Identification of Pseudomonas aeruginosa by a duplex real-time polymerase chain reaction assay targeting the ecfX and the gyrB genes

Phenotypic identification of Gram-negative bacteria from respiratory specimens of patients with cystic fibrosis carries a high risk of misidentification. Molecular identification techniques that use single-gene targets are also susceptible to error, including cross-reaction issues with other Gram-negative organisms. In this study, we have designed a Pseudomonas aeruginosa duplex real-time polymerase chain reaction (PCR) (PAduplex) assay targeting the ecfX and the gyrB genes. The PAduplex was evaluated against a panel of 91 clinical and environmental isolates that were presumptively identified as P. aeruginosa. The results were compared with those obtained using a commercial biochemical identification kit and several other P. aeruginosa PCR assays. The results showed that the PAduplex assay is highly suitable for routine identification of P. aeruginosa isolates from clinical or environmental samples. The 2-target format provides simultaneous confirmation of P. aeruginosa identity where both the ecfX and gyrB PCR reactions are positive and may also reduce the potential for false negatives caused by sequence variation in primer or probe targets.

High resolution X-ray spectroscopy in fast electron transport studies

A detailed knowledge of the physical phenomena underlying the generation and the transport of fast electrons generated in high-intensity laser-matter interactions is of fundamental importance for the fast ignition scheme for inertial confinement fusion.

Here we report on an experiment carried out with the VULCAN Petawatt beam and aimed at investigating the role of collisional return currents in the dynamics of the fast electron beam. To that scope, in the experiment counter-propagating electron beams were generated by double-sided irradiation of layered target foils containing a Ti layer. The experimental results were obtained for different time delays between the two laser beams as well as for single-sided irradiation of the target foils. The main diagnostics consisted of two bent mica crystal spectrometers placed at either side of the target foil. High-resolution X-ray spectra of the Ti emission lines in the range from the Ly alpha to the K alpha line were recorded. In addition, 2D X-ray images with spectral resolution were obtained by means of a novel diagnostic technique, the energy-encoded pin-hole camera, based on the use of a pin-hole array equipped with a CCD detector working in single-photon regime. The spectroscopic measurements suggest a higher target temperature for well-aligned laser beams and a precise timing between the two beams. The experimental results are presented and compared to simulation results.

Application of Evidence Theory and Discounting Techniques to Aerospace Design

Critical decisions are made by decision-makers throughout
the life-cycle of large-scale projects. These decisions are crucial as they
have a direct impact upon the outcome and the success of projects. To aid
decision-makers in the decision making process we present an evidential
reasoning framework. This approach utilizes the Dezert-Smarandache
theory to fuse heterogeneous evidence sources that suffer from levels
of uncertainty, imprecision and conflicts to provide beliefs for decision
options. To analyze the impact of source reliability and priority upon
the decision making process, a reliability discounting technique and a
priority discounting technique, are applied. A maximal consistent subset
is constructed to aid in dening where discounting should be applied.
Application of the evidential reasoning framework is illustrated using a
case study based in the Aerospace domain.

Transforming Growth Factor-beta superfamily:evaluation as breast cancer biomarkers and preventive agents

The Transforming Growth Factor-beta (TGFbeta) superfamily of cytokines is comprised of a number of structurally-related, secreted polypeptides that regulate a multitude of cellular processes including proliferation, differentiation and neoplastic transformation. These growth regulatory molecules induce ligand-mediated hetero-oligomerization of distinct type II and type I serine/threonine kinase receptors that transmit signals predominantly through receptor-activated Smad proteins but also induce Smad-independent pathways. Ligands, receptors and intracellular mediators of signaling initiated by members of the TGFbeta family are expressed in the mammary gland and disruption of these pathways may contribute to the development and progression of human breast cancer. Since many facets of TGFbeta and breast cancer have been recently reviewed in several articles, except for discussion of recent developments on some aspects of TGFbeta, the major focus of this review will be on the role of activins, inhibins, BMPs, nodal and MIS-signaling in breast cancer with emphasis on their utility as potential diagnostic, prognostic and therapeutic targets.

Experimental and Numerical Benchmarking of an Improved Impeller Meanline Modelling Method for Automotive Turbocharger Centrifugal Compressors

After the development of a new single-zone meanline modelling technique, benchmarking of the technique and the modelling methods used during its development are presented. The new meanline model had been developed using the results of three automotive turbocharger centrifugal compressors, and single passage CFD models based on their geometry.

The target of the current study was to test the new meanline modelling method on two new centrifugal compressor stages, again from the automotive turbocharger variety. Furthermore the single passage CFD modelling method used in the previous study would be again employed here and also benchmarked.

The benchmarking was twofold; firstly test the overall performance prediction accuracy of the single-zone meanline model. Secondly, test the detailed performance estimation of the CFD model using detailed interstage static pressure tappings.

The final component of this study exposed the weaknesses in the current modelling methods used (explicitly during this study). The non-axisymmetric flow field at the leading and trailing edges for the two compressors was measured and is presented here for the complete compressor map, highlighting the distortion relative to the tongue.

Advanced materials for recognition and capture of whole cells and microorganisms

Selective cell recognition and capture has recently attracted significant interest due to its potential importance for clinical, diagnostic, environmental, and security applications. Current methods for cell isolation from complex samples are largely dependent on cell size and density, with limited application scope as many of the target cells do not exhibit appreciable differences in this respect. The most recent and forthcoming developments in the area of selective recognition and capture of whole cells, based on natural receptors, as well as synthetic materials utilising physical and chemical properties of the target cell or microorganism, are highlighted. Particular focus is given to the development of cell complementary surfaces using the cells themselves as templating agents, by means of molecular imprinting, and their combination with sensing platforms for rapid cell detection in complex media. The benefits and challenges of each approach are discussed and a perspective of the future of this research area is given.

Panning for Gold: The Standardizing Work of Filling “Autistic” Shells – Using institutional ethnography to explore textually mediated health relations in the diagnostic process of autism.

Health reform practices in Canada and elsewhere have restructured the purpose and use of diagnostic labels and the processes of naming such labels. Diagnoses are no longer only a means to tell doctors and patients what may be wrong and indicate potential courses of treatment; some diagnoses activate specialized services and supports for persons with a disability and those who provide care for them. In British Columbia, a standardized process of diagnosis with the outcome of an autism spectrum disorder gives access to government provided health care and educational services and supports. Such processes enter individuals into a complex of text mediated relations, regulated by the principles of evidence-based medicine. However, the diagnosis of autism in children is notoriously uncertain. Because of this ambiguity, standardizing the diagnostic process creates a hurdle in gaining help and support for parents who have children with problems that could lead to a diagnosis on the autism spectrum. Such processes and their organizing relations are problematized, explored and explicated below. Grounded in the epistemological and ontological shift offered by Dorothy E. Smith (1987; 1990a; 1999; 2005), this article reports on the findings of an institutional ethnographic study that explored the diagnostic process of autism in British Columbia. More specifically, this article focuses on the processes involved in going from mothers talking from their experience about their childrens problems to the formalized and standardized, and thus “virtually” produced, diagnoses that may or may not give access to services and supports in different systems of care. Two psychologists, a developmental pediatrician, a social worker – members of a specialized multidisciplinary assessment team – and several mothers of children with a diagnosis on the autism spectrum were interviewed. The implications of standardizing the diagnosis process of a disability that is not clear-cut and has funding attached are discussed. This ethnography also provides a glimpse of the implications of current and ongoing reforms in the state-supported health care system in British Columbia, and more generally in Canada, for people’s everyday doings.

Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype-phenotype correlations, codon bias and dominant-negative effects

The adaptor protein-2 sigma subunit (AP2sigma;2) is pivotal for clathrin-mediated endocytosis of plasma membrane constituents such as the calcium-sensing receptor (CaSR). Mutations of the AP2sigma;2 Arg15 residue result in familial hypocalciuric hypercalcaemia type 3 (FHH3), a disorder of extracellular calcium (Ca<inf>o</inf>²⁺) homeostasis. To elucidate the role of AP2sigma;2 in Ca<inf>o</inf>²⁺ regulation, we investigated 65 FHH probands, without other FHH-associated mutations, for AP2sigma;2 mutations, characterized their functional consequences and investigated the genetic mechanisms leading to FHH3. AP2sigma;2 mutations were identified in 17 probands, comprising 5 Arg15Cys, 4 Arg15His and 8 Arg15Leu mutations. A genotype-phenotype correlation was observed with the Arg15Leu mutation leading to marked hypercalcaemia. FHH3 probands harboured additional phenotypes such as cognitive dysfunction. All three FHH3-causing AP2sigma;2 mutations impaired CaSR signal transduction in a dominant-negative manner. Mutational bias was observed at the AP2sigma;2 Arg15 residue as other predicted missense substitutions (Arg15Gly, Arg15Pro and Arg15Ser), which also caused CaSR loss-of-function, were not detected in FHH probands, and these mutations were found to reduce the numbers of CaSR-expressing cells. FHH3 probands had significantly greater serum calcium (sCa) and magnesium (sMg) concentrations with reduced urinary calcium to creatinine clearance ratios (CCCR) in comparison with FHH1 probands with CaSR mutations, and a calculated index of sCa × sMg/100 × CCCR, which was ≥ 5.0, had a diagnostic sensitivity and specificity of 83 and 86%, respectively, for FHH3. Thus, our studies demonstrate AP2sigma;2 mutations to result in a more severe FHH phenotype with genotype-phenotype correlations, and a dominant-negative mechanism of action with mutational bias at the Arg15 residue.

Combining Bio- and Chemo-catalysis for the Sustainable Production of Chemicals

The combination of bio- and chemo-catalysis to form a single synthetic route is a powerful methodology for the improvement of chemical synthesis. The extreme methods of biocatalysis (whole cell and isolated enzyme) fulfill very different roles. Biocatalysis by isolated enzymes enables highly efficient chemical transformations of extremely high selectivity and low contamination; however, conditions and substrates are limited to a narrow range. Whole cell biocatalysis enables the conversion of crude substrates, such as those derived from biomass; however, the products tend to be impure and delivered in dilute aqueous solution. Chemocatalysis is a well-established technique, and the addition of chemical catalysis and chemocatalytic methods to biocatalysis enables synthetic chemists to avoid the shortcomings of a biocatalytic step. For example, in enzymatic catalysis the addition of a chemical catalyst can allow the conversion of a racemic alcohol to an enantiopure, instead of racemic, product. In whole cell biocatalysis chemical reagents can assist the separation, transformation, and further isolation of the functionality of interest. The cooperation of bio- and chemocatalysts enables sustainable production of chemicals that would be impossible using biocatalysis alone, while achieving selectivities and using substrates not currently possible with chemocatalysis alone.

Diagnostic value of increased sensitivity by massively parallel sequencing

Routine molecular diagnostics modalities are unable to confidently detect low frequency mutations (<5-15%) that may indicate response to targeted therapies. We confirm the presence of a low frequency NRAS mutation in a rectal cancer patient using massively parallel sequencing when previous Sanger sequencing results proved negative and Q-PCR testing inconclusive. There is increasing evidence that these low frequency mutations may confer resistance to anti-EGFR therapy. In view of negative/inconclusive Sanger sequencing and Q-PCR results for NRAS mutations in a KRAS wt rectal case, the diagnostic biopsy and 4 distinct subpopulations of cells in the resection specimen after conventional chemo/radiotherapy were massively parallel sequenced using the Ion Torrent PGM. DNA was derived from FFPE rectal cancer tissue and amplicons produced using the Cancer Hotspot Panel V2 and sequenced using semiconductor technology. NRAS mutations were observed at varying frequencies in the patient biopsy (12.2%) and all four subpopulations of cells in the resection with an average frequency of 7.3% (lowest 2.6%). The results of the NGS also provided the mutational status of 49 other genes that may have prognostic or predictive value, including KRAS and PIK3CA. NGS technology has been postulated in diagnostics because of its capability to generate results in large panels of clinically meaningful genes in a cost-effective manner. This case illustrates another potential advantage of this technology: its use for detecting low frequency mutations that may influence therapeutic decisions in cancer treatment.

Prostate cancer radiotherapy: potential applications of metal nanoparticles for imaging and therapy

Prostate cancer (CaP) is the most commonly diagnosed cancer in males. There have been dramatic technical advances in radiotherapy delivery, enabling higher doses of radiotherapy to primary cancer, involved lymph nodes and oligometastases with acceptable normal tissue toxicity. Despite this, many patients relapse following primary radical therapy, and novel treatment approaches are required. Metal nanoparticles are agents that promise to improve diagnostic imaging and image-guided radiotherapy and to selectively enhance radiotherapy effectiveness in CaP. We summarize current radiotherapy treatment approaches for CaP and consider pre-clinical and clinical evidence for metal nanoparticles in this condition.

Prostate cancer (CaP) is the most commonly diagnosed cancer in males and is responsible for more than 10,000 deaths each year in the UK.1 Technical advances in radiotherapy delivery, including image-guided intensity-modulated radiotherapy (IG-IMRT), have enabled the delivery of higher radiation dose to the prostate, which has led to improved biochemical control. Further improvements in cancer imaging during radiotherapy are being developed with the advent of MRI simulators and MRI linear accelerators.2–4

Nanotechnology promises to deliver significant advancements across numerous disciplines.5 The widest scope of applications are from the biomedical field including exogenous gene/drug delivery systems, advanced biosensors, targeted contrast agents for diagnostic applications and as direct therapeutic agents used in combination with existing treatment modalities.6–11 This diversity of application is especially evident within cancer research, with a myriad of experimental anticancer strategies currently under investigation.

This review will focus specifically on the potential of metal-based nanoparticles to augment the efficacy of radiotherapy in CaP, a disease where radiotherapy constitutes a major curative treatment modality.12 Furthermore, we will also address the clinical state of the art for CaP radiotherapy and consider how these treatments could be best combined with nanotherapeutics to improve cancer outcomes.

Identification of diagnostic biomarkers for infection in premature neonates

Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity, and extraneous medical interventions. Additionally premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes, and antimicrobial toxicity. Currently initial diagnosis is based upon clinical suspicion accompanied by nonspecific clinical signs and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates that are associated with inflammation, coagulation, and fibrinolysis. Specifically P- and E-selectins, interleukin 2 soluble receptor alpha, interleukin 18, neutrophil elastase, urokinase plasminogen activator and its cognate receptor, and C-reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.