Mapping and controlling molecular processes: The application of control theory and system identification algorithms to ASOPS and other fast pulse spectroscopies

Asynchronous Optical Sampling (ASOPS) [1,2] and frequency comb spectrometry [3] based on dual Ti:saphire resonators operated in a master/slave mode have the potential to improve signal to noise ratio in THz transient and IR sperctrometry. The multimode Brownian oscillator time-domain response function described by state-space models is a mathematically robust framework that can be used to describe the dispersive phenomena governed by Lorentzian, Debye and Drude responses. In addition, the optical properties of an arbitrary medium can be expressed as a linear combination of simple multimode Brownian oscillator functions. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing the recorded THz transients in the time or frequency domain will be outlined [4,5]. Since a femtosecond duration pulse is capable of persistent excitation of the medium within which it propagates, such approach is perfectly justifiable. Several de-noising routines based on system identification will be shown. Furthermore, specifically developed apodization structures will be discussed. These are necessary because due to dispersion issues, the time-domain background and sample interferograms are non-symmetrical [6-8]. These procedures can lead to a more precise estimation of the complex insertion loss function. The algorithms are applicable to femtosecond spectroscopies across the EM spectrum. Finally, a methodology for femtosecond pulse shaping using genetic algorithms aiming to map and control molecular relaxation processes will be mentioned.

Assessing the vulnerability of food crop systems in Africa to climate change

Africa is thought to be the region most vulnerable to the impacts of climate variability and change. Agriculture plays a dominant role in supporting rural livelihoods and economic growth over most of Africa. Three aspects of the vulnerability of food crop systems to climate change in Africa are discussed: the assessment of the sensitivity of crops to variability in climate, the adaptive capacity of farmers, and the role of institutions in adapting to climate change. The magnitude of projected impacts of climate change on food crops in Africa varies widely among different studies. These differences arise from the variety of climate and crop models used, and the different techniques used to match the scale of climate model output to that needed by crop models. Most studies show a negative impact of climate change on crop productivity in Africa. Farmers have proved highly adaptable in the past to short- and long-term variations in climate and in their environment. Key to the ability of farmers to adapt to climate variability and change will be access to relevant knowledge and information. It is important that governments put in place institutional and macro-economic conditions that support and facilitate adaptation and resilience to climate change at local, national and transnational level.

Comparison of energy evaluation systems and a mechanistic model for milk production by dairy cattle offered fresh grass-based diets

Grass-based diets are of increasing social-economic importance in dairy cattle farming, but their low supply of glucogenic nutrients may limit the production of milk. Current evaluation systems that assess the energy supply and requirements are based on metabolisable energy (ME) or net energy (NE). These systems do not consider the characteristics of the energy delivering nutrients. In contrast, mechanistic models take into account the site of digestion, the type of nutrient absorbed and the type of nutrient required for production of milk constituents, and may therefore give a better prediction of supply and requirement of nutrients. The objective of the present study is to compare the ability of three energy evaluation systems, viz. the Dutch NE system, the agricultural and food research council (AFRC) ME system, and the feed into milk (FIM) ME system, and of a mechanistic model based on Dijkstra et al. [Simulation of digestion in cattle fed sugar cane: prediction of nutrient supply for milk production with locally available supplements. J. Agric. Sci., Cambridge 127, 247-60] and Mills et al. [A mechanistic model of whole-tract digestion and methanogenesis in the lactating dairy cow: model development, evaluation and application. J. Anim. Sci. 79, 1584-97] to predict the feed value of grass-based diets for milk production. The dataset for evaluation consists of 41 treatments of grass-based diets (at least 0.75 g ryegrass/g diet on DM basis). For each model, the predicted energy or nutrient supply, based on observed intake, was compared with predicted requirement based on observed performance. Assessment of the error of energy or nutrient supply relative to requirement is made by calculation of mean square prediction error (MSPE) and by concordance correlation coefficient (CCC). All energy evaluation systems predicted energy requirement to be lower (6-11%) than energy supply. The root MSPE (expressed as a proportion of the supply) was lowest for the mechanistic model (0.061), followed by the Dutch NE system (0.082), FIM ME system (0.097) and AFRCME system(0.118). For the energy evaluation systems, the error due to overall bias of prediction dominated the MSPE, whereas for the mechanistic model, proportionally 0.76 of MSPE was due to random variation. CCC analysis confirmed the higher accuracy and precision of the mechanistic model compared with energy evaluation systems. The error of prediction was positively related to grass protein content for the Dutch NE system, and was also positively related to grass DMI level for all models. In conclusion, current energy evaluation systems overestimate energy supply relative to energy requirement on grass-based diets for dairy cattle. The mechanistic model predicted glucogenic nutrients to limit performance of dairy cattle on grass-based diets, and proved to be more accurate and precise than the energy systems. The mechanistic model could be improved by allowing glucose maintenance and utilization requirements parameters to be variable. (C) 2007 Elsevier B.V. All rights reserved.

Application of one-list capture-recapture models to scrapie surveillance data in Great Britain

In this paper, we apply one-list capture-recapture models to estimate the number of scrapie-affected holdings in Great Britain. We applied this technique to the Compulsory Scrapie Flocks Scheme dataset where cases from all the surveillance sources monitoring the presence of scrapie in Great Britain, the abattoir survey, the fallen stock survey and the statutory reporting of clinical cases, are gathered. Consequently, the estimates of prevalence obtained from this scheme should be comprehensive and cover all the different presentations of the disease captured individually by the surveillance sources. Two estimators were applied under the one-list approach: the Zelterman estimator and Chao's lower bound estimator. Our results could only inform with confidence the scrapie-affected holding population with clinical disease; this moved around the figure of 350 holdings in Great Britain for the period under study, April 2005-April 2006. Our models allowed the stratification by surveillance source and the input of covariate information, holding size and country of origin. None of the covariates appear to inform the model significantly. Crown Copyright (C) 2008 Published by Elsevier B.V. All rights reserved.

Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments

Establishing the mechanisms by which microbes interact with their environment, including eukaryotic hosts, is a major challenge that is essential for the economic utilisation of microbes and their products. Techniques for determining global gene expression profiles of microbes, such as microarray analyses, are often hampered by methodological restraints, particularly the recovery of bacterial transcripts (RNA) from complex mixtures and rapid degradation of RNA. A pioneering technology that avoids this problem is In Vivo Expression Technology (IVET). IVET is a 'promoter-trapping' methodology that can be used to capture nearly all bacterial promoters (genes) upregulated during a microbe-environment interaction. IVET is especially useful because there is virtually no limit to the type of environment used (examples to date include soil, oomycete, a host plant or animal) to select for active microbial promoters. Furthermore, IVET provides a powerful method to identify genes that are often overlooked during genomic annotation, and has proven to be a flexible technology that can provide even more information than identification of gene expression profiles. A derivative of IVET, termed resolvase-IVET (RIVET), can be used to provide spatio-temporal information about environment-specific gene expression. More recently, niche-specific genes captured during an IVET screen have been exploited to identify the regulatory mechanisms controlling their expression. Overall, IVET and its various spin-offs have proven to be a valuable and robust set of tools for analysing microbial gene expression in complex environments and providing new targets for biotechnological development.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

Application of computer-aided facilities management (CAFM) for intelligent buildings operation

Purpose – The purpose of this paper is to investigate the concepts of intelligent buildings (IBs), and the opportunities offered by the application of computer-aided facilities management (CAFM) systems. Design/methodology/approach – In this paper definitions of IBs are investigated, particularly definitions that are embracing open standards for effective operational change, using a questionnaire survey. The survey further investigated the extension of CAFM to IBs concepts and the opportunities that such integrated systems will provide to facilities management (FM) professionals. Findings – The results showed variation in the understanding of the concept of IBs and the application of CAFM. The survey showed that 46 per cent of respondents use a CAFM system with a majority agreeing on the potential of CAFM in delivery of effective facilities. Research limitations/implications – The questionnaire survey results are limited to the views of the respondents within the context of FM in the UK. Practical implications – Following on the many definitions of an IB does not necessarily lead to technologies of equipment that conform to an open standard. This open standard and documentation of systems produced by vendors is the key to integrating CAFM with other building management systems (BMS) and further harnessing the application of CAFM for IBs. Originality/value – The paper gives experience-based suggestions for both demand and supply sides of the service procurement to gain the feasible benefits and avoid the currently hindering obstacles, as the paper provides insight to the current and future tools for the mobile aspects of FM. The findings are relevant for service providers and operators as well.

Contextual prerequisites for the application of ILS principles to the building services industry

Purpose – This paper proposes assessing the context within which integrated logistic support (ILS) can be implemented for whole life performance of building services systems. Design/methodology/approach – The use of ILS within a through-life business model (TLBM) is a better framework to achieve a well-designed, constructed and managed product. However, for ILS to be implemented in a TLBM for building services systems, the practices, tools and techniques need certain contextual prerequisites tailored to suit the construction industry. These contextual prerequisites are discussed. Findings – The case studies conducted reinforced the contextual importance of prime contracting, partnering and team collaboration for the application of ILS techniques. The lack of data was a major hindrance to the full realisation of ILS techniques within the case studies. Originality/value – The paper concludes with the recognition of the value of these contextual prerequisites for the use of ILS techniques within the building industry.

Application of integrated GPS and GIS technology for reducing construction waste and improving construction efficiency

This paper presents a study on applying an integrated Global Position System (GPS) and Geographacial Information System (GIS) technology to the reduction of construction waste. During the study, a prototype study is developed from automatic data capture system such as the barcoding system for construction material and equipment (M&E) management onsite, whilst the integrated GPS and GIS technology is combined to the M&E system based on the Wide Area Network (WAN). Then, a case study is conducted to demonstrate the deployment of the system. Experimental results indicate that the proposed system can minimize the amount of onsite material wastage.

Application of semiquantitative proteomics techniques to the Maillard reaction

Proteomic tools-in particular, mass spectrometry (MS)-have advanced significantly in recent years, and the identification of proteins within complex mixtures is now a routine procedure. Quantitative methods of analysis are less well advanced and continue to develop. These include the use of stable isotope ratio approaches, isotopically labeled peptide standards, and nonlabeling methods. This paper summarizes the use of MS as a proteomics tool to identify and semiquantify proteins and their modified forms by using examples of relevance to the Maillard reaction. Finally, some challenges for the future are presented.

Conceptualisation of an application of adaptive synthetic socioeconomic agents for intelligent network control

The deployment of Quality of Service (QoS) techniques involves careful analysis of area including: those business requirements; corporate strategy; and technical implementation process, which can lead to conflict or contradiction between those goals of various user groups involved in that policy definition. In addition long-term change management provides a challenge as these implementations typically require a high-skill set and experience level, which expose organisations to effects such as “hyperthymestria” [1] and “The Seven Sins of Memory”, defined by Schacter and discussed further within this paper. It is proposed that, given the information embedded within the packets of IP traffic, an opportunity exists to augment the traffic management with a machine-learning agent-based mechanism. This paper describes the process by which current policies are defined and that research required to support the development of an application which enables adaptive intelligent Quality of Service controls to augment or replace those policy-based mechanisms currently in use.

The application of the Hilbert spectrum to the analysis of electromyographic signals

This paper investigates the application of the Hilbert spectrum (HS), which is a recent tool for the analysis of nonlinear and nonstationary time-series, to the study of electromyographic (EMG) signals. The HS allows for the visualization of the energy of signals through a joint time-frequency representation. In this work we illustrate the use of the HS in two distinct applications. The first is for feature extraction from EMG signals. Our results showed that the instantaneous mean frequency (IMNF) estimated from the HS is a relevant feature to clinical practice. We found that the median of the IMNF reduces when the force level of the muscle contraction increases. In the second application we investigated the use of the HS for detection of motor unit action potentials (MUAPs). The detection of MUAPs is a basic step in EMG decomposition tools, which provide relevant information about the neuromuscular system through the morphology and firing time of MUAPs. We compared, visually, how MUAP activity is perceived on the HS with visualizations provided by some traditional (e.g. scalogram, spectrogram, Wigner-Ville) time-frequency distributions. Furthermore, an alternative visualization to the HS, for detection of MUAPs, is proposed and compared to a similar approach based on the continuous wavelet transform (CWT). Our results showed that both the proposed technique and the CWT allowed for a clear visualization of MUAP activity on the time-frequency distributions, whereas results obtained with the HS were the most difficult to interpret as they were extremely affected by spurious energy activity. (c) 2008 Elsevier Inc. All rights reserved.

Application of molecular biological methods for studying probiotics and the gut flora

Increasingly, the microbiological scientific community is relying on molecular biology to define the complexity of the gut flora and to distinguish one organism from the next. This is particularly pertinent in the field of probiotics, and probiotic therapy, where identifying probiotics from the commensal flora is often warranted. Current techniques, including genetic fingerprinting, gene sequencing, oligonucleotide probes and specific primer selection, discriminate closely related bacteria with varying degrees of success. Additional molecular methods being employed to determine the constituents of complex microbiota in this area of research are community analysis, denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel electrophoresis (TGGE), fluorescent in situ hybridisation (FISH) and probe grids. Certain approaches enable specific aetiological agents to be monitored, whereas others allow the effects of dietary intervention on bacterial populations to be studied. Other approaches demonstrate diversity, but may not always enable quantification of the population. At the heart of current molecular methods is sequence information gathered from culturable organisms. However, the diversity and novelty identified when applying these methods to the gut microflora demonstrates how little is known about this ecosystem. Of greater concern is the inherent bias associated with some molecular methods. As we understand more of the complexity and dynamics of this diverse microbiota we will be in a position to develop more robust molecular-based technologies to examine it. In addition to identification of the microbiota and discrimination of probiotic strains from commensal organisms, the future of molecular biology in the field of probiotics and the gut flora will, no doubt, stretch to investigations of functionality and activity of the microflora, and/or specific fractions. The quest will be to demonstrate the roles of probiotic strains in vivo and not simply their presence or absence.