CAPLib - A 'thin layer' message passing library to support computational mechanics codes on distributed memory parallel systems

The Computer Aided Parallelisation Tools (CAPTools) [Ierotheou, C, Johnson SP, Cross M, Leggett PF, Computer aided parallelisation tools (CAPTools)-conceptual overview and performance on the parallelisation of structured mesh codes, Parallel Computing, 1996;22:163±195] is a set of interactive tools aimed to provide automatic parallelisation of serial FORTRAN Computational Mechanics (CM) programs. CAPTools analyses the user's serial code and then through stages of array partitioning, mask and communication calculation, generates parallel SPMD (Single Program Multiple Data) messages passing FORTRAN. The parallel code generated by CAPTools contains calls to a collection of routines that form the CAPTools communications Library (CAPLib). The library provides a portable layer and user friendly abstraction over the underlying parallel environment. CAPLib contains optimised message passing routines for data exchange between parallel processes and other utility routines for parallel execution control, initialisation and debugging. By compiling and linking with different implementations of the library, the user is able to run on many different parallel environments. Even with today's parallel systems the concept of a single version of a parallel application code is more of an aspiration than a reality. However for CM codes the data partitioning SPMD paradigm requires a relatively small set of message-passing communication calls. This set can be implemented as an intermediate `thin layer' library of message-passing calls that enables the parallel code (especially that generated automatically by a parallelisation tool such as CAPTools) to be as generic as possible. CAPLib is just such a `thin layer' message passing library that supports parallel CM codes, by mapping generic calls onto machine specific libraries (such as CRAY SHMEM) and portable general purpose libraries (such as PVM an MPI). This paper describe CAPLib together with its three perceived advantages over other routes: - as a high level abstraction, it is both easy to understand (especially when generated automatically by tools) and to implement by hand, for the CM community (who are not generally parallel computing specialists); - the one parallel version of the application code is truly generic and portable; - the parallel application can readily utilise whatever message passing libraries on a given machine yield optimum performance.

Development of a technique to measure the residual strength of woodworm infested timber

This paper presents a study of the residual strength of Pinus sylvestris, which has been subject to attack by the furniture beetle (Anobium punctatum). It is relatively easy to stop the infestation, but difficult to assess the structural soundness of the remaining timber. Removal and replacement of affected structural elements is usually difficult and expensive, particularly in buildings of historic interest. Current on-site assessment procedures are limited. The main object of the study was to develop an on-site test of timber quality: a test which can be carried out on the surface and also at varying depths into the timber. It is based on a probe pull-out technique using a portable load-measuring device. Pull-out force values have been correlated with both strength and energy absorbed as measured by compression testing on laboratory samples of both sound and infested timber. These two relationships are significant and could be used to assess whether remedial work is needed. In addition, work on the use of artificial borings to simulate the natural worming of timber is presented and the findings discussed.

Reuseable Silicon IP Cores for Discrete Wavelet Transform Applications

Architectures and methods for the rapid design of silicon cores for implementing discrete wavelet transforms over a wide range of specifications are described. These architectures are efficient, modular, scalable, and cover orthonormal and biorthogonal wavelet transform families. They offer efficient hardware utilization by exploiting a number of core wavelet filter properties and allow the creation of silicon designs that are highly parameterized, including in terms of wavelet type and wordlengths. Control circuitry is embedded within these systems allowing them to be cascaded for any desired level of decomposition without any interface glue logic. The time to produce chip designs for a specific wavelet application is typically less than a day and these are comparable in area and performance to handcrafted designs. They are also portable across a wide range of silicon foundries and suitable for field programmable gate array and programmable logic data implementation. The approach described has also been extended to wavelet packet transforms.

Performance analysis of an improved power-saving medium access protocol for IEEE 802.11 point coordination function WLAN

Wireless enabled portable devices must operate with the highest possible energy efficiency while still maintaining a minimum level and quality of service to meet the user's expectations. The authors analyse the performance of a new pointer-based medium access control protocol that was designed to significantly improve the energy efficiency of user terminals in wireless local area networks. The new protocol, pointer controlled slot allocation and resynchronisation protocol (PCSAR), is based on the existing IEEE 802.11 point coordination function (PCF) standard. PCSAR reduces energy consumption by removing the need for power saving stations to remain awake and listen to the channel. Using OPNET, simulations were performed under symmetric channel loading conditions to compare the performance of PCSAR with the infrastructure power saving mode of IEEE 802.11, PCF-PS. The simulation results demonstrate a significant improvement in energy efficiency without significant reduction in performance when using PCSAR. For a wireless network consisting of an access point and 8 stations in power saving mode, the energy saving was up to 31% while using PCSAR instead of PCF-PS, depending upon frame error rate and load. The results also show that PCSAR offers significantly reduced uplink access delay over PCF-PS while modestly improving uplink throughput.

Design of silicon IP cores for biorthogonal wavelet transforms

A methodology for rapid silicon design of biorthogonal wavelet transform systems has been developed. This is based on generic, scalable architectures for the forward and inverse wavelet filters. These architectures offer efficient hardware utilisation by combining the linear phase property of biorthogonal filters with decimation and interpolation. The resulting designs have been parameterised in terms of types of wavelet and wordlengths for data and coefficients. Control circuitry is embedded within these cores that allows them to be cascaded for any desired level of decomposition without any interface logic. The time to produce silicon designs for a biorthogonal wavelet system is only the time required to run synthesis and layout tools with no further design effort required. The resulting silicon cores produced are comparable in area and performance to hand-crafted designs. These designs are also portable across a range of foundries and are suitable for FPGA and PLD implementations.

Rapid design of biorthogonal wavelet transforms

A rapid design methodology for biorthogonal wavelet transform cores has been developed based on a generic, scaleable architecture for wavelet filters. The architecture offers efficient hardware utilisation by combining the linear phase property of biorthogonal filters with decimation in a MAC-based implementation. The design has been captured in VHDL and parameterised in terms of wavelet type, data word length and coefficient word length. The control circuit is embedded within the cores and allows them to be cascaded without any interface glue logic for any desired level of decomposition. The design time to produce silicon layout of a biorthogonal wavelet system is typically less than a day. The silicon cores produced are comparable in area and performance to hand-crafted designs, The designs are portable across a range of foundries and are also applicable to FPGA and PLD implementations.

La visión artificial, un nuevo aliado para el análisis de imágenes artísticas

En este estudio se evalúa el rendimiento de los métodos de Bag-of-Visualterms (BOV) para la clasificación automática de imágenes digitales de la base de datos del artista Miquel Planas. Estas imágenes intervienen en la ideación y diseño de su producción escultórica. Constituye un interesante desafío dada la dificultad de la categorización de escenas cuando éstas difieren más por los contenidos semánticos que por los objetos que contienen. Hemos empleado un método de reconocimiento basado en Kernels introducido por Lazebnik, Schmid y Ponce en 2006. Los resultados son prometedores, en promedio, la puntuación del rendimiento es aproximadamente del 70%. Los experimentos sugieren que la categorización automática de imágenes basada en métodos de visión artificial puede proporcionar principios objetivos en la catalogación de imágenes y que los resultados obtenidos pueden ser aplicados en diferentes campos de la creación artística.

Spatial characterization of salt accumulation in early stage limestone weathering using probe permeametry

This research characterizes the weathering of natural building stone using an unsteady-state portable probe permeameter. Variations between the permeability properties of fresh rock and the same rocks after the early stages of a salt weathering simulation are used to examine the effects of salt accumulation on spatial variations in surface rock permeability properties in two limestones from Spain. The Fraga and Tudela limestones are from the Ebro basin and are of Miocene age. Both stone types figure largely in the architectural heritage of Spain and, in common with many other building limestones, they are prone to physical damage from salt crystallization in pore spaces. To examine feedbacks associated with salt accumulation during the early stages of this weathering process, samples of the two stone types were subjected to simulated salt weathering under laboratory conditions using magnesium sulphate and sodium chloride at concentrations of 5% and 15%. Permeability mapping and statistical analysis (aspatial statistics and spatial prediction) before and after salt accumulation are used to assess changes in the spatial variability of permeability and to correlate these changes with salt movement, porosity change, potential rock deterioration and textural characteristics. Statistical analyses of small-scale permeability measurements are used to evaluate the drivers for decay and hence aid the prediction of the weathering behaviour of the two limestones.

Optical Fiber Refractive Index Sensor for Chloride Ion Monitoring

The development of a reflective, gold-coated long-period grating-based sensor for the measurement of chloride ions in solution is discussed. The sensor scheme is based around a long-period fiber grating (LPG)-based Michelson interferometer where the sensor was calibrated and evaluated in the laboratory using sodium chloride solutions, over a wide range of concentrations, from 0.01 to 4.00 M. The grating response creates shifts in the spectral characteristic of the interferometer, formed using the LPG and a reflective surface on the distal end of the fiber, due to the change of refracting index of the solution surrounding it. It was found that the sensitivity of the device could be enhanced over that obtained from a bare fiber by coating the LPG-based interferometer with gold nanoparticles and the results of a cross-comparison of performance were obtained and details discussed. The approach will be explored as a basis to create a portable, low-power device, developed with the potential for installation in concrete structures to determine the ingress of chloride ions, operating through monitoring the refractive index change.

Basking is affected by season and influences oxygen consumption in desert-living striped mice

Small mammals that inhabit arid and temporally unproductive environments use several methods to conserve energy. Here, we investigate the energetic role of sun basking in striped mice Rhabdomys pumilio from the Succulent Karoo desert in South Africa. We observed mice in front of their nests for 140 h and recorded the time they spent basking during the non-breeding (dry) and the breeding (wet) seasons. We measured temperature changes in model mice to provide an indication of the heat that can be absorbed from the sun. Finally, we measured the oxygen consumption (circle dot O-2) of mice at their basking sites in the field both in the sun and in the shade. This was accomplished using a portable respirometry system with a metabolism chamber, which could be placed in and out of the sun. Observations showed that mice basked more often during the non-breeding than during the breeding season. During the former season, mice spent an average of 11.9 +/- 1.1 min (se) in the morning and 5.5 +/- 0.5 min in the afternoon per day basking. Within the metabolism chamber, circle dot O-2 decreased when the animal was in the sunshine compared with the shade. This effect occurred independent of the ambient temperature (T-a), indicating that a significant amount of radiant energy was absorbed from the sun. Basking may be an alternative to other energy-acquisition behaviours, such as foraging, which might be particularly useful at times when food is scarce.

Comparative repeatability of two handheld fractional exhaled nitric oxide monitors.

Background The use of portable fractional exhaled nitric oxide (FENO) devices is increasingly common in the diagnosis and management of allergic airways inflammation. Methods We tested two handheld FENO devices, to determine (a) if there was adequate intradevice repeatability to allow the use of single breath testing, and (b) if the devices could be used interchangeably. In a mixed pediatric population, including normal, asthmatic, and children with peanut allergies, 858 paired values were collected from the NIOX-MINO® and/or the NObreath® devices. Results The NIOX-MINO® showed excellent repeatability (mean difference of 0.1 with 95% limits of agreement between -7.93 to 7.72?ppb), while the NObreath® showed good repeatability (mean difference of -1.61 with 95% limits of agreement between -14.1 and 10.8?ppb). Intradevice repeatability was good but not adequate and the NIOX-MINO® systematically produced higher results than the NObreath® [mean difference of 7.8?ppb with 95% limits of agreement from -11.55 to 27.52?ppb (-33% to 290%)]. Conclusions Our results support the manufacturer's advice that single breath testing is appropriate for the NIOX-MINO®. NObreath® results indicate that the mean of more than one breath should be utilized. The devices cannot be used interchangeably. Pediatr Pulmonol. © 2011 Wiley Periodicals, Inc.

A comparative study of qualitative immunochemical screening assays for the combined measurement of T-2/HT-2 in cereals and cereal-based products

Many different immunochemical platforms exist for the screening of naturally occurring contaminants in food from the low cost enzyme linked immunosorbent assays (ELISA) to the expensive instruments such as optical biosensors based on the phenomenon of surface plasmon resonance (SPR). The primary aim of this study was to evaluate and compare a number of these platforms to assess their accuracy and precision when applied to naturally contaminated samples containing HT-2/T-2 mycotoxins. Other important factors considered were the speed of analysis, ease of use (sample preparation techniques and use of the equipment) and ultimately the cost implications. The three screening procedures compared included an SPR biosensor assay, a commercially available ELISA and an enzyme-linked immunomagnetic electrochemical array (ELIME array). The qualitative data for all methods demonstrated very good overall agreements with each other, however on comparison with mass spectrometry confirmatory results, the ELISA and SPR assay performed slightly better than the ELIME array, exhibiting an overall agreement of 95.8% compared to 91.7%. Currently, SPR is more costly than the other two platforms and can only be used in the laboratory whereas in theory both the ELISA and ELIME array are portable and can be used in the field, but ultimately this is dependent on the sample preparation techniques employed. Sample preparative techniques varied for all methods evaluated, the ELISA was the most simple to perform followed by that of the SPR method. The ELIME array involved an additional clean-up step thereby increasing both the time and cost of analysis. Therefore in the current format, field use would not be an option for the ELIME array. In relation to speed of analysis, the ELISA outperformed the other methods.

Tobramycin Inhalation Powder™:a novel drug delivery system for treating chronic Pseudomonas aeruginosa infection in cystic fibrosis

Lung disease in cystic fibrosis (CF) is typified by the development of chronic airways infection culminating in bronchiectasis and progression to end-stage respiratory disease. Pseudomonas aeruginosa, a ubiquitous gram-negative bacteria, is the archetypical CF pathogen and is associated with an accelerated clinical decline. The development and widespread use of chronic suppressive aerosolized antibacterial therapies, in particular Tobramycin Inhalation Solution (TIS), in CF has contributed to reduced lung function decline and improved survival. However, the requirement for the aerosolization of these agents through nebulizers has been associated with increased treatment burden, reduced quality of life and remain a barrier to broader uptake. Tobramycin Inhalation Powder (TIP™) has been developed by Novartis with the express purpose of delivering the same benefits as TIS in a time-effective manner. Administered via the T-326™ (Novartis) Inhaler in four individual 28-mg capsules, TIP can be administered in a quarter of the time of traditional nebulizers and is inherently portable. In clinical studies, TIP has been shown to be safe, result in equivalent or superior reductions in P. aeruginosa sputum density and produce similar improvements in pulmonary function. TIP offers significant advantages in time saving, portability and convenience over traditional nebulized TIS with comparable clinical outcomes for individuals with CF.

Investigating Hydraulically Active Fractures in A Shallow Meta-Sedimentary Bedrock Aquifer Using Single Well Tracer Testing, Mount Stewart, Northern Ireland

Knowledge of groundwater flow/mass transport, in poorly productive aquifers which underlie over 65% of the island of Ireland, is necessary for effective management of catchment water quality and aquatic ecology. This research focuses on a fractured low-grade Ordovician/Silurian greywacke sequence which underlies approximately 25% of the northern half of Ireland. Knowledge of the unit’s hydrogeological properties remain largely restricted to localised single well open hole “transmissivity” values. Current hydrogeological conceptual models of the Greywacke view the bulk of groundwater flowing through fractures in an otherwise impermeable bedrock mass.
Core analysis permits fracture characterisation, although not all identified fractures may be involved in groundwater flow. Traditional in-situ hydraulic characterisation relies on cumbersome techniques such as packer testing or geophysical borehole logging (e.g. flowmeters). Queen’s University Belfast is currently carrying out hydraulic characterization of 16 boreholes at its Greywacke Hydrogeological Research Site at Mount Stewart, Northern Ireland.
Development of dye dilution methods, using a recently-developed downhole fluorometer, provided a portable, user-friendly, and inexpensive means of detecting hydraulically active intervals in open boreholes. Measurements in a 55m deep hole, three days following fluorescent dye injection, demonstrated the ability of the technique to detect two discrete hydraulically active intervals corresponding to zones identified by caliper and heat-pulse flowmeter logs. High resolution acoustic televiewer logs revealed the zones to correspond to two steeply dipping fractured intervals. Results suggest the rock can have effective porosities of the order of 0.1%.
Study findings demonstrate dye dilution’s utility in characterizing groundwater flow in fractured aquifers. Tests on remaining holes will be completed at different times following injection to identify less permeable fractures and develop an improved understanding of the structural controls on groundwater flow in the uppermost metres of competent bedrock.

Development and validation of an ultrasensitive fluorescence planar waveguide biosensor for the detection of paralytic shellfish toxins in marine algae

Marine dinoflagellates of the genera Alexandrium are well known producers of the potent neurotoxic paralytic shellfish toxins that can enter the food web and ultimately present a serious risk to public health in addition to causing huge economic losses. Direct coastal monitoring of Alexandrium spp. can provide early warning of potential shellfish contamination and risks to consumers and so a rapid, sensitive, portable and easy-to-use assay has been developed for this purpose using an innovative planar waveguide device. The disposable planar waveguide is comprised of a transparent substrate onto which an array of toxin-protein conjugates is deposited, assembled in a cartridge allowing the introduction of sample, and detection reagents. The competitive assay format uses a high affinity antibody to paralytic shellfish toxins with a detection signal generated via a fluorescently labelled secondary antibody. The waveguide cartridge is analysed by a simple reader device and results are displayed on a laptop computer. Assay speed has been optimised to enable measurement within 15 min. A rapid, portable sample preparation technique was developed for Alexandrium spp. in seawater to ensure analysis was completed within a short period of time. The assay was validated and the LOD and CCß were determined as 12 pg/mL and 20 pg/mL respectively with an intra-assay CV of 11.3% at the CCß and an average recovery of 106%. The highly innovative assay was proven to accurately detect toxin presence in algae sampled from the US and European waters at an unprecedented cell density of 10 cells/L. © 2012 Elsevier B.V. All rights reserved.