End-to-end versus hop-by-hop state refresh in soft state signaling protocols

The concept of soft state (i.e., the state that will expire unless been refreshed) has been widely used in the design of network signaling protocols. The approaches of refreshing state in multi-hop networks can be classified to end-to-end (E2E) and hop-by-hop (HbH) refreshes. In this article we propose an effective Markov chain based analytical model for both E2E and HbH refresh approaches. Simulations verify the analytical models, which can be used to study the impacts of link characteristics on the performance (e.g., state synchronization and message overhead), as a guide on configuration and optimization of soft state signaling protocols. © 2009 IEEE.

Optical coherence tomography confirmed resolution of macular edema in a diabetic patient after hemodialysis

Purpose: The authors report the first case, to their knowledge, of resolution of diffuse macular edema after hemodialysis, which has been confirmed by optical coherence tomography. Methods: A 53-year-old white woman with type 2 diabetes developed worsening macular edema and was examined in the ophthalmology clinic and scheduled for macular grid laser photocoagulation. The laser, however, was deferred for 4 weeks because she had also developed end-stage renal failure and required hemodialysis. Results: When she was reviewed in the ophthalmology clinic 4 weeks later for laser therapy, it was found that her macular edema had resolved, vision had improved, and laser was unnecessary. Review at 6 months showed that the macular edema remains resolved. Conclusion: Ophthalmologists should be aware that hemodialysis may reduce macular edema in such patients. Copyright © by Ophthalmic Communications Society Inc.

Enhanced slotted aloha protocols for underwater sensor networks with large propagation delay

Recently underwater sensor networks (UWSN) attracted large research interests. Medium access control (MAC) is one of the major challenges faced by UWSN due to the large propagation delay and narrow channel bandwidth of acoustic communications used for UWSN. Widely used slotted aloha (S-Aloha) protocol suffers large performance loss in UWSNs, which can only achieve performance close to pure aloha (P-Aloha). In this paper we theoretically model the performances of S-Aloha and P-Aloha protocols and analyze the adverse impact of propagation delay. According to the observation on the performances of S-Aloha protocol we propose two enhanced S-Aloha protocols in order to minimize the adverse impact of propagation delay on S-Aloha protocol. The first enhancement is a synchronized arrival S-Aloha (SA-Aloha) protocol, in which frames are transmitted at carefully calculated time to align the frame arrival time with the start of time slots. Propagation delay is taken into consideration in the calculation of transmit time. As estimation error on propagation delay may exist and can affect network performance, an improved SA-Aloha (denoted by ISA-Aloha) is proposed, which adjusts the slot size according to the range of delay estimation errors. Simulation results show that both SA-Aloha and ISA-Aloha perform remarkably better than S-Aloha and P-Aloha for UWSN, and ISA-Aloha is more robust even when the propagation delay estimation error is large. © 2011 IEEE.

Recombinant protein production in yeast:methods and protocols

In the last few years, significant advances have been made in understanding how a yeast cell responds to the stress of producing a recombinant protein, and how this information can be used to engineer improved host strains. The molecular biology of the expression vector, through the choice of promoter, tag and codon optimization of the target gene, is also a key determinant of a high-yielding protein production experiment. Recombinant Protein Production in Yeast: Methods and Protocols examines the process of preparation of expression vectors, transformation to generate high-yielding clones, optimization of experimental conditions to maximize yields, scale-up to bioreactor formats and disruption of yeast cells to enable the isolation of the recombinant protein prior to purification. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Extended-range, low coherence dual wavelength interferometry using a superfluorescent fibre source and chirped fibre Bragg gratings

We describe an all-fibre, passive scheme for making extended range interferometric measurements based on the dual wavelength technique. The coherence tuned interferometer network is illuminated with a single superfluorescent fibre source at 1.55 μm and the two wavelengths are synthesised at the output by means of chirped fibre Bragg gratings. We demonstrate an unambiguous sensing range of 270 μm, with a dynamic range of 2.7 × 105.

Fibre Bragg grating sensor interrogation using an acousto-optic tunable filter and low-coherence interferometry

We describe how an acousto-optic tunable filter can be used to both demultiplex the signals from multiple fibre Bragg grating sensors and simultaneously provide wide bandwidth signal demodulation in a system using interferometric wavelength shift detection. In an experimental demonstration, the approach provided a noise limited strain resolution of 24.9 nε Hz -1/2 at 15 Hz. © 2007 IOP Publishing Ltd.

Coherence imaging by use of a Newton rings sampling function

We show that, with suitable optics in the arm of a Michelson interferometer, orthogonal galvo-scanning mirrors build a sampling function in the form of Newton rings when the two interferometer arms are matched. Using a low-coherence source, one can obtain transversal depth-resolved images. A fast display procedure using a storage oscilloscope was devised based on this method.

Advances in characterisation, calibration and data processing speed of optical coherence tomography systems

This thesis describes advances in the characterisation, calibration and data processing of optical coherence tomography (OCT) systems. Femtosecond (fs) laser inscription was used for producing OCT-phantoms. Transparent materials are generally inert to infra-red radiations, but with fs lasers material modification occurs via non-linear processes when the highly focused light source interacts with the materials. This modification is confined to the focal volume and is highly reproducible. In order to select the best inscription parameters, combination of different inscription parameters were tested, using three fs laser systems, with different operating properties, on a variety of materials. This facilitated the understanding of the key characteristics of the produced structures with the aim of producing viable OCT-phantoms. Finally, OCT-phantoms were successfully designed and fabricated in fused silica. The use of these phantoms to characterise many properties (resolution, distortion, sensitivity decay, scan linearity) of an OCT system was demonstrated. Quantitative methods were developed to support the characterisation of an OCT system collecting images from phantoms and also to improve the quality of the OCT images. Characterisation methods include the measurement of the spatially variant resolution (point spread function (PSF) and modulation transfer function (MTF)), sensitivity and distortion. Processing of OCT data is a computer intensive process. Standard central processing unit (CPU) based processing might take several minutes to a few hours to process acquired data, thus data processing is a significant bottleneck. An alternative choice is to use expensive hardware-based processing such as field programmable gate arrays (FPGAs). However, recently graphics processing unit (GPU) based data processing methods have been developed to minimize this data processing and rendering time. These processing techniques include standard-processing methods which includes a set of algorithms to process the raw data (interference) obtained by the detector and generate A-scans. The work presented here describes accelerated data processing and post processing techniques for OCT systems. The GPU based processing developed, during the PhD, was later implemented into a custom built Fourier domain optical coherence tomography (FD-OCT) system. This system currently processes and renders data in real time. Processing throughput of this system is currently limited by the camera capture rate. OCTphantoms have been heavily used for the qualitative characterization and adjustment/ fine tuning of the operating conditions of OCT system. Currently, investigations are under way to characterize OCT systems using our phantoms. The work presented in this thesis demonstrate several novel techniques of fabricating OCT-phantoms and accelerating OCT data processing using GPUs. In the process of developing phantoms and quantitative methods, a thorough understanding and practical knowledge of OCT and fs laser processing systems was developed. This understanding leads to several novel pieces of research that are not only relevant to OCT but have broader importance. For example, extensive understanding of the properties of fs inscribed structures will be useful in other photonic application such as making of phase mask, wave guides and microfluidic channels. Acceleration of data processing with GPUs is also useful in other fields.

On the Coherence Between Probability and Possibility Measures

* This paper is supported by CICYT (Spain) under Project TIN 2005-08943-C02-01.

Developing Agent Interaction Protocols with PRALU

The purpose of the paper is to explore the possibility of applying existing formal theories of description and design of distributed and concurrent systems to interaction protocols for real-time multi-agent systems. In particular it is shown how the language PRALU, proposed for description of parallel logical control algorithms and rooted in the Petri net formalism, can be used for the modeling of complex concurrent conversations between agents in a multi-agent system. It is demonstrated with a known example of English auction on how to specify an agent interaction protocol using considered means.

Fiber optically integrated cost-effective spectrometer for optical coherence tomography

A tilted fiber Bragg grating (TFBG) was integrated as the dispersive element in a high performance biomedical imaging system. The spectrum emitted by the 23 mm long active region of the fiber is projected through custom designed optics consisting of a cylindrical lens for vertical beam collimation and successively by an achromatic doublet onto a linear detector array. High resolution tomograms of biomedical samples were successfully acquired by the frequency domain OCT-system. Tomograms of ophthalmic and dermal samples obtained by the frequency domain OCT-system were obtained achieving 2.84 μm axial and 10.2 μm lateral resolution. The miniaturization reduces costs and has the potential to further extend the field of application for OCT-systems in biology, medicine and technology. © 2014 SPIE.

Simultaneous en-face imaging of two layers in human retina by low-coherence reflectometry

We show that with a fiberized multiple Michelson-interferometer-type configuration, transverse images from several layers in the human eye can be simultaneously obtained. We demonstrate the principle by producing simultaneous 100×100 pixel en-face images of a 4 mm×4 mm region on a postmortem retina for two depth positions 250 µm apart.

Quantitative optical coherence tomography for characterization of microscopic structures with varying refractive index

In this paper we have done back to back comparison of quantitive phase and refractive index from a microscopic image of waveguide previously obtained by Allsop et al. Paper also shows microscopic image of the first 3 waveguides from the sample. Tomlins et al. have demonstrated use of femtosecond fabricated artefacts as OCT calibration samples. Here we present the use of femtosecond waveguides, inscribed with optimized parameters, to test and calibrate the sensitivity of the OCT systems.