Peptide mass fingerprinting using field-programmable gate arrays

The reconfigurable computing paradigm, which exploits the flexibility and versatility of field-programmable gate arrays (FPGAs), has emerged as a powerful solution for speeding up time-critical algorithms. This paper describes a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-TOF instruments. The hardware-implemented algorithms for denoising, baseline correction, peak identification, and deisotoping, running on a Xilinx Virtex-2 FPGA at 180 MHz, generate a mass fingerprint that is over 100 times faster than an equivalent algorithm written in C, running on a Dual 3-GHz Xeon server. The results obtained using the FPGA implementation are virtually identical to those generated by a commercial software package MassLynx

Replication Technique for Studying Microstructure in Fossil Enamel

The present paper describes a two stage impression technique using a silicone elastomer suitable for field replication studies; which requires high dimensional stability, defined resolution, and being capable of reproducing inaccessible details. A test object consisting of etched pearlite possessed fine detail [\u3e1μm to \u3c0.1μm] which was suitable for testing negative/ positive replica combinations. Coltene President light-body impression material was capable of resolving parallel side depressions of widths ≧0.2μm, and it possesses very good dimensional stability with time, allowing the production of positive casts to be deferred for several months. Low viscosity Spurr resin reproduced this detail, and flowed into inaccessible sites. Although there was evidence of bulk contraction on curing, there was no significant shrinkage on flat [linear] surfaces or in vertical relief dimensions. Replicas of fractured hominid teeth showed good surface detail, and reproduction of inaccessible three-dimensional features on enamel surfaces. Enamel prism shape was pattern 3

Virtual Werribee : a planning support tool

Virtual Werribee is collaborative research in applying 3-D modelling and visualisation as a planning support tool in comparison to 2-D plans and drawings. It was a joint initiative involving Deakin University and the Wyndham City Council to demonstrate the use of 3-D visualisation for planning process in the actual context of a planning authority in Australia. The objective of this project was to assist the council in preparing for the revised Local Structure Plan. By reconstructing the council&rsquo;s data into easily understood information, 3-D model and visualisation served as a verification and discussion tool for decision making. The integration of wider site context also provided a better understanding of the surrounding development areas. This could equip other stakeholders as well as the community to participate in council&rsquo;s planning agenda activities, such as increasing the urban density and building heights limit.Virtual Werribee included the development planning agenda, categorised as new, re-development and hypothetical. The modelling process progressed with sufficient data from the council. Some changes to the initial plan were made, including the use of CAD modelling software instead of GIS software, and production of a block model with selected detail buildings, instead of a full draped 3-D model. The council decided that the block model would be sufficient for their planning purposes. This was determined while taking into consideration the available facilities at the council.The potentials of the model as a planning tool were demonstrated in this paper, and further compared to the council&rsquo;s existing materials prepared by the project developers. The advantages of the 3-D interactive model and visualisation over the conventional materials have provided the council officer with a tool for better empowerment in the planning process. This was also evident in the increasing engagement level between the officer and the model as the process developed. As a result of this, the project scope has also expanded, finally covering the entire city.While Virtual Werribee has the potential to better communicate council&rsquo;s planning agendas to the stakeholders and the community, the key factor, coupled with its visualisation components, was its interactive capability. Property layers with aerial site image that provided a realistic background served as a virtual city platform for different users. Although limited in its analytic capability found in GIS software, this model offered high visualisation content to assist visual impact assessment through its interactive mode along with a series of still images and a simulation movie.<br /

MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

Electronic Consultation at the National Assembly for Wales

Significant developments are occurring in the domain of electronic government within the UK – the use of ICT to enable re-structuring of governmental processes. In this paper we look at that subset of e-Government known as electronic democracy. In particular, we describe how electronic consultation, an important facet of electronic democracy, is being used to procure ideas from partnership organisations and citizenry in relation to the policy formulation processes at a devolved regional assembly in the UK – the National Assembly for Wales (NAfW). We utilise a process model of governance focused around the concept of the policy cycle. This process is currently being enabled at the NAfW through the development of a series of bespoke ICT systems. Such forms of ICT innovation are seen by many to be significant ways in which government may re-engage with its populace, address issues of social exclusion in the area of democratic participation and generally re-energise the democratic process

Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research

Beyond Access: Bridging the Digital Divide

This paper describes the theoretical underpinnings of an ongoing research project that is examining the relationship between e-Democracy and the ‘digital divide’. The literature surrounding the Digital Divide is reviewed, and the importance of equitable physical access to ICTs in the drive to bridge the issue of social exclusion examined. It is argued that any discussion of the phenomenon of the digital divide must look beyond equitable physical access and take into consideration issues mentioned separately in the literature – ‘real access’, ‘reach’ and ‘socially responsible connectivity’

Galectin-3 interacts with the cell surface glycoprotein CD146 (MCAM, MUC18) and induces secretion of metastasis-promoting cytokines from vascular endothelial cells

The galactoside-binding protein galectin-3 is increasingly recognized as an important player in cancer development, progression, and metastasis via its interactions with various galactoside-terminated glycans. We have shown previously that circulating galectin-3, which is increased up to 30-fold in cancer patients, promotes blood-borne metastasis in an animal cancer model. This effect is partly attributable to the interaction of galectin-3 with unknown receptor(s) on vascular endothelial cells and causes endothelial secretion of several metastasis-promoting cytokines. Here we sought to identify the galectin-3-binding molecule(s) on the endothelial cell surface responsible for the galectin-3-mediated cytokine secretion. Using two different galectin-3 affinity purification processes, we extracted four cell membrane glycoproteins, CD146/melanoma cell adhesion molecule (MCAM)/MUC18, CD31/platelet endothelial cell adhesion molecule-1 (PECAM-1), CD144/VE-cadherin, and CD106/Endoglin, from vascular endothelial cells. CD146 was the major galectin-3-binding ligand and strongly co-localized with galectin-3 on endothelial cell surfaces treated with exogenous galectin-3. Moreover, galectin-3 bound to N-linked glycans on CD146 and induced CD146 dimerization and subsequent activation of AKT signaling. siRNA-mediated suppression of CD146 expression completely abolished the galectin-3-induced secretion of IL-6 and G-CSF cytokines from the endothelial cells. Thus, CD146/MCAM is the functional galectin-3-binding ligand on endothelial cell surfaces responsible for galectin-3-induced secretion of metastasis-promoting cytokines. We conclude that CD146/MCAM interactions with circulating galectin-3 may have an important influence on cancer progression and metastasis