ProxiMAX Randomisation:a new technology for non-degenerate saturation mutagenesis of contiguous codons

ProxiMAX randomisation achieves saturation mutagenesis of contiguous codons without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, it uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents and as such, requires no specialised chemistry, reagents nor equipment. When particular residues are known to affect protein activity/specificity, their combinatorial replacement with all 20 amino acids, or a subset thereof, can provide a rapid route to generating proteins with desirable characteristics. Conventionally, saturation mutagenesis replaced key codons with degenerate ones. Although simple to perform, that procedure resulted in unnecessarily large libraries, termination codons and inherent uneven amino acid representation. ProxiMAX randomisation is an enzyme-based technique that can encode unbiased representation of all or selected amino acids or else can provide required codons in pre-defined ratios. Each saturated position can be defined independently of the others. ProxiMAX randomisation is achieved via saturation cycling: an iterative process comprising blunt end ligation, amplification and digestion with a Type IIS restriction enzyme. We demonstrate both unbiased saturation of a short 6-mer peptide and saturation of a hypervariable region of a scfv antibody fragment, where 11 contiguous codons are saturated with selected codons, in pre-defined ratios. As such, ProxiMAX randomisation is particularly relevant to antibody engineering. The development of ProxiMAX randomisation from concept to reality is described.

Discovering knowledge structures in mind maps of mental health risks

This thesis addressed the problem of risk analysis in mental healthcare, with respect to the GRiST project at Aston University. That project provides a risk-screening tool based on the knowledge of 46 experts, captured as mind maps that describe relationships between risks and patterns of behavioural cues. Mind mapping, though, fails to impose control over content, and is not considered to formally represent knowledge. In contrast, this thesis treated GRiSTs mind maps as a rich knowledge base in need of refinement; that process drew on existing techniques for designing databases and knowledge bases. Identifying well-defined mind map concepts, though, was hindered by spelling mistakes, and by ambiguity and lack of coverage in the tools used for researching words. A novel use of the Edit Distance overcame those problems, by assessing similarities between mind map texts, and between spelling mistakes and suggested corrections. That algorithm further identified stems, the shortest text string found in related word-forms. As opposed to existing approaches’ reliance on built-in linguistic knowledge, this thesis devised a novel, more flexible text-based technique. An additional tool, Correspondence Analysis, found patterns in word usage that allowed machines to determine likely intended meanings for ambiguous words. Correspondence Analysis further produced clusters of related concepts, which in turn drove the automatic generation of novel mind maps. Such maps underpinned adjuncts to the mind mapping software used by GRiST; one such new facility generated novel mind maps, to reflect the collected expert knowledge on any specified concept. Mind maps from GRiST are stored as XML, which suggested storing them in an XML database. In fact, the entire approach here is ”XML-centric”, in that all stages rely on XML as far as possible. A XML-based query language allows user to retrieve information from the mind map knowledge base. The approach, it was concluded, will prove valuable to mind mapping in general, and to detecting patterns in any type of digital information.

The interrogation and multiplexing of long period grating curvature sensors using a Bragg grating based, derivative spectroscopy technique

A long period grating is interrogated with a fibre Bragg grating using a derivative spectroscopy technique. A quasi-linear relationship between the output of the sensing scheme and the curvature experienced by the long period grating is demonstrated, with a sensitivity of 5.05 m and with an average curvature resolution of 2.9 × 10-2 m-1. In addition, the feasibility of multiplexing an in-line series of long period gratings with this interrogation scheme is demonstrated with two pairs of fibre Bragg gratings and long period gratings. With this arrangement the cross-talk error between channels was less than ± 2.4 × 10-3 m-1.

Biochemical sensor based on a novel all-fibre cavity ring down spectroscopy technique incorporating a tilted fibre Bragg grating

A novel all-fibre cavity ring down spectroscopy technique is proposed where a tilt fibre Bragg grating (TFBG) or long-period grating (LPG) in the cavity provides sensitivity to surrounding medium. Such configuration with an LPG as the representative was theoretically analyzed. Two spectral bands were identified employable for sensing of surrounding refractive index for a weak LPG while only one band existed for a strong LPG. A TFBG, with enhanced sensitivity compared to usual LPGs, was used in a ring down cavity of 1 m constructed with 2 fibre Bragg gratings as the reflectors and the decay time changed from 220 to 450 ns when the TFBG was immersed into water from air.

A novel sensor interrogation technique using chirped fiber grating based sagnac loop

We demonstrate a novel and simple sensor interrogation scheme for fiber Bragg grating (FBG) based sensing systems. In this scheme, a chirped FBG based Sagnac loop is used as a wavelength-dependent receiver, and a stable and linear readout response is realised. It is a signijkant advantage of this scheme that the sensitivity and the measurement wavelength range can be easily adjhsted by controlling the chirp of the FBG or using an optical delay line in the Sagnac loop.

Self-mixing-based demodulation technique for dynamic fiber Bragg grating strain sensors

We report a novel demodulation scheme for the detection of small Bragg wavelength shifts in a fiber Bragg grating strain sensor by exploiting the optical feedback reflected from the grating structure back into a 1310 nm laser diode integrating a photodiode. The dynamic strain generated by a mechanical vibrator is applied transversely to the fiber Bragg grating and the desired longitudinal strain values inferred from the detected sawtooth-like optical feedback signals. Preliminary results demonstrate the feasibility of this demodulation technique for strain measurement which could be further extended to fiber Bragg grating-based sensors for the detection of different measurands in general.

A novel sensor interrogation technique using chirped fiber grating based Sagnac loop

We demonstrate a novel and simple sensor interrogation scheme for fiber Bragg grating (FBG) based sensing systems. In this scheme, a chirped FBG based Sagnac loop is used as a wavelength-dependent receiver, and a stable and linear readout response is realised. It is a signijkant advantage of this scheme that the sensitivity and the measurement wavelength range can be easily adjhsted by controlling the chirp of the FBG or using an optical delay line in the Sagnac loop.

Self-mixing-based demodulation technique for dynamic fiber Bragg grating strain sensors

We report a novel demodulation scheme for the detection of small Bragg wavelength shifts in a fiber Bragg grating strain sensor by exploiting the optical feedback reflected from the grating structure back into a 1310 nm laser diode integrating a photodiode. The dynamic strain generated by a mechanical vibrator is applied transversely to the fiber Bragg grating and the desired longitudinal strain values inferred from the detected sawtooth-like optical feedback signals. Preliminary results demonstrate the feasibility of this demodulation technique for strain measurement which could be further extended to fiber Bragg grating-based sensors for the detection of different measurands in general.

The interrogation and multiplexing of long period grating curvature sensors using a Bragg grating based, derivative spectroscopy technique

A long period grating is interrogated with a fibre Bragg grating using a derivative spectroscopy technique. A quasi-linear relationship between the output of the sensing scheme and the curvature experienced by the long period grating is demonstrated, with a sensitivity of 5.05 m and with an average curvature resolution of 2.9 × 10-2 m-1. In addition, the feasibility of multiplexing an in-line series of long period gratings with this interrogation scheme is demonstrated with two pairs of fibre Bragg gratings and long period gratings. With this arrangement the cross-talk error between channels was less than ± 2.4 × 10-3 m-1.

Internet search:subdivision-based interactive query expansion and the soft semantic web

The expansion of the Internet has made the task of searching a crucial one. Internet users, however, have to make a great effort in order to formulate a search query that returns the required results. Many methods have been devised to assist in this task by helping the users modify their query to give better results. In this paper we propose an interactive method for query expansion. It is based on the observation that documents are often found to contain terms with high information content, which can summarise their subject matter. We present experimental results, which demonstrate that our approach significantly shortens the time required in order to accomplish a certain task by performing web searches.

A technique for incorporating dynamic paths in lab-based mobile evaluations

Increasingly, lab evaluations of mobile applications are incorporating mobility. The inclusion of mobility alone, however, is insufficient to generate a realistic evaluation context since real-life users will typically be required to monitor their environment while moving through it. While field evaluations represent a more realistic evaluation context, such evaluations pose difficulties, including data capture and environmental control, which mean that a lab-based evaluation is often a more practical choice. This paper describes a novel evaluation technique that mimics a realistic mobile usage context in a lab setting. The technique requires that participants monitor their environment and change the route they are walking to avoid dynamically changing hazards (much as reallife users would be required to do). Two studies that employed this technique are described, and the results (which indicate the technique is useful) are discussed.

Biochemical sensor based on a novel all-fibre cavity ring down spectroscopy technique incorporating a tilted fibre Bragg grating

A novel all-fibre cavity ring down spectroscopy technique is demonstrated where a tilted fibre Bragg grating in the cavity provides sensitivity to surrounding refractive index. A decay time of 450ns was attained when sensing water.

Liquid core fibre Bragg grating based refractive index sensor formed by femtosecond assisted chemical etching technique

We report the fabrication of a refractive index (RI) sensor based on a liquid core fibre Bragg grating (FBG). A micro-slot FBG was created in standard telecom optical fibre employing the tightly focused femtosecond laser inscription aided chemical etching. A micro-slot with dimensions of 5.74(h) × 125(w) × 1388.72(l) μm was engraved across the whole fibre and along 1mm long FBG which gives advantage of a relatively robust liquid core waveguide. The device performed the refractive index sensitivity up to about 742.72 nm/RIU. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Drying kinetic analysis of municipal solid waste using modified page model and pattern search method

This work studied the drying kinetics of the organic fractions of municipal solid waste (MSW) samples with different initial moisture contents and presented a new method for determination of drying kinetic parameters. A series of drying experiments at different temperatures were performed by using a thermogravimetric technique. Based on the modified Page drying model and the general pattern search method, a new drying kinetic method was developed using multiple isothermal drying curves simultaneously. The new method fitted the experimental data more accurately than the traditional method. Drying kinetic behaviors under extrapolated conditions were also predicted and validated. The new method indicated that the drying activation energies for the samples with initial moisture contents of 31.1 and 17.2 % on wet basis were 25.97 and 24.73 kJ mol−1. These results are useful for drying process simulation and industrial dryer design. This new method can be also applied to determine the drying parameters of other materials with high reliability.