Efficient Bayesian inference for learning in the Ising linear perceptron and signal detection in CDMA

Efficient new Bayesian inference technique is employed for studying critical properties of the Ising linear perceptron and for signal detection in code division multiple access (CDMA). The approach is based on a recently introduced message passing technique for densely connected systems. Here we study both critical and non-critical regimes. Results obtained in the non-critical regime give rise to a highly efficient signal detection algorithm in the context of CDMA; while in the critical regime one observes a first-order transition line that ends in a continuous phase transition point. Finite size effects are also studied. © 2006 Elsevier B.V. All rights reserved.

A study of liquid-liquid extraction in a sieve plate column

The literature relating to sieve plate liquid extraction columns and relevant hydrodynamic phenomena have been surveyed. Mass transfer characteristics during drop formation, rise and coalescence, and related models were also reviewed. Important design parameters i.e. flooding, dispersed phase hold-up, drop size distribution, mean drop size, coalescence/flocculation zone height beneath a plate and jetting phenomena were investigated under non-mass transfer and mass transfer conditions in a 0.45m diameter, 2.3m high sieve plate column. This column had provision for four different plate designs, and variable plate spacing and downcomer heights, and the system used was Clairsol `350' (dispersed) - acetone - deionised water (continuous) with either direction of mass transfer. Drop size distributions were best described by the functions proposed by Gal-or, and then Mugele-Evans. Using data from this study and the literature, correlations were developed for dispersed phase hold-up, mean drop size in the preferred jetting regime and in the non-jetting regime, and coalescence zone height. A method to calculate the theoretical overall mass transfer coefficient allowing for the range of drop sizes encountered in the column gave the best fit to experimental data. This applied the drop size distribution diagram to estimate the volume percentage of stagnant, circulating and oscillating drops in the drop population. The overall coefficient Kcal was then calculated as the fractional sum of the predicted individual single drop coefficients and their proportion in the drop population. In a comparison between the experimental and calculated overall mass transfer coefficients for cases in which all the drops were in the oscillating regime (i.e. 6.35mm hole size plate), and for transfer from the dispersed(d) to continuous(c) phase, the film coefficient kd predicted from the Rose-Kintner correlation together with kc from that of Garner-Tayeban gave the best representation. Droplets from the 3.175mm hole size plate, were of a size to be mainly circulating and oscillating; a combination of kd from the Kronig-Brink (circulating) and Rose-Kintner (oscillating) correlations with the respective kc gave the best agreement. The optimum operating conditions for the SPC were identified and a procedure proposed for design from basic single drop data.

Bayesian data assimilation

This thesis addresses data assimilation, which typically refers to the estimation of the state of a physical system given a model and observations, and its application to short-term precipitation forecasting. A general introduction to data assimilation is given, both from a deterministic and' stochastic point of view. Data assimilation algorithms are reviewed, in the static case (when no dynamics are involved), then in the dynamic case. A double experiment on two non-linear models, the Lorenz 63 and the Lorenz 96 models, is run and the comparative performance of the methods is discussed in terms of quality of the assimilation, robustness "in the non-linear regime and computational time. Following the general review and analysis, data assimilation is discussed in the particular context of very short-term rainfall forecasting (nowcasting) using radar images. An extended Bayesian precipitation nowcasting model is introduced. The model is stochastic in nature and relies on the spatial decomposition of the rainfall field into rain "cells". Radar observations are assimilated using a Variational Bayesian method in which the true posterior distribution of the parameters is approximated by a more tractable distribution. The motion of the cells is captured by a 20 Gaussian process. The model is tested on two precipitation events, the first dominated by convective showers, the second by precipitation fronts. Several deterministic and probabilistic validation methods are applied and the model is shown to retain reasonable prediction skill at up to 3 hours lead time. Extensions to the model are discussed.

New oil modified acrylic polymer for pH sensitive drug release:experimental results and statistical analysis

We report results of an experimental study, complemented by detailed statistical analysis of the experimental data, on the development of a more effective control method of drug delivery using a pH sensitive acrylic polymer. New copolymers based on acrylic acid and fatty acid are constructed from dodecyl castor oil and a tercopolymer based on methyl methacrylate, acrylic acid and acryl amide were prepared using this new approach. Water swelling characteristics of fatty acid, acrylic acid copolymer and tercopolymer respectively in acid and alkali solutions have been studied by a step-change method. The antibiotic drug cephalosporin and paracetamol have also been incorporated into the polymer blend through dissolution with the release of the antibiotic drug being evaluated in bacterial stain media and buffer solution. Our results show that the rate of release of paracetamol getss affected by the pH factor and also by the nature of polymer blend. Our experimental data have later been statistically analyzed to quantify the precise nature of polymer decay rates on the pH density of the relevant polymer solvents. The time evolution of the polymer decay rates indicate a marked transition from a linear to a strictly non-linear regime depending on the whether the chosen sample is a general copolymer (linear) or a tercopolymer (non-linear). Non-linear data extrapolation techniques have been used to make probabilistic predictions about the variation in weight percentages of retained polymers at all future times, thereby quantifying the degree of efficacy of the new method of drug delivery.

Nanophotonics of optical fibers

This review is concerned with nanoscale effects in highly transparent dielectric photonic structures fabricated from optical fibers. In contrast to those in plasmonics, these structures do not contain metal particles, wires, or films with nanoscale dimensions. Nevertheless, a nanoscale perturbation of the fiber radius can significantly alter their performance. This paper consists of three parts. The first part considers propagation of light in thin optical fibers (microfibers) having the radius of the order of 100 nanometers to 1 micron. The fundamental mode propagating along a microfiber has an evanescent field which may be strongly expanded into the external area. Then, the cross-sectional dimensions of the mode and transmission losses are very sensitive to small variations of the microfiber radius. Under certain conditions, a change of just a few nanometers in the microfiber radius can significantly affect its transmission characteristics and, in particular, lead to the transition from the waveguiding to non-waveguiding regime. The second part of the review considers slow propagation of whispering gallery modes in fibers having the radius of the order of 10–100 microns. The propagation of these modes along the fiber axis is so slow that they can be governed by extremely small nanoscale changes of the optical fiber radius. This phenomenon is exploited in SNAP (surface nanoscale axial photonics), a new platform for fabrication of miniature super-low-loss photonic integrated circuits with unprecedented sub-angstrom precision. The SNAP theory and applications are overviewed. The third part of this review describes methods of characterization of the radius variation of microfibers and regular optical fibers with sub-nanometer precision.

Sub-critical regime of femtosecond inscription

We apply well known nonlinear diffraction theory governing focusing of a powerful light beam of arbitrary shape in medium with Kerr nonlinearity to the analysis of femtosecond (fs) laser processing of dielectric in sub-critical (input power less than the critical power of selffocusing) regime. Simple analytical expressions are derived for the input beam power and spatial focusing parameter (numerical aperture) that are required for achieving an inscription threshold. Application of non-Gaussian laser beams for better controlled fs inscription at higher powers is also discussed. © 2007 Optical Society of America.

DNA chip designed antisense oligodeoxynucleotides targeting EGFR MRNA for brain tumour therapy

Glioblastoma multiforme (GBM) is a malignant brain tumour for which there is currently no effective treatment regime. It is thought to develop due to the overexpression of a number of genes, including the epidermal growth factor receptor (EGFR), which is found in over 40% of GBM. Novel forms of treatment such as antisense therapy may allow for the specific inhibition of aberrant genes and thus they are optimistic therapies for future treatment of GBM. Oligodeoxynucleotides (ODNs) are small pieces of DNA that are often modified to increase their stability to nucleases and can be targeted to the aberrant gene in order to inhibit it and thus prevent its transcription into protein. By specifically binding to mRNA in an antisense manner, they can bring about its degradation by a variety of mechanisms including the activation of RNase H and thus have great potential as therapeutic agents. One of the main drawbacks to the utilisation of this therapy so far is the lack of techniques that can successfully predict accessible regions on the target mRNA that the ODNs can bind to. DNA chip technology has been utilised here to predict target sequences on the EGFR mRNA and these ODNs (AS 1 and AS2) have been tested in vitro for their stability, uptake into cells and their efficacy on cellular growth, EGFR protein and mRNA. Studies showed that phosphorothioate and 2'O-methyl ODNs were significantly more stable than phosphodiester ODNs both in serum and serum-free conditions and that the mechanism of uptake into A431 cells was temperature dependent and more efficient with the use of optimised lipofectin. Efficacy results show that AS 1 and AS2 phosphorothioate antisense ODNs were capable of inhibiting cell proliferation by 69% ±4% and 65% ±4.5% respectively at 500nM in conjunction with a non-toxic dose of lipofectinTM used to enhance cellular delivery. Furthermore, control ODN sequences, 2' O-methyl derivatives and a third ODN sequence, that was found not to be capable of binding efficiently to the EGFR mRNA by DNA chip technology, showed no significant effect on cell proliferation. AS 1 almost completely inhibited EGFR protein levels within 48 hours with two doses of 500nM AS 1 with no effect on other EGFR family member proteins or by control sequences. RNA analysis showed a decrease in mRNA levels of 32.4% ±0.8% but techniques require further optimisation to confirm this. As there are variations found between human glioblastoma in situ and those developed as xenografts, analysis of effect of AS 1 and AS2 was performed on primary tumour cell lines derived from glioma patients. ODN treatment showed a specific knockdown of cell growth compared to any of the controls used. Furthermore, combination therapies were tested on A431 cell growth to determine the advantage of combining different antisense approaches and that of conventional drugs. Results varied between the combination treatments but indicated that with optimisation of treatment regimes and delivery techniques that combination therapies utilising antisense therapies would be plausible.

Mouse splenocyte proliferation and its modulation by sex steroids

Concanavalin A, a T cell mitogen enhanced DNA synthesis in murine splenocytes. Amongst the early signals prior to this event was an increase in cytosolic calcium derived from both intra- and extracellular sources. The requirements for extracellular calcium persisted for four hours after the lectin administration which itself was needed for six hours. Putative calcium channel antagonists and calmodulin inhibitors blocked ihe increase in DNA synthesis. The calcium signal was mimicked by application of the ionophore, A23187, although no increase in DNA synthesis occurred. An activator of protein kinase C, 12-0- tetradecanoylphorbol 13-acetate, had little effect in isolation but the combined application of these two agents greatly enhanced DNA synthesis. The natural mediators of these events are presumed to be inositol trisphosphate and diacylglycerol derived from phosphatidylinositol bisphosphate hydrolysis. Lectin application and protein kinase C activation both increased intracellular pH possibly as a result of Na'l'/H"'' exchange since amiloride an inhibitor of this antiporter inhibited lectin induced DNA synthesis. The calcium and hydrogen ionic changes occur within minutes of lectin application; the protracted requirement for this mitogen suggests further signalling mechanisms occur to elicit maximum DNA synthesis in these cells. Gonadectomy caused an increase in thymic and splenic weight. Spleno-cytes derived from castrated mice showed no change in mitogen response whereas those from ovariectomised mice demonstrated a reduced lectin sensitivity. Testosterone, 5 a dihydrotestosterone, a and 0 oestradiol all inhibited lectin induced DNA synthesis but only at pharmacological concentrations. Testosterone glucuronide and cholesterol were without effect Studies with mouse serum fractions of differing steroidal status were unable to confirm the presence or absence of serum factors which might mediate the effects of steroid on lymphoid cells, all fractions tested inhibited lymphocyte transformation. Both interleukin-2 and lipopolysaccharide induced splenocyte mitogene-sis was also impaired by high steroid concentrations in vitro, suggesting that steroids mediate their effect by a non-specific, non-receptor-mediated event.

Non-periodic quasi-stable nonlinear optical carrier pulses with sliding chirp-free points for transmission at 40 Gbit/s rate

In this paper, we demonstrate the possibility of reaching a quasi-stable nonlinear transmission regime with carrier pulses of 12.5 ps width in multi-channel 40 Gbit/s systems. The quasi-stable pulses that are presented in this work for the first time are not dispersion-managed solitons, and are indeed supported by a large normal span average dispersion and misbalanced optical amplification, and representing a new type of nonlinear carrier.

Sub-critical regime of femtosecond inscription

We apply well known nonlinear diffraction theory governing focusing of a powerful light beam of arbitrary shape in medium with Kerr nonlinearity to the analysis of femtosecond (fs) laser processing of dielectric in sub-critical (input power less than the critical power of selffocusing) regime. Simple analytical expressions are derived for the input beam power and spatial focusing parameter (numerical aperture) that are required for achieving an inscription threshold. Application of non-Gaussian laser beams for better controlled fs inscription at higher powers is also discussed. © 2007 Optical Society of America.

Regulating the expression of eEF1A to decipher its non canonical functions in eukaryotic cells

The canonical function of eEF1A is delivery of the aminoacylated tRNA to the A site of the ribosome during protein translation, however, it is also known to be an actin binding protein. As well as this actin binding function, eEF1A has been shown to be involved in other cellular processes such as cell proliferation and apoptosis. It has long been thought that the actin cytoskeleton and protein synthesis are linked and eEF1A has been suggested to be a candidate protein to form this link, though very little is understood about the relationship between its two functions. Overexpression of eEF1A has also been shown to be implicated in many different types of cancers, especially cancers that are metastatic, therefore it is important to further understand how eEF1A can affect both translation and the organisation of the actin cytoskeleton. To this end, we aimed to determine the effects of reduced expression of eEF1A on both translation and its non canonical functions in CHO cells. We have shown that reduced expression of eEF1A in this cell system results in no change in protein synthesis, however results in an increased number of actin stress fibres and other proteins associated with these fibres such as myosin IIA, paxillin and vinculin. Cell motility and attachment are also affected by this reduction in eEF1A protein expression. The organisational and motility phenotypes were found to be specific to eEF1A by transforming the cells with plasmids containing either human eEF1A1 or eEF1A2. Though the mechanisms by which these effects are regulated have not yet been established, this data provides evidence to show that the translation and actin binding functions of eEF1A are independent of each other as well as being suggestive of a role for eEF1A in cell motility as supported by the observation that overexpression of eEF1A protein tends to be associated with the cancer cells that are metastatic.

Phytoestrogen-ind uced glucose uptake and cellular proliferation in L6 myotubesadipocyte function

Aims: Oestrogens are known to act on a number of tissues throughout the body via classical oestrogen receptors, alpha (ER-a) and beta (ER-beta). Previous research has shown that oestrogens can regulate skeletal muscle glucose uptake cellular proliferation. Thus, oestrogens and related molecules provide an interesting focus for research into possible therapies for the treatment of metabolic disorders and sarcopenia. Enterodiol and enterolactone are plant derived mammalian enterolignans which share a struc- tural similarity to the human oestrogen oestradiol. Methods: In the present study we incubated the differentiated rat skeletal muscle cell line L6 concentration ranges of both com- pounds in the presence/absence of oestrogen receptor antagonists and measured glucose uptake using the non-metabolised glucose analogue 2-NBDG. Cellular proliferation was also measured using a modified MTS assay. Results: Enterolactone was seen to cause a significant increase in cellular proliferation after 48h (a maximal 25% at 0.1nmol/l), in an ER-a dependent mechanism. Incubation with 10nmol/l and 100nmol/l enterodiol caused significant increases in 2-NBDG (5000% compared with control, p < 0.001) and 2h glucose depletion from media (15% increase compared with control, p < 0.05), also in an ER-a dependent way. These results suggest these dietary derived oestrogen-like molecules might be of potential use in targeting metabolic disorders or sarcopenia. Conclusion: We can report here that the phytoestrogen derived molecules enterodiol and enterolactone interact with ER-a in the myotubes to regulate glucose uptake and cellular proliferation respectively.