Geometric optimization methods for the analysis of gene expression data

DNA microarrays provide such a huge amount of data that unsupervised methods are required to reduce the dimension of the data set and to extract meaningful biological information. This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data. The paper first presents an overview of the most popular algorithms to perform ICA. These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed. This study indicates that ICA significantly outperforms Principal Component Analysis (PCA).

An approach to scenario analysis of the sustainability of an industrial sector applied to clothing and textiles in the UK

Companies aiming to be 'sustainability leaders' in their sector and governments wanting to support their ambitions need a means to assess the changes required to make a significant difference in the impact of their whole sector. Previous work on scenario analysis/scenario planning demonstrates extensive developments and applications, but as yet few attempts to integrate the 'triple bottom line' concerns of sustainability into scenario planning exercises. This paper, therefore, presents a methodology for scenario analysis of large change to an entire sector. The approach includes calculation of a 'triple bottom line graphic equaliser' to allow exploration and evaluation of the trade-offs between economic, environmental and social impacts. The methodology is applied to the UK's clothing and textiles sector, and results from the study of the sector are summarised. In reflecting on the specific study, some suggestions are made about future application of a similar methodology, including a template of candidate solutions that may lead to significant reduction in impacts. © 2007 Elsevier Ltd. All rights reserved.

A comparison of methods for the coupled analysis of floating structures

The dynamic analysis of a deepwater floating platform and the associated mooring/riser system should ideally be fully coupled to ensure a reliable response prediction. It is generally held that a time domain analysis is the only means of capturing the various coupling and nonlinear effects accurately. However, in recent work it has been found that for an ultra-deepwater floating system (2000m water depth), the highly efficient frequency domain approach can provide highly accurate response predictions. One reason for this is the accuracy of the drag linearization procedure over both first and second order motions, another reason is the minimal geometric nonlinearity displayed by the mooring lines in deepwater. In this paper, the aim is to develop an efficient analysis method for intermediate water depths, where both mooring/vessel coupling and geometric nonlinearity are of importance. It is found that the standard frequency domain approach is not so accurate for this case and two alternative methods are investigated. In the first, an enhanced frequency domain approach is adopted, in which line nonlinearities are linearized in a systematic way. In the second, a hybrid approach is adopted in which the low frequency motion is solved in the time domain while the high frequency motion is solved in the frequency domain; the two analyses are coupled by the fact that (i) the low frequency motion affects the mooring line geometry for the high frequency motion, and (ii) the high frequency motion affects the drag forces which damp the low frequency motion. The accuracy and efficiency of each of the methods are systematically compared. Copyright © 2007 by ASME.

Poroelastic indentation analysis for hydrated biological tissues

Indentation techniques are employed for the measurement of mechanical properties of a wide range of materials. In particular, techniques focused at small length-scales, such as nanoindentation and AFM indentation, allow for local characterization of material properties in heterogeneous materials including natural tissues and biomimetic materials. Typical elastic analysis for spherical indentation is applicable in the absence of time-dependent deformation, but is inappropriate for materials with time-dependent responses. Recent analyses for the viscoelastic indentation problem, based on elastic-viscoelastic correspondence, have begun to address the issue of time-dependent deformation during an indentation test. The viscoelastic analysis has been shown to fit experimental indentation data well, and has been demonstrated as useful for characterization of viscoelasticity in polymeric materials and in hydrated mineralized tissues. However, a viscoelastic analysis is not necessarily sufficient for multi-phase materials with fluid flow. In the current work, a poroelastic analysis-based on fluid motion through a porous elastic network-is used to examine spherical indentation creep responses of hydrated biological materials. Both analytical and finite element approaches are considered for the poroelastic Hertzian indentation problem. Modeling results are compared with experimental data from nanoindentation of hydrated bone immersed in water and polar solvents (ethanol, methanol, acetone). Baseline (water-immersed) bone responses are characterized using the poroelastic model and numerical results are compared with altered hydration states due to polar solvents. © 2007 Materials Research Society.

Design of carbon nanotubes based microwave applications employing mechanical resonance analysis

Carbon nanotubes (CNTs) have good mechanical properties and unique structural, electronic, thermal, and optical characteristics. In this work, we present the results of our investigations of a resonator device based on embedded vertical CNT arrays. The device's design is based on the mechanical resonance of the tubes. CoventorWare FEA tools have been used to simulate the mechanical resonance frequencies of the vertical nanotubes arrays integrated on a silicon substrate. ©2008 IEEE.

Fourier analysis and gabor filtering for texture analysis and local reconstruction of general shapes

Since the pioneering work of Gibson in 1950, Shape- From-Texture has been considered by researchers as a hard problem, mainly due to restrictive assumptions which often limit its applicability. We assume a very general stochastic homogeneity and perspective camera model, for both deterministic and stochastic textures. A multi-scale distortion is efficiently estimated with a previously presented method based on Fourier analysis and Gabor filters. The novel 3D reconstruction method that we propose applies to general shapes, and includes non-developable and extensive surfaces. Our algorithm is accurate, robust and compares favorably to the present state of the art of Shape-From- Texture. Results show its application to non-invasively study shape changes with laid-on textures, while rendering and retexturing of cloth is suggested for future work. © 2009 IEEE.

Automated meshing for aero-thermal analysis of complex automotive geometries

Successful product development, especially in motorsport, increasingly depends not just on the ability to simulate aero-thermal behavior of complex geometrical configurations, but also the ability to automate these simulations within a workflow and perform as many simulations as possible within constrained time frames. The core of these aero-thermal simulations - and usually the main bottleneck - is generating the computational mesh. This paper describes recent work aimed at developing a mesh generator which can reliably produce meshes for geometries of essentially arbitrary complexity in an automated manner and fast enough to keep up with the pace of an engineering development program. Our goal is to be able to script the mesh generation within an automated workflow - and forget it. © 2011 SAE International.

Analysis of CFRP strap-strengthened reinforced concrete beams using the modified compression field theory (MCFT)

External, prestressed carbon fiber reinforced polymer (CFRP) straps can be used to enhance the shear strength of existing reinforced concrete beams. In order to effectively design a strengthening system, a rational predictive theory is required. The current work investigates the ability of the modified compression field theory (MCFT) to predict the behavior of rectangular strap strengthened beams where the discrete CFRP strap forces are approximated as a uniform vertical stress. An unstrengthened control beam and two strengthened beams were tested to verify the predictions. The experimental results suggest that the MCFT could predict the general response of a strengthened beam with a uniform strap spacing < 0.9d. However, whereas the strengthened beams failed in shear, the MCFT predicted flexural failures. It is proposed that a different compression softening model or the inclusion of a crack width limit is required to reflect the onset of shear failures in the strengthened beams.

The analysis of impact forces in randomly vibrating elastic systems

This work is concerned with the characteristics of the impact force produced when two randomly vibrating elastic bodies collide with each other, or when a single randomly vibrating elastic body collides with a stop. The impact condition includes a non-linear spring, which may represent, for example, a Hertzian contact, and in the case of a single body, closed form approximate expressions are derived for the duration and magnitude of the impact force and for the maximum deceleration at the impact point. For the case of two impacting bodies, a set of algebraic equations are derived which can be solved numerically to yield the quantities of interest. The approach is applied to a beam impacting a stop, a plate impacting a stop, and to two impacting beams, and in each case a comparison is made with detailed numerical simulations. Aspects of the statistics of impact velocity are also considered, including the probability that the impact velocity will exceed a specified value within a certain time. © 2012 Elsevier Ltd. All rights reserved.

Analysis of asphalt concrete permeability data using representative pore size

The permeability of asphalt concrete has been the subject of much study by pavement engineers over the last decade. The work undertaken has tended to focus on high air voids as the primary indicator of permeable asphalt concrete. This paper presents a simple approach for understanding the parameters that affect permeability. Principles explained by Taylor in 1956 in channel theory work for soils are used to derive a new parameter-representative pore size. Representative pore size is related to the air voids in the compacted mix and the D75 of the asphalt mix grading curve. Collected Superpave permeability data from published literature and data collected by the writers at the Queensland Department of Transport and Main Roads is shown to be better correlated with representative pore size than air voids, reducing the scatter considerably. Using the database of collected field and laboratory permeability values an equation is proposed that pavement engineers can use to estimate the permeability of in-place pavements. © 2011 ASCE.

Management and Analysis of Unstructured Construction Data Types

Compared with structured data sources that are usually stored and analyzed in spreadsheets, relational databases, and single data tables, unstructured construction data sources such as text documents, site images, web pages, and project schedules have been less intensively studied due to additional challenges in data preparation, representation, and analysis. In this paper, our vision for data management and mining addressing such challenges are presented, together with related research results from previous work, as well as our recent developments of data mining on text-based, web-based, image-based, and network-based construction databases.

Data Analysis on Complicated Construction Data Sources: Vision, Research, and Recent Developments

Compared with construction data sources that are usually stored and analyzed in spreadsheets and single data tables, data sources with more complicated structures, such as text documents, site images, web pages, and project schedules have been less intensively studied due to additional challenges in data preparation, representation, and analysis. In this paper, our definition and vision for advanced data analysis addressing such challenges are presented, together with related research results from previous work, as well as our recent developments of data analysis on text-based, image-based, web-based, and network-based construction sources. It is shown in this paper that particular data preparation, representation, and analysis operations should be identified, and integrated with careful problem investigations and scientific validation measures in order to provide general frameworks in support of information search and knowledge discovery from such information-abundant data sources.

Stall warning by blade pressure signature analysis

At low mass flow rates axial compressors suffer from flow instabilities leading to stall and surge. The inception process of these instabilities has been widely researched in the past - primarily with the aim of predicting or averting stall onset. In recent times, attention has shifted to conditions well before stall and has focussed on the level of irregularity in the blade passing signature in the rotor tip region. In general, this irregularity increases in intensity as the flow rate through the compressor is reduced. Attempts have been made to develop stall warning/avoidance procedures based on the level of the flow irregularity, but little effort has been made to characterise the irregularity, or to understand its underlying causes. Work on this project has revealed for the first time that the increase in irregularity in the blade passing signature is highly dependent on both tip-clearance and eccentricity. In a compressor with small, uniform, tip-clearance, the increase in blade passing irregularity which accompanies a reduction in flow rate will be modest. If the tip-clearance is enlarged, however, there will be a sharp rise in irregularity at all circumferential locations. In a compressor with eccentric tip-clearance, the increase in irregularity will only occur in the part of the annulus where the tip-clearance is largest, regardless of the average clearance level. In this paper, some attention is also given to the question of whether this irregularity observed in the pre-stall flow field is due to random turbulence, or to some form of coherent flow structure. Detailed flow measurements reveal that the latter is the case. From these findings, it is clear that a stall warning system based on blade passing signature irregularity will not be viable in an aero-engine where tip-clearance size and eccentricity change during each flight cycle and over the life of the compressor. Copyright © 2011 by ASME.

Biofluid behaviour in 3D microchannel systems: Numerical analysis and design development of 3D microchannel biochip separators

This paper describes the design and development cycle of a 3D biochip separator and the modelling analysis of flow behaviour in the biochip microchannel features. The focus is on identifying the difference between 2D and 3D implementations as well as developing basic forms of 3D microfluidic separators. Five variants, based around the device are proposed and analysed. These include three variations of the branch channels (circular, rectangular, disc) and two variations of the main channel (solid and concentric). Ignoring the initial transient behaviour and assuming steady state flow has been established, the efficiencies of the flow between the main and side channels for the different designs are analysed and compared with regard to relevant biomicrofluidic laws or effects (bifurcation law, Fahraeus effect, cell-free phenomenon, bending channel effect and laminar flow behaviour). The modelling results identify flow features in microchannels, a constriction and bifurcations and show detailed differences in flow fields between the various designs. The manufacturing process using injection moulding for the initial base case design is also presented and discussed. The work reported here is supported as part of the UK funded 3D-MINTEGRATION project. © 2010 IEEE.