Discrete wavelets transform for signal denoising in capillary electrophoresis with electrochemiluminescence detection

Discrete wavelets transform (DWT). was applied to noise on removal capillary electrophoresis-electrochemiluminescence (CE-ECL) electropherograms. Several typical wavelet transforms, including Haar, Daublets, Coiflets, and Symmlets, were evaluated. Four types of determining threshold methods, fixed form threshold, rigorous Stein's unbiased estimate of risk (rigorous SURE), heuristic SURE and minimax, combined with hard and soft thresholding methods were compared. The denoising study on synthetic signals showed that wave Symmlet 4 with a level decomposition of 5 and the thresholding method of heuristic SURE-hard provide the optimum denoising strategy. Using this strategy, the noise on CE-ECL electropherograms could be removed adequately. Compared with the Savitzky-Golay and Fourier transform denoising methods, DWT is an efficient method for noise removal with a better preservation of the shape of peaks.

Comparative study on CO2 emissions from different types of alpine meadows during grass exuberance period

Potentilla fruticosa scrub, Kobresia humilis meadow and Kobresia tibetica meadow are widely distributed on the Qinghai-Tibet Plateau. During the grass exuberance period from 3 July to 4September, based on close chamber-GC method, a study on CO2 emissions from different treatments was conducted in these meadows at Haibei research station, CAS. Results indicated that mean CO2emission rates from various treatments were 672.09+152.37 mgm-2h-1 for FC (grass treatment); 425.41+191.99 mgrn-2h-1 for FJ (grass exclusion treatment); 280.36+174.83 mgrn-2h-1 for FL (grass and roots exclusion treatment); 838.95+237.02 mgm-2h-1 for GG (scrub+grass treatment); 528.48+205.67 mgm-2h-1for GC (grass treatment); 268.97 ±99.72 mgm-2h-1 for GL (grass and roots exclusion treatment); and 659.20±94.83 mgm-2h-1 for LC (grass treatment), respectively (FC, FJ, FL, GG, GC, GL, LC were the Chinese abbreviation for various treatments). Furthermore, Kobresia humilis meadow, Potentilla fruticosa scrub meadow and Kobresia tibetica meadow differed greatly in average CO2 emission rate of soil-plant system, in the order of GG＞FC＞LC＞GC. Moreover, in Kobresia humilis meadow,heterotrophic and autotrophic respiration accounted for 42% and 58% of the total respiration of soil-plant system respectively, whereas, in Potentilla fruticosa scrub meadow, heterotrophic and autotrophic respiration accounted for 32% and 68% of total system respiration from G-G; 49% and 51%from GC. In addition, root respiration from Kobresia humilis meadow approximated 145 mgCO2m-2h-1,contributed 34% to soil respiration. During the experiment period, Kobresia humilis meadow and Potentilla fruticosa scrub meadow had a net carbon fixation of 111.11 grn-2 and 243.89 grn-2,respectively. Results also showed that soil temperature was the main factor which influenced CO2 emission from alpine meadow ecosystem, significant correlations were found between soil temperature at 5 cm depth and CO2 emission from GG, GC, FC and FJ treatments. In addition, soil moisture may be the inhibitory factor of CO2 emission from Kobresia tibetica meadow, and more detailed analyses should be done in further research.

Effect of annual weeds on the growth of perennial grass mixtures in the alpine region of the Qinghai-Tibetan Plateau

In the alpine region of the Tibetan Plateau, five perennial grass cultivars, Bromus inermis (B), Elymus nutans (E), Clinelymus nutans (C), Agropyron cristatum (A), and Poa crymophila (P) were combined into nine communities with different compositions and ratios, B+C, E+A, B+E+A, E+B+C,C+E+A,B+E+C+A,B+C+A+P,B+E+A+P and E+C+A+P. Each combination was sown in six 10 X 10 m plots with three hand-weeded plots and three natural-growing plots in a completely randomised design in 1998. A field experiment studied the performance of these perennial grass combinations under the competitive interference of annual weeds in 3 consecutive years from 1998 to 2000. The results showed that annual weeds occupied more space and suppressed the growth of the grasses due to earlier germination and quicker growth in the establishment year, but this pattern changed in the second and third years. Leaf area indexes (LAIs) of grasses were greatly decreased by the competitive interference of weeds, and the negative effect of weeds on LAIs of grasses declined and stabilised in the second and third years. E+B+C, B+E+C+A, and B+E+A+P possessed relatively higher LAIs (P < 0.05) among all grass combinations and their LAIs were close to five when the competitive interference of weeds was removed. Grasses were competitively inferior to weeds in the establishment year, although their competitive ability (aggressivities) increased throughout the growing season. In the second and third years, grasses were competitively superior to weeds, and their competitive ability decreased from May until August and increased in September. Dry matter (DM) yields of grasses were reduced by 29.8-74.1% in the establishment year, 11.0-64.9% in the second year, and 16.0-55.8% in the third year by the competitive interference of weeds. B+E+C+A and B+E+A+P can produce around 14 t/ha of DM yields, significantly higher (P < 0.05) than the production of the other grass combinations in the second and third years after the competitive interference of weeds was removed. It was preliminarily concluded that removal of competitive interference of weeds increased the LAIs of all grass swards and improved the light interception of grasses, thus promoting the production of perennial grass pastures. The germination stage of the grasses in the establishment year was the critical period for weeding and suppression of weeds should occur at an early stage of plant growth. The grass combinations of B+E+C+A and B+E+A+P were productive and can be extensively established in the alpine regions of the Tibetan Plateau. Two or three growing seasons will be needed before determining success of establishment of grass mixtures under the alpine conditions of the Tibetan Plateau.

Effect of N fertilizer on the productivity and nutritive values of perennial grass mixtures in the alpine region of Qinghai-Tibetan Plateau, China

A study was conducted on grass mixtures that included smooth bromegrass (SB) + drooping wild ryegrass (DW), smooth bromegrass + Siberian wild ryegrass (SW) + crested wheatgrass (CW) and smooth bromegrass + Siberian wild ryegrass + drooping wild ryegrass + crested wheatgrass in the alpine region of Qinghai-Tibetan Plateau. The study was conducted from 1998 to 2000 to investigate the effects of N application rates and growing year on herbage dry matter (DM) yield and nutritive values. Herbage DM production increased linearly with N application rates. The effect of N application on DM yields was greater (P < 0.05) in the 2nd and 3rd production years than in the establishment year. Dry matter yields of SB + SW + CW and SB + SW + DW + CW can reach as high as 15 000 kg ha(-1) at 345 kg ha(-1) N rate in the 3rd growing year. With increased N application rates, crude protein (CP) contents and 48 h in sacco DM degradability of grasses increased (P < 0.05). No effect (P > 0.05) of N application was detected on organic matter (OM) and acid detergent fibre (ADF) concentration. It can be concluded that for increased biomass production in the alpine region of the Qinghai-Tibetan Plateau, a minimum of 345 kg N ha(-1) should be applied to grass stands in three split application of 115 kg N ha(-1), in early June, early July and late July

Productivity and persistence of perennial grass mixtures under competition from annual weeds in the alpine region of the Qinghai-Tibetan Plateau

In the alpine region of the Qinghai-Tibetan Plateau four indigenous perennial grass species Bromus inermis (BI), Elymus sibiricus (ES), Elymus nutans (EN) and Agropyron cristatum (AC) were cultivated as three mixtures with different compositions and seeding rates, BI + EN, BI + ES + AC and BI + ES + EN + AC. From 1998 to 2001 there were three different weeding treatments: never weeded (CK); weeded on three occasions in the first year (1-y) and weeded on three occasions in both the first and second year (2-y) and their effect of grass combination and interactions on sward productivity and persistence was measured. Intense competitive interference by weedy annuals reduced dry matter (DM) yield of the swards. Grass combination significantly affected sward DM yields, leaf area index (LAI) and foliar canopy cover and also species composition DM and LAI, and species plant cover. Interaction between weeding treatments and grass combination was significant for sward DM yield, LAI and canopy cover, but not on species composition for DM, LAI or species plant cover. Grass mixture BI + ES + EN + AC gave the highest sward DM yield and LAI for both weeding and non-weeding treatments. Species ES and EN were competitively superior to the others. Annual weedy forbs must be controlled to obtain productive and stable mixtures of perennial grasses, and germination/emergence is the most important time for removal. Weeding three times (late May, late June and mid-July) in the establishment year is enough to maintain the production and persistence of perennial grass mixtures in the following growing seasons. Extra weeding three times in the second growing year makes only a slight improvement in productivity.

Influence of grazing intensity on performance of perennial grass mixtures in the alpine region of the Tibetan Plateau

Effects of grazing intensity on leaf photosynthetic rate (Pn), specific leaf area (SLA), individual tiller density, sward leaf area index (LAI), harvested herbage DM, and species composition in grass mixtures (Clinelymus nutans + Bromus inermis, Elymus nutans + Bromus inermis + Agropyron cristatum and Elymus nutans + Clinelymus nutans + Bromus inermis + Agropyron cristatum) were studied in the alpine region of the Tibetan Plateau. Four grazing intensities (GI), expressed as feed utilisation rates (UR) by Tibetan lambs were imposed as follows: (1) no grazing; (2) 30% UR as light grazing; (3) 50% UR as medium grazing; and (4) 70% UR as high grazing. Leaf Pn rate and tiller density of grasses increased (P < 0.05), while sward LAI and harvested herbage DM declined (P < 0.05) with the increments of GI, although no effect of GI on SLA was observed. With increasing GI, Elymus nutans and Clinelymus nutans increased but Bromus inermis and Agropyron cristatum decreased in swards, LAI and DM contribution. Whether being grazed or not, Elymus nutans + Clinelymus nutans + Bromus inermis + Agropyron cristatum was the most productive sward among the grass mixtures. Thus, two well-performed grass species (Elymus nutans and Clinelymus nutans) and the most productive mixture of four species should be investigated further as the new feed resources in the alpine grazing system of the Tibetan Plateau. Light grazing intensity of 30% UR was recommended for these grass mixtures when swards, LAI, herbage DM harvested, and species compatibility were taken into account.

Metabolic Engineering, metabolite profiling and machine learning to investigate the phloem-mobile signal in systemic acquired resistance in tobacco

Draper, J., Darby, R.M., Beckmann, M., Maddison, A.L., Mondhe, M., Sheldrick, C., Taylor, J., Goodacre, R., and Kell, D.B. (2002) Metabolic Engineering, metabolite profiling and machine learning to investigate the phloem-mobile signal in systemic acquired resistance in tobacco. First International Congress on Plant Metabolomics, Wageningen, The Netherlands

Cloning and characterization of a putative fructosyltransferase and two putative invertase genes from the temperate grass Lolium temulentum L.

J. A. Gallagher, A. J. Cairns and C. J. Pollock (2004). Cloning and characterization of a putative fructosyltransferase and two putative invertase genes from the temperate grass Lolium temulentum L. Journal of Experimental Botany, 55 (397) pp.557-569 Sponsorship: BBSRC RAE2008

Use of semiconductor optical amplifiers in signal processing applications

We describe a 42.6 Gbit/s all-optical pattern recognition system which uses semiconductor optical amplifiers (SOAs). A circuit with three SOA-based logic gates is used to identify the presence of specific port numbers in an optical packet header.

Digital signal processing and artificial intelligence for the automated classification of food allergy

As a by-product of the ‘information revolution’ which is currently unfolding, lifetimes of man (and indeed computer) hours are being allocated for the automated and intelligent interpretation of data. This is particularly true in medical and clinical settings, where research into machine-assisted diagnosis of physiological conditions gains momentum daily. Of the conditions which have been addressed, however, automated classification of allergy has not been investigated, even though the numbers of allergic persons are rising, and undiagnosed allergies are most likely to elicit fatal consequences. On the basis of the observations of allergists who conduct oral food challenges (OFCs), activity-based analyses of allergy tests were performed. Algorithms were investigated and validated by a pilot study which verified that accelerometer-based inquiry of human movements is particularly well-suited for objective appraisal of activity. However, when these analyses were applied to OFCs, accelerometer-based investigations were found to provide very poor separation between allergic and non-allergic persons, and it was concluded that the avenues explored in this thesis are inadequate for the classification of allergy. Heart rate variability (HRV) analysis is known to provide very significant diagnostic information for many conditions. Owing to this, electrocardiograms (ECGs) were recorded during OFCs for the purpose of assessing the effect that allergy induces on HRV features. It was found that with appropriate analysis, excellent separation between allergic and nonallergic subjects can be obtained. These results were, however, obtained with manual QRS annotations, and these are not a viable methodology for real-time diagnostic applications. Even so, this was the first work which has categorically correlated changes in HRV features to the onset of allergic events, and manual annotations yield undeniable affirmation of this. Fostered by the successful results which were obtained with manual classifications, automatic QRS detection algorithms were investigated to facilitate the fully automated classification of allergy. The results which were obtained by this process are very promising. Most importantly, the work that is presented in this thesis did not obtain any false positive classifications. This is a most desirable result for OFC classification, as it allows complete confidence to be attributed to classifications of allergy. Furthermore, these results could be particularly advantageous in clinical settings, as machine-based classification can detect the onset of allergy which can allow for early termination of OFCs. Consequently, machine-based monitoring of OFCs has in this work been shown to possess the capacity to significantly and safely advance the current state of clinical art of allergy diagnosis

Application of signal detection methods to fisheries management

The abundance of many commercially important fish stocks are declining and this has led to widespread concern on the performance of traditional approach in fisheries management. Quantitative models are used for obtaining estimates of population abundance and the management advice is based on annual harvest levels (TAC), where only a certain amount of catch is allowed from specific fish stocks. However, these models are data intensive and less useful when stocks have limited historical information. This study examined whether empirical stock indicators can be used to manage fisheries. The relationship between indicators and the underlying stock abundance is not direct and hence can be affected by disturbances that may account for both transient and persistent effects. Methods from Statistical Process Control (SPC) theory such as the Cumulative Sum (CUSUM) control charts are useful in classifying these effects and hence they can be used to trigger management response only when a significant impact occurs to the stock biomass. This thesis explores how empirical indicators along with CUSUM can be used for monitoring, assessment and management of fish stocks. I begin my thesis by exploring various age based catch indicators, to identify those which are potentially useful in tracking the state of fish stocks. The sensitivity and response of these indicators towards changes in Spawning Stock Biomass (SSB) showed that indicators based on age groups that are fully selected to the fishing gear or Large Fish Indicators (LFIs) are most useful and robust across the range of scenarios considered. The Decision-Interval (DI-CUSUM) and Self-Starting (SS-CUSUM) forms are the two types of control charts used in this study. In contrast to the DI-CUSUM, the SS-CUSUM can be initiated without specifying a target reference point (‘control mean’) to detect out-of-control (significant impact) situations. The sensitivity and specificity of SS-CUSUM showed that the performances are robust when LFIs are used. Once an out-of-control situation is detected, the next step is to determine how much shift has occurred in the underlying stock biomass. If an estimate of this shift is available, they can be used to update TAC by incorporation into Harvest Control Rules (HCRs). Various methods from Engineering Process Control (EPC) theory were tested to determine which method can measure the shift size in stock biomass with the highest accuracy. Results showed that methods based on Grubb’s harmonic rule gave reliable shift size estimates. The accuracy of these estimates can be improved by monitoring a combined indicator metric of stock-recruitment and LFI because this may account for impacts independent of fishing. The procedure of integrating both SPC and EPC is known as Statistical Process Adjustment (SPA). A HCR based on SPA was designed for DI-CUSUM and the scheme was successful in bringing out-of-control fish stocks back to its in-control state. The HCR was also tested using SS-CUSUM in the context of data poor fish stocks. Results showed that the scheme will be useful for sustaining the initial in-control state of the fish stock until more observations become available for quantitative assessments.

Akt signal transduction dysfunction in the 3xTg-AD mouse model of Alzheimer's disease

Alzheimer’s disease (AD) is an incurable neurodegenerative disorder, accounting for over 60% of all cases of dementia. The primary risk factor for AD is age, however several genetic and environmental factors are also involved. The pathological characteristics of AD include extracellular deposition of the beta-amyloid peptide (Aβ) and intraneuronal accumulation of neurofibrillary tangles (NFTs) made of aggregated paired helical filaments (PHFs) of the hyperphosphorylated tau protein, along with synaptic loss and neuronal death. There are numerous biochemical mechanisms involved in AD pathogenesis, however the reigning hypothesis points to toxic oligomeric Aβ species as the primary causative factor in a cascade of events leading to neuronal stress and dyshomeostasis that initiate abnormal regulation of tau. The insulin and IGF-1 receptors (IR, IGF-1R) are the primary activators of PI3- K/Akt through which they regulate cell growth, development, glucose metabolism, and learning and memory. Work in our lab and others shows increased Akt activity and phosphorylation of its downstream targets in AD brain, along with insulin and insulin-like growth factor-1 signalling (IIS) dysfunction. This is supported by studies of AD models in vivo and in vitro. Our group and others hypothesise that Aβ activates Akt through IIS to initiate a negative feedback mechanism that desensitises neurons to insulin/IGF-1, and sustains activation of Akt. In this study the functions of endogenous Akt, IR, and the insulin receptor substrate (IRS-1) were examined in relationship to Aβ and tau pathology in the 3xTg-AD mouse model, which contains three mutant human transgenes associated with familial AD or dementia. The 3xTg-AD mouse develops Aβ and tau pathology in a spatiotemporal manner that best recapitulates the progression of AD in human brain. Western blotting and immunofluorescent microscopy techniques were utilised in vivo and in vitro, to examine the relationship between IIS, Akt, and AD pathology. I first characterised in detail AD pathology in 3xTg-AD mice, where an age-related accumulation of intraneuronal Aβ and tau was observed in the hippocampal formation, amygdala, and entorhinal cortex, and at late stages (18 months), extracellular amyloid plaques and NFTs, primarily in the subiculum and the CA1 layer of the hippocampal formation. Increased activity of Akt, detected with antibody to phosphoSer473-Akt, was increased in 3xTg-AD mice compared to age-matched non-transgenic mice (non-Tg), and in direct correlation to the accumulation of Aβ and tau in neuronal somatodendritic compartments. Akt phosphorylates tau at residue Ser214 within a highly specific consensus sequence for Akt phosphorylation, and phosphoSer214-tau strongly decreases microtubule (MT) stabilisation by preventing tau-MT binding. PhosphoSer214-tau increased concomitantly with this in the same age-related and region-specific fashion. Polarisation of tau phosphorylation was observed, where PHF-1 (tauSer396/404) and phosphoSer214-tau both appeared early in 3xTg-AD mice in distinct neuronal compartments: PHF-1 in axons, and phosphoSer214-tau in neuronal soma and dendrites. At 18 months, phosphoSer214-tau strongly colocalised with NFTs positive for the PHF- 1 and AT8 (tauSer202/Thr205) phosphoepitopes. IR was decreased with age in 3xTg-AD brain and in comparison to age-matched non-Tg, and this was specific for brain regions containing Aβ, tau, and hyperactive Akt. IRS-1 was similarly decreased, and both proteins showed altered subcellular distribution. Phosphorylation of IRS-1Ser312 is a strong indicator of IIS dysfunction and insulin resistance, and was increased in 3xTg-AD mice with age and in relation to pathology. Of particular note was our observation that abberant IIS and Akt signalling in 3xTg-AD brain related to Aβ and tau pathology on a gross anatomical level, and specifically localised to the brain regions and circuitry of the perforant path. Finally, I conducted a preliminary study of the effects of synthetic Aβ oligomers on embryonic rat hippocampus neuronal cultures to support these results and those in the literature. Taken together, these novel findings provide evidence for IIS and Akt signal transduction dysfunction as the missing link between Aβ and tau pathogenesis, and contribute to the overall understanding of the biochemical mechanisms of AD.

All-optical signal processing using semiconductor optical amplifiers for next generation optical networks

This thesis details an experimental and simulation investigation of some novel all-optical signal processing techniques for future optical communication networks. These all-optical techniques include modulation format conversion, phase discrimination and clock recovery. The methods detailed in this thesis use the nonlinearities associated with semiconductor optical amplifiers (SOA) to manipulate signals in the optical domain. Chapter 1 provides an introduction into the work detailed in this thesis, discusses the increased demand for capacity in today’s optical fibre networks and finally explains why all-optical signal processing may be of interest for future optical networks. Chapter 2 discusses the relevant background information required to fully understand the all-optical techniques demonstrated in this thesis. Chapter 3 details some pump-probe measurement techniques used to calculate the gain and phase recovery times of a long SOA. A remarkably fast gain recovery is observed and the wavelength dependent nature of this recovery is investigated. Chapter 4 discusses the experimental demonstration of an all-optical modulation conversion technique which can convert on-off- keyed data into either duobinary or alternative mark inversion. In Chapter 5 a novel phase sensitive frequency conversion scheme capable of extracting the two orthogonal components of a quadrature phase modulated signal into two separate frequencies is demonstrated. Chapter 6 investigates a novel all-optical clock recovery technique for phase modulated optical orthogonal frequency division multiplexing superchannels and finally Chapter 7 provides a brief conclusion.

Biomethane production from grass silage: laboratory assessment to maximise yields

On-farm biogas production is typically associated with forage maize as the biomass source. Digesters are designed and operated with the focus of optimising the conditions for this feedstock. Thus, such systems may not be ideally suited to the digestion of grass. Ireland has ca. 3.85 million ha of grassland. Annual excess grass, surplus to livestock requirements, could potentially fuel an anaerobic digestion industry. Biomethane associated with biomass from 1.1 % of grassland in Ireland, could potentially generate over 10 % renewable energy supply in transport. This study aims to identify and optimise technologies for the production of biomethane from grass silage. Mono-digestion of grass silage and co-digestion with slurry, as would occur on Irish farms, is investigated in laboratory trials. Grass silage was shown to have 7 times greater methane potential than dairy slurry on a fresh weight basis (107 m3 t-1 v 16 m3 t-1). However, comprehensive trace element profiles indicated that cobalt, iron and nickel are deficient in mono-digestion of grass silage at a high organic loading rate (OLR) of 4.0 kg VS m-3 d-1. The addition of a slurry co-substrate was beneficial due to its wealth of essential trace elements. To stimulate hydrolysis of high lignocellulose grass silage, particle size reduction (physical) and rumen fluid addition (biological) were investigated. In a continuous trial, digestion of grass silage of <1 cm particle size achieved a specific methane yield of 371 L CH4 kg-1 VS when coupled with rumen fluid addition. The concept of demand driven biogas was also examined in a two-phase digestion system (leaching with UASB). When demand for electricity is low it is recommended to disconnect the UASB from the system and recirculate rumen fluid to increase volatile fatty acid (VFA) and soluble chemical oxygen demand (SCOD) production whilst minimising volatile solids (VS) destruction. At times of high demand for electricity, connection of the UASB increases the destruction of volatiles and associated biogas production. The above experiments are intended to assess a range of biogas production options from grass silage with a specific focus on maximising methane yields and provide a guideline for feasible design and operation of on-farm digesters in Ireland.