits targeted for flexible and lightweight applications. © 2008 American Institute of Physics.

Integration of holographic sensors into microfluidics for the real-time pH sensing of L. casei metabolism

We describe developments in the integration of analyte specific holographic sensors into PDMS-based microfluidic devices for the purpose of continuous, low-impact monitoring of extra-cellular change in micro-bioreactors. Holographic sensors respond to analyte concentration via volume change, which makes their reduction in size and integration into spatially confined fluidics difficult. Through design and process modification many of these constraints have been addressed, and a microfluidics-based device capable of real-time monitoring of the pH change caused by Lactobacillus casei fermentation is presented as a general proof-of-concept for a wide array of possible devices.