Ultra-trace detection of diagnostically important biomarkers using functionalised-Surface Enhanced Raman Spectroscopy (SERS)

Here we report an ultrasensitive method for detecting bio-active compounds in biological samples by means of functionalised nanoparticles interrogated by surface enhanced Raman spectroscopy (SERS). This method is applicable to the recovery and detection of many diagnostically important peptidyl analytes such as insulin, human growth hormone, growth factors (IGFs) and erythropoietin (EPO), as well as many small molecule analytes and metabolites. Our method, developed to detect EPO, demonstrates its utility in a complex yet well defined biological system. Recombinant human EPO (rhEPO) and EPO analogues have successfully been used to treat anaemia in end-stage renal failure, chronic disorders and infections, cancer and AIDS. Current methods for EPO testing are lengthy, laborious and relatively insensitive to low concentrations. In our rapid screening methodology, gold nanoparticles were functionalised with anti-EPO antibodies to provide very high selectivity towards the EPO protein in urine. These “smart sensor” nanoparticles interact with and trap EPO. Subsequent SERS screening allows for the detection and quantisation of ultra trace amounts (<<10-15 M) of EPO in urine samples with minimal sample preparation. We present data showing that the SERS spectrum differentiates between human endogenous EPO and rhEPO in unpurified urine, and potentially distinguishes between purified EPO isoforms. The elimination of sample preparation and direct screening in biological fluids significantly reduces the time required by current methods. Antibody recognition against a variety of biological targets and the availability of portable commercial SERS analysers for rapid onsite testing suggest broad diagnostic applicability in a flexible analytical platform.

Dynamic contrast-enhanced magnetic resonance imaging as a biomarker for the pharmacological response of PTK787/ZK 222584, an inhibitor of the vascular endothelial growth factor receptor tyrosine kinases, in patients with advanced colorectal cancer and liver metastases: Results from two phase I studies

Purpose: PTK787/ZK 222584 (PTK/ZK), an orally active inhibitor of vascular endothelial growth factor (VEGF) receptor tyrosine kinases, inhibits VEGF-mediated angiogenesis. The pharmacodynamic effects of PTK/ZK were evaluated by assessing changes in contrast-enhancement parameters of metastatic liver lesions using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in patients with advanced colorectal cancer treated in two ongoing, dose-escalating phase I studies. Patients and Methods: Twenty-six patients had DCE-MRI performed at baseline, day 2, and at the end of each 28-day cycle. Doses of oral PTK/ZK ranged from 50 to 2000 mg once daily. Tumor permeability and vascularity were assessed by calculating the bidirectional transfer constant (Ki). The percentage of baseline Ki (% of baseline Ki) at each time point was compared with pharmacokinetic and clinical end points. Results: A significant negative correlation exists between the % of baseline Ki and increase in PTK/ZK oral dose and plasma levels (P = .01 for oral dose; P = .0001 for area under the plasma concentration curve at day 2). Patients with a best response of stable disease had a significantly greater reduction in Ki at both day 2 and at the end of cycle 1 compared with progressors (mean difference in % of baseline Ki, 47%, P = .004%; and 51%, P = .006; respectively). The difference in % of baseline Ki remained statistically significant after adjusting for baseline WHO performance status. Conclusion: These findings should help to define a biologically active dose of PTK/ZK. These results suggest that DCE-MRI may be a useful biomarker for defining the pharmacological response and dose of angiogenesis inhibitiors, such as PTK/ZK, for further clinical development. © 2003 by American Society of Clinical Oncology.

In vitro assessment of surface congruency and integration of chondrocytes at adjacent edges of micro-fabricated clefts on cartilage

Osteochondral grafts are common treatment options for joint focal defects due to their excellent functionality. However, the difficulty is matching the topography of host and graft(s) surfaces flush to one another. Incongruence could lead to disintegration particularly when the gap reaches subchondoral region. The aim of this study is therefore to investigate cell response to gap geometry when forming cartilage-cartilage bridge at the interface. The question is what would be the characteristics of such a gap if the cells could bridge across to fuse the edges? To answer this, osteochondral plugs devoid of host cells were prepared through enzymatic decellularization and artificial clefts of different sizes were created on the cartilage surface using laser ablation. High density pellets of heterologous chondrocytes were seeded on the defects and cultured with chondrogenic differentiation media for 35 days. The results showed that the behavior of chondrocytes was a function of gap topography. Depending on the distance of the edges two types of responses were generated. Resident cells surrounding distant edges demonstrated superficial attachment to one side whereas clefts of 150 to 250 µm width experienced cell migration and anchorage across the interface. The infiltration of chondrocytes into the gaps provided extra space for their proliferation and laying matrix; as the result faster filling of the initial void space was observed. On the other hand, distant and fit edges created an incomplete healing response due to the limited ability of differentiated chondrocytes to migrate and incorporate within the interface. It seems that the initial condition of the defects and the curvature profile of the adjacent edges were the prime determinants of the quality of repair; however, further studies to reveal the underlying mechanisms of cells adapting to and modifying the new environment would be of particular interest.

In vivo confocal microscopy of the ocular surface : from bench to bedside

In vivo confocal microscopy (IVCM) is an emerging technology that provides minimally invasive, high resolution, steady-state assessment of the ocular surface at the cellular level. Several challenges still remain but, at present, IVCM may be considered a promising technique for clinical diagnosis and management. This mini-review summarizes some key findings in IVCM of the ocular surface, focusing on recent and promising attempts to move “from bench to bedside”. IVCM allows prompt diagnosis, disease course follow-up, and management of potentially blinding atypical forms of infectious processes, such as acanthamoeba and fungal keratitis. This technology has improved our knowledge of corneal alterations and some of the processes that affect the visual outcome after lamellar keratoplasty and excimer keratorefractive surgery. In dry eye disease, IVCM has provided new information on the whole-ocular surface morphofunctional unit. It has also improved understanding of pathophysiologic mechanisms and helped in the assessment of prognosis and treatment. IVCM is particularly useful in the study of corneal nerves, enabling description of the morphology, density, and disease- or surgically induced alterations of nerves, particularly the subbasal nerve plexus. In glaucoma, IVCM constitutes an important aid to evaluate filtering blebs, to better understand the conjunctival wound healing process, and to assess corneal changes induced by topical antiglaucoma medications and their preservatives. IVCM has significantly enhanced our understanding of the ocular response to contact lens wear. It has provided new perspectives at a cellular level on a wide range of contact lens complications, revealing findings that were not previously possible to image in the living human eye. The final section of this mini-review provides a focus on advances in confocal microscopy imaging. These include 2D wide-field mapping, 3D reconstruction of the cornea and automated image analysis.

Performance of buried tunnels subjected to surface blast incorporating fluid structure interaction

This paper uses finite element techniques to investigate the performance of buried tunnels subjected to surface blasts incorporating fully coupled Fluid Structure Interaction and appropriate material models which simulate strain rate effects. Modelling techniques are first validated against existing experimental results and then used to treat the blast induced shock wave propagation and tunnel response in dry and saturated sands. Results show that the tunnel buried in saturated sand responds earlier than that in dry sand. Tunnel deformations decrease with distance from explosive in both sands, as expected. In the vicinity of the explosive, the tunnel buried in saturated sand suffered permanent deformation in both axial and circumferential directions, whereas the tunnel buried in dry sand recovered from most of the axial deformation. Overall, response of the tunnel in saturated sand is more severe for a given blast event and shows the detrimental effect of pore water on the blast response of buried tunnels. The validated modelling techniques developed in this paper can be used to investigate the blast response of tunnels buried in dry and saturated sands.

Response to “Comment on ‘Indications of energetic consequences of decoherence at short times for scattering from open quantum systems’” [AIP Advances 1, 049101 (2011)]

The Comment by Mayers and Reiter criticizes our work on two counts. Firstly, it is claimed that the quantum decoherence effects that we report in consequence of our experimental analysis of neutron Compton scattering from H in gaseous H2 are not, as we maintain, outside the framework of conventional neutron scatteringtheory. Secondly, it is claimed that we did not really observe such effects, owing to a faulty analysis of the experimental data, which are claimed to be in agreement with conventional theory. We focus in this response on the critical issue of the reliability of our experimental results and analysis. Using the same standard Vesuvio instrument programs used by Mayers et al., we show that, if the experimental results for H in gaseous H2 are in agreement with conventional theory, then those for D in gaseous D2 obtained in the same way cannot be, and vice-versa. We expose a flaw in the calibration methodology used by Mayers et al. that leads to the present disagreement over the behaviour of H, namely the ad hoc adjustment of the measured H peak positions in TOF during the calibration of Vesuvio so that agreement is obtained with the expectation of conventional theory. We briefly address the question of the necessity to apply the theory of open quantum systems.

Blast response and vulnerability assessment of piled foundations

This research treated the response of pile foundations to blast loads. The influence of important parameters was investigated. The research techniques and the results will enable safer design of pile foundations that are vulnerable to blast loads.

Epithelial-mesenchymal interconversions in normal ovarian surface epithelium and ovarian carcinomas : an exception to the norm

Cancer that arises from the ovarian surface epithelium (OSE) accounts for approximately 90% of human ovarian cancer, and is the fourth leading cause of cancer-related deaths among women in developed countries. The pathophysiology of epithelial ovarian cancer is still unclear because of the poor understanding of the complex nature of its development and the unusual mechanism(s) of disease progression. Recent studies have reported epithelial-mesenchymal transition (EMT) in cultured OSE and ovarian cancer cell lines in response to various stimuli, but our understanding of the importance of these observations for normal ovarian physiology and cancer progression is not well established. This review highlights the current literature on EMT-associated events in normal OSE and ovarian cancer cell lines, and discusses its implication for normal ovarian function as well as acquisition of neoplastic phenotypes. The pathological changes in OSE in response to EMT during neoplastic transformation and the contribution of hormones, growth factors, and cytokines that initiate and drive EMT to sustain normal ovarian function, as well as cancer development and progression are also discussed. Finally, emphasis is placed on the clinical implications of EMT and potential therapeutic opportunities that may arise from these observations have been proposed.

The use of phospholipid fatty acid analysis to measure impact of acid rock drainage on microbial communities in sediments

The impact of acid rock drainage (ARD) and eutrophication on microbial communities in stream sediments above and below an abandoned mine site in the Adelaide Hills, South Australia, was quantified by PLFA analysis. Multivariate analysis of water quality parameters, including anions, soluble heavy metals, pH, and conductivity, as well as total extractable metal concentrations in sediments, produced clustering of sample sites into three distinct groups. These groups corresponded with levels of nutrient enrichment and/or concentration of pollutants associated with ARD. Total PLFA concentration, which is indicative of microbial biomass, was reduced by >70% at sites along the stream between the mine site and as far as 18 km downstream. Further downstream, however, recovery of the microbial abundance was apparent, possibly reflecting dilution effect by downstream tributaries. Total PLFA was >40% higher at, and immediately below, the mine site (0-0.1 km), compared with sites further downstream (2.5-18 km), even after accounting for differences in specific surface area of different sediment samples. The increased microbial population in the proximity of the mine source may be associated with the presence of a thriving iron-oxidizing bacteria community as a consequence of optimal conditions for these organisms while the lower microbial population further downstream corresponded with greater sediments' metal concentrations. PCA of relative abundance revealed a number of PLFAs which were most influential in discriminating between ARD-polluted sites and the rest of the sites. These PLFA included the hydroxy fatty acids: 2OH12:0, 3OH12:0, 2OH16:0; the fungal marker: 18:2ω6; the sulfate-reducing bacteria marker 10Me16:1ω7; and the saturated fatty acids 12:0, 16:0, 18:0. Partial constrained ordination revealed that the environmental parameters with the greatest bearing on the PLFA profiles included pH, soluble aluminum, total extractable iron, and zinc. The study demonstrated the successful application of PLFA analysis to rapidly assess the toxicity of ARD-affected waters and sediments and to differentiate this response from the effects of other pollutants, such as increased nutrients and salinity.

Security analysis of the non-aggressive challenge response of the DNP3 Protocol using a CPN Model

Distributed Network Protocol Version 3 (DNP3) is the de-facto communication protocol for power grids. Standard-based interoperability among devices has made the protocol useful to other infrastructures such as water, sewage, oil and gas. DNP3 is designed to facilitate interaction between master stations and outstations. In this paper, we apply a formal modelling methodology called Coloured Petri Nets (CPN) to create an executable model representation of DNP3 protocol. The model facilitates the analysis of the protocol to ensure that the protocol will behave as expected. Also, we illustrate how to verify and validate the behaviour of the protocol, using the CPN model and the corresponding state space tool to determine if there are insecure states. With this approach, we were able to identify a Denial of Service (DoS) attack against the DNP3 protocol.

Physisorption-induced electron scattering on the surface of carbon-metal core-shell nanowire arrays for hydrogen sensing

Palladium is sputtered on multi-walled carbon nanotube forests to form carbon-metal core-shell nanowire arrays. These hybrid nanostructures exhibited resistive responses when exposed to hydrogen with an excellent baseline recovery at room temperature. The magnitude of the response is shown to be tuneable by an applied voltage. Unlike the charge-transfer mechanism commonly attributed to Pd nanoparticle-decorated carbon nanotubes, this demonstrates that the hydrogen response mechanism of the multi-walled carbon nanotube-Pd core-shell nanostructure is due to the increase in electron scattering induced by physisorption of hydrogen. These hybrid core-shell nanostructures are promising for gas detection in hydrogen storage applications.

Thinning vertical graphenes, tuning electrical response : from semiconducting to metallic

A simple, uniquely plasma-enabled and environment-friendly process to reduce the thickness of vertically standing graphenes to only 4–5 graphene layers and arranging them in dense, ultra-large surface area, ultra-open-edge-length, self-organized and interconnected networks is demonstrated. The approach for the ultimate thickness reduction to 1–2 graphene layers is also proposed. The vertical graphene networks are optically transparent and show tunable electric properties from semiconducting to semi-metallic and metallic at room and near-room temperature, thus recovering semi-metallic properties of a single-layer graphene.

Nanowire sensor response to reactive gas environment

The response of an originally developed catalytic sensor with a Nb2 O5 nanowire array at its outer surface to the varying density of O atoms is experimentally and numerically studied. This technique can be used to measure one order of magnitude lower densities of O atoms and achieve a stable linear response in a significantly broader pressure range compared to conventional catalytic probes with a flat surface. The nanostructured outer surface also acts as a thermal barrier against sensor overheating. This approach is generic and can be used for reactive species detection in other reactive gas environments.

Surface plasmon enhancement of optical absorption in thin-film silicon solar cells

Strong electromagnetic field enhancement that occurs under conditions of the surface plasmon excitation in metallic nanoparticles deposited on a semiconductor surface is a very efficient and promising tool for increasing the optical absorption within semiconductor solar cells and, hence, their photocurrent response. The enhancement of the optical absorption in thin-film silicon solar cells via the excitation of localized surface plasmons in spherical silver nanoparticles is investigated. Using the effective medium model, the effect of the nanoparticle size and the surface coverage on that enhancement is analyzed. The optimum configuration and the nanoparticle parameters leading to the maximum enhancement in the optical absorption and the photocurrent response in a single p-n junction silicon cell are obtained. The effect of coupling between the silicon layer and the surface plasmon fields on the efficiency of the above enhancement is quantified as well.

Catalytic probes with nanostructured surface for gas/discharge diagnostics : a study of a probe signal behaviour

Catalytic probes are used for plasma diagnostics in order to quantify the density of neutral atoms. The probe response primarily depends on the probe material and its surface morphology. Here we report on the design, operation and modelling of the response of niobium pentoxide sensors with a flat and nanowire (NW) surfaces. These sensors were used to detect neutral oxygen atoms in the afterglow region of an inductively coupled rf discharge in oxygen. A very different response of the flat-surface and NW probes to the varying densities of oxygen atoms was explained by modelling heat conduction and taking into account the associated temperature gradients. It was found that the nanostructure probe can measure in a broader range than the flat oxide probe due to an increase in the surface to volume ratio, and the presence of nanostructures which act as a thermal barrier against sensor overheating. These results can be used for the development of the new generation of catalytic probes for gas/discharge diagnostics in a range of industrial and environmental applications.