Identification of double bond position in lipids : From GC to OzID

Recent developments in mass spectrometry and chromatography provide new possibilities for the identification and in some instances quantification of a wide range of lipids in complex matrices. These advances in analytical technologies have provided a tantalizing glimpse of the true structural diversity of lipids in nature and have reinvigorated interest in the role of lipids in biology. While technological advances have been impressive, difficulties in the ready identification of sites of unsaturation (i.e., double bond position) within these molecules presents a significant impediment to understanding lipid biochemistry. This is of particular importance given the growing body of literature suggesting that the presence of naturally occurring lipid double bond isomers can have a significant influence, both positive and negative, on the development of pathologies such as cancer, cardiovascular disease and type 2 diabetes. This article provides a critical review of the Current suite of analytical approaches to the challenge of identification of the position of carbon-carbon double bonds in intact lipids. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Identification and Validity of Accelerometer Cut-Points for Toddlers

The purpose of this study was to derive ActiGraph cut-points for sedentary (SED), light-intensity physical activity (LPA), and moderate-to-vigorous physical activity (MVPA) in toddlers and evaluate their validity in an independent sample. The predictive validity of established preschool cut-points were also evaluated and compared. Twenty-two toddlers (mean age = 2.1 years ± 0.4 years) wore an ActiGraph accelerometer during a videotaped 20-min play period. Videos were subsequently coded for physical activity (PA) intensity using the modified Children's Activity Rating Scale (CARS). Receiver operating characteristic (ROC) curve analyses were conducted to determine cut-points. Predictive validity was assessed in an independent sample of 18 toddlers (mean age = 2.3 ± 0.4 years). From the ROC curve analyses, the 15-s count ranges corresponding to SED, LPA, and MVPA were 0–48, 49–418, and >418 counts/15 s, respectively. Classification accuracy was fair for the SED threshold (ROC-AUC = 0.74, 95% confidence interval = 0.71–0.76) and excellent for MVPA threshold (ROC-AUC = 0.90, 95% confidence interval = 0.88–0.92). In the cross-validation sample, the toddler cut-point and established preschool cut-points significantly overestimated time spent in SED and underestimated time in spent in LPA. For MVPA, mean differences between observed and predicted values for the toddler and Pate cut-points were not significantly different from zero. In summary, the ActiGraph accelerometer can provide useful group-level estimates of MVPA in toddlers. The results support the use of the Pate cut-point of 420 counts/15 s for MVPA.

Relevation! : an open source system for information retrieval relevance assessment

Relevation! is a system for performing relevance judgements for information retrieval evaluation. Relevation! is web-based, fully configurable and expandable; it allows researchers to effectively collect assessments and additional qualitative data. The system is easily deployed allowing assessors to smoothly perform their relevance judging tasks, even remotely. Relevation! is available as an open source project at: http://ielab.github.io/relevation.

Methodology for developing real-time motorway traffic risk identification models using individual-vehicle data

Most of existing motorway traffic safety studies using disaggregate traffic flow data aim at developing models for identifying real-time traffic risks by comparing pre-crash and non-crash conditions. One of serious shortcomings in those studies is that non-crash conditions are arbitrarily selected and hence, not representative, i.e. selected non-crash data might not be the right data comparable with pre-crash data; the non-crash/pre-crash ratio is arbitrarily decided and neglects the abundance of non-crash over pre-crash conditions; etc. Here, we present a methodology for developing a real-time MotorwaY Traffic Risk Identification Model (MyTRIM) using individual vehicle data, meteorological data, and crash data. Non-crash data are clustered into groups called traffic regimes. Thereafter, pre-crash data are classified into regimes to match with relevant non-crash data. Among totally eight traffic regimes obtained, four highly risky regimes were identified; three regime-based Risk Identification Models (RIM) with sufficient pre-crash data were developed. MyTRIM memorizes the latest risk evolution identified by RIM to predict near future risks. Traffic practitioners can decide MyTRIM’s memory size based on the trade-off between detection and false alarm rates. Decreasing the memory size from 5 to 1 precipitates the increase of detection rate from 65.0% to 100.0% and of false alarm rate from 0.21% to 3.68%. Moreover, critical factors in differentiating pre-crash and non-crash conditions are recognized and usable for developing preventive measures. MyTRIM can be used by practitioners in real-time as an independent tool to make online decision or integrated with existing traffic management systems.

Five-level Z-source diode-clamped inverter

This study proposes a five-level Z-source diode-clamped inverter designed with two intermediate Z-source networks connected between the dc input sources and rear-end inverter circuitry. By partially shorting the Z-source networks, new operating states not previously reported for two-level Z-source inverter are introduced here for operating the proposed inverter with voltage buck-boost energy conversion ability and five-level phase voltage switching. These characteristic features are in fact always ensured at the inverter terminal output by simply adopting a properly designed carrier modulation scheme, which always inserts two partial shoot-through states per half carrier cycle for smooth balanced operation. Theoretical findings and practical issues identified are eventually verified by constructing a scaled down laboratory prototype for testing.

Five-level current-source inverters with buck-boost and inductive-current balancing capabilities

This paper presents new five-level current-source inverters (CSIs) with voltage/current buck-boost capability, unlike existing five-level CSIs where only voltage-boost operation is supported. The proposed inverters attain self-inductive-current-balancing per switching cycle at their dc front ends without having to include additional balancing hardware or complex control manipulation. The inverters can conveniently be controlled by using the well-established phase-shifted carrier modulation scheme with only two additional linear references and a mapping logic table needed. Existing modulators can therefore be conveniently retrofitted for controlling the presented inverters. By appropriately coordinating the inverter gating signals, their implementations can be realized by using the least number of components without degrading performance. These enhanced features of the inverters have already been verified in simulation and experimentally using a scaled-down laboratory platform.

Z-source-inverter-based flexible distributed generation system solution for grid power quality improvement

Distributed generation (DG) systems are usually connected to the grid using power electronic converters. Power delivered from such DG sources depends on factors like energy availability and load demand. The converters used in power conversion do not operate with their full capacity all the time. The unused or remaining capacity of the converters could be used to provide some ancillary functions like harmonic and unbalance mitigation of the power distribution system. As some of these DG sources have wide operating ranges, they need special power converters for grid interfacing. Being a single-stage buck-boost inverter, recently proposed Z-source inverter (ZSI) is a good candidate for future DG systems. This paper presents a controller design for a ZSI-based DG system to improve power quality of distribution systems. The proposed control method is tested with simulation results obtained using Matlab/Simulink/PLECS and subsequently it is experimentally validated using a laboratory prototype.

An investigation of Staphylococcus aureus and related species from flood affected and other environmental sources

This research investigated the microbial air quality of flooded houses in Brisbane suburbs following the January 2011 flood event. Flood waters can carry and spread human pathogenic bacteria, and these organisms can be dispersed into residential air by aerosolisation. This study found that the bacterial load was significantly different for indoor and outdoor areas of flood affected houses, but no significant differences were observed between flooded and non-flooded houses. This could be due to the rapid clean-up of flooded houses following the event. Molecular methods were used to identify and characterise staphylococcal species in residential air of flooded and non-flooded houses. A major finding was the diverse population of airborne staphylococci as well as the high rate of methicillin-resistance in these strains. By determining the genetic relatedness of residential air sourced staphylococci, a potential source for pathogenic strains can be identified.

Tumor cells are the source of osteopontin and bone sialoprotein expression in human breast cancer

Bone sialoprotein (BSP) and osteopontin (OPN) are secreted glycoproteins with a conserved Arg-Gly-Asp (RGD) integrin-binding motif and are expressed predominantly in bone. The RGD tripeptide is commonly present in extracellular attachment proteins and has been shown to mediate the attachment of osteosarcoma cells and osteoclasts. To determine the origin and incidence of BSP and OPN mRNA expression in primary tumor, a cohort of archival, primary invasive breast carcinoma specimens was analyzed. BSP transcripts were detected in 65% and OPN transcripts in 77% of breast cancers examined. In general, BSP and OPN transcripts were detected in both invasive and in situ carcinoma components. The transcripts were not detected in surrounding stromal cells or in peritumoral macrophages. Despite its abundance in carcinomas, BSP expression was not detected in a panel of 11 human breast cancer cell lines (MCF-7, T47D, SK-Br-3, MDA-MB-453, MDA-MB- 231, MDA-MB-436, BT549, MCF-7(AOR), Hs578T, MDA-MB-435, and LCC15-MB) and OPN expression was detected only in two of these (MDA-MB-435 and LCC15-MB). To examine the possibility that expression of these genes was down-regulated in cell culture, several cell lines were grown as nude mouse xenografts in vivo; however, these tumors also failed to express BSP. OPN expression was identified in all cell lines grown as nude mouse xenografts. Our data suggest that in human primary breast tumors, the origin of BSP and OPN mRNA is predominantly the breast cancer cells and that expression of these transcripts is influenced by the tumor environment.

Optimising the cell source and biomaterials for the generation of vascularized adipose tissue in vivo

We initially described a rat chamber model with an inserted arteriovenous pedicle which spontaneously generates 3-dimensional vascularized connective tissue (Tanaka Y et al., Br J Plast Surg 2000; 53: 51-7). More recently we have developed a murine chamber model containing reconstituted basement membrane (Matrigel®) and FGF-2 that generates vascularized adipose tissue in vivo (Cronin K et al., Plast Reconstr Surg 2004; in press). We have extended this work to assess the cellular and matrix requirements for the Matrigel®- induced neo-adipogenesis. We found that chambers sealed to host fat were unable to grow new adipose tissue. In these chambers the Matrigel® became vascularized with maximal outgrowth of vessels extending to the periphery at 6 weeks. A small amount of adipose tissue was found adjacent to the vessels, most likely arising from periadventitial adipose tissue. In contrast, chambers open to interaction with endogenous adipose tissue showed abundant new fat, and partial exposure to adjacent adipose tissue clearly showed neo-adipogenesis only in this area. Addition of small amounts of free fat to the closed chamber containing Matrigel® was able to induce neo-adipogenesis. Addition of small pieces of human fat also caused neo-adipogenesis in immunocompromised (SCID) mice. Also, we found Matrigel® to induce adipogenesis of Lac-Z-tagged (Rosa-26) murine bone marrow-derived mesenchymal stem cells, and cells similar to these have been isolated from human adipose tissue. Given that Matrigel® is a mouse product and cannot be used in humans, we have started investigating alternative matrix scaffolds for adipogenesis such as the PDA-approved PLGA, collagen and purified components derived from Matrigel®, such as laminin-1. The optimal conditions for adipogenesis with these matrices are still being elucidated. In conclusion, we have demonstrated that a precursor cell source inside the chamber is essential for the generation of vascularized adipose tissue in vivo. This technique offers unique potential for the reconstruction of soft tissue defects and may enable the generation of site-specific tissue using the correct microenvironment.

Two-photon fluorescence spectroscopy for identification of healthy and malignant biological tissues

Two-photon fluorescence spectroscopy has been performed on rat skeletal muscles to investigate the effect of fixation processes on the micro-environments of the endogenous fluorophors in rat skeletal muscles. The two-photon fluorescence spectra measured for different fixation periods show a differential among those samples that were fixed in water, formalin and methanol, respectively. The results imply that two-photon fluorescence spectroscopy can be a potential technique for identification of healthy and malignant biological tissues.

STI-GMaS : an open-source environment for simulation of sexually-transmitted infections

Background Sexually-transmitted pathogens often have severe reproductive health implications if treatment is delayed or absent, especially in females. The complex processes of disease progression, namely replication and ascension of the infection through the genital tract, span both extracellular and intracellular physiological scales, and in females can vary over the distinct phases of the menstrual cycle. The complexity of these processes, coupled with the common impossibility of obtaining comprehensive and sequential clinical data from individual human patients, makes mathematical and computational modelling valuable tools in developing our understanding of the infection, with a view to identifying new interventions. While many within-host models of sexually-transmitted infections (STIs) are available in existing literature, these models are difficult to deploy in clinical/experimental settings since simulations often require complex computational approaches. Results We present STI-GMaS (Sexually-Transmitted Infections – Graphical Modelling and Simulation), an environment for simulation of STI models, with a view to stimulating the uptake of these models within the laboratory or clinic. The software currently focuses upon the representative case-study of Chlamydia trachomatis, the most common sexually-transmitted bacterial pathogen of humans. Here, we demonstrate the use of a hybrid PDE–cellular automata model for simulation of a hypothetical Chlamydia vaccination, demonstrating the effect of a vaccine-induced antibody in preventing the infection from ascending to above the cervix. This example illustrates the ease with which existing models can be adapted to describe new studies, and its careful parameterisation within STI-GMaS facilitates future tuning to experimental data as they arise. Conclusions STI-GMaS represents the first software designed explicitly for in-silico simulation of STI models by non-theoreticians, thus presenting a novel route to bridging the gap between computational and clinical/experimental disciplines. With the propensity for model reuse and extension, there is much scope within STI-GMaS to allow clinical and experimental studies to inform model inputs and drive future model development. Many of the modelling paradigms and software design principles deployed to date transfer readily to other STIs, both bacterial and viral; forthcoming releases of STI-GMaS will extend the software to incorporate a more diverse range of infections.

Experimental and finite element analysis to identify the source of vibration of a coach

This paper presents an investigation on the cause of severe vibration problem of a coach with four-cylinder engine running at an idle state using vibration and impact hammer modal experiments to obtain the main vibration frequency components and the natural characteristics of the coach. The vibration results indicate that the main vibration component comes from the vibration transmitted from the engine to the chassis frame, which is closely related with the engine idle speed. Based on structural simulation analysis of the coach’s chassis frame and comparison with modal testing, the coach severe vibration problem was due to coupling resonance between the engine idle frequency and the fourth natural frequency of the chassis frame. The solution to eliminate the vibration problem is provided by changing the local structure stiffness of the chassis frame. The contribution of this paper lies in providing a solution to solve similar problems.

A novel identification method for ultra trace detection of biomolecules using functionalised Surface Enhanced Raman Spectroscopy (SERS)

This thesis developed a new method for measuring extremely low amounts of organic and biological molecules, using Surface enhanced Raman Spectroscopy. This method has many potential applications, e.g. medical diagnosis, public health, food provenance, antidoping, forensics and homeland security. The method development used caffeine as the small molecule example, and erythropoietin (EPO) as the large molecule. This method is much more sensitive and specific than currently used methods; rapid, simple and cost effective. The method can be used to detect target molecules in beverages and biological fluids without the usual preparation steps.

Effects of wireless sensor network uncertainties on output-only modal analysis employing merged data of multiple tests

The use of Wireless Sensor Networks (WSNs) for vibration-based Structural Health Monitoring (SHM) has become a promising approach due to many advantages such as low cost, fast and flexible deployment. However, inherent technical issues such as data asynchronicity and data loss have prevented these distinct systems from being extensively used. Recently, several SHM-oriented WSNs have been proposed and believed to be able to overcome a large number of technical uncertainties. Nevertheless, there is limited research verifying the applicability of those WSNs with respect to demanding SHM applications like modal analysis and damage identification. Based on a brief review, this paper first reveals that Data Synchronization Error (DSE) is the most inherent factor amongst uncertainties of SHM-oriented WSNs. Effects of this factor are then investigated on outcomes and performance of the most robust Output-only Modal Analysis (OMA) techniques when merging data from multiple sensor setups. The two OMA families selected for this investigation are Frequency Domain Decomposition (FDD) and data-driven Stochastic Subspace Identification (SSI-data) due to the fact that they both have been widely applied in the past decade. Accelerations collected by a wired sensory system on a large-scale laboratory bridge model are initially used as benchmark data after being added with a certain level of noise to account for the higher presence of this factor in SHM-oriented WSNs. From this source, a large number of simulations have been made to generate multiple DSE-corrupted datasets to facilitate statistical analyses. The results of this study show the robustness of FDD and the precautions needed for SSI-data family when dealing with DSE at a relaxed level. Finally, the combination of preferred OMA techniques and the use of the channel projection for the time-domain OMA technique to cope with DSE are recommended.