Reliable and robust molecular sexing of the hen harrier (Circus cyaneus) using PCR-RFLP of the CHD1 gene

The hen harrier (Circus cyaneus) is a bird of prey that is persecuted in the United Kingdom, and there is a need for a DNA-based individual identification and sexing system for the use in forensic investigations. This study reports a new set of PCR primers for the chromo-helicase-DNA-binding protein 1 gene, which allows sexing using PCR-RFLP. Instead of exonic primers that amplify across a large intron, this set consists of a primer within the intron, enabling reduction in amplicon sizes from 356 to 212 bp and 565 to 219 bp in W and Z chromosomes. DNA degradation and dilution experiments demonstrate that this set is significantly more robust than one that amplifies across the intron, and sequencing of the intronic primer-binding region across several individuals shows that it is highly conserved. While our objective is to incorporate this primer set into an STR-based individualization kit, it may in the meantime prove useful in forensic or conservation studies

A literature review of applied adaptive design methodology within the field of oncology in randomised controlled trials and a proposed extension to the CONSORT guidelines

Background: The application of adaptive design methodology within a clinical trial setting is becoming increasingly popular. However the application of these methods within trials is not being reported as adaptive designs hence making it more difficult to capture the emerging use of these designs. Within this review, we aim to understand how adaptive design methodology is being reported, whether these methods are explicitly stated as an 'adaptive design' or if it has to be inferred and to identify whether these methods are applied prospectively or concurrently. Methods: Three databases; Embase, Ovid and PubMed were chosen to conduct the literature search. The inclusion criteria for the review were phase II, phase III and phase II/III randomised controlled trials within the field of Oncology that published trial results in 2015. A variety of search terms related to adaptive designs were used. Results: A total of 734 results were identified, after screening 54 were eligible. Adaptive designs were more commonly applied in phase III confirmatory trials. The majority of the papers performed an interim analysis, which included some sort of stopping criteria. Additionally only two papers explicitly stated the term 'adaptive design' and therefore for most of the papers, it had to be inferred that adaptive methods was applied. Sixty-five applications of adaptive design methods were applied, from which the most common method was an adaptation using group sequential methods. Conclusion: This review indicated that the reporting of adaptive design methodology within clinical trials needs improving. The proposed extension to the current CONSORT 2010 guidelines could help capture adaptive design methods. Furthermore provide an essential aid to those involved with clinical trials

Concussion assessment in the Emergency Department: A preliminary study for a quality improvement project

Background In sport, concussion is assessed using the Sports Concussion Assessment Tool (SCAT) 5 and managed with return to play guidelines. Similar, user-friendly tools are rarely, if ever, used in the emergency department (ED). Objectives To evaluate a modified concussion assessment tool designed for the ED (ED-CAT) in patients presenting with a head injury and to identify variables that predict 30-day reattendance. Methods A preliminary, prospective, evaluation in a quality improvement project was conducted in one hospital in South Wales. Patients were recruited if they were over 13 years, and either did not have an ED-CT head scan or had a scan with no acute changes. The primary outcome was 30-day reattendance. Results 40 patients were recruited, 18 of whom had a CT scan. 37 were discharged on the same day with advice, two discharged the next day and one was admitted. Three (7.5%) patients reattended the department. Predictors of reattendance were headache score (median 3.0 vs 5.0; p<0.05), pressure in head score (2.0 vs 5.0; p<0.05), nausea/vomiting score (1.0 vs 3.0; p<0.05), dizziness score (1.0 vs 4.0; p<0.05), blurred vision score (0 vs 4.0; p<0.01), balance problems score (0 vs 4.0; p<0.05), sensitivity to light and confusion score (0 vs 4.0; p<0.01), orientation score (1. 0 vs 0; p<0.05) and immediate memory score (5.0 vs 4.0; p<0.05). Conclusions Key symptoms and signs predicted 30-day reattendance. The ED-CAT requires validation and refinement in a larger population to produce a short, practical, user-friendly, relevant tool for ED head injury assessment

Designing Energy-Efficient Heat Recovery Networks using Mixed-Integer Nonlinear Optimisation

Many industrial processes involve heating and cooling liquids: a quarter of the EU 2012 energy consumption came from industry and industry uses 73% of this energy on heating and cooling. We discuss mixed-integer nonlinear optimisation and its applications to energy efficiency. Our particular emphasis is on algorithms and solution techniques enabling optimisation for large-scale industrial networks. As a first application, optimising heat exchangers networks may increase efficiency in industrial plants. We develop deterministic global optimisation algorithms for a mixed-integer nonlinear optimisation model that simultaneously incorporates utility cost, equipment area, and hot/cold stream matches. We automatically recognise and exploit special mathematical structures common in heat recovery. We also computationally demonstrate the impact on the global optimisation solver ANTIGONE and benchmark large-scale test cases against heuristic approaches. As a second application, we discuss special structure in nonconvex quadratically-constrained optimisation problems, particularly through the lens of stream mixing and intermediate blending on process systems engineering networks. We take a parametric approach to uncovering topological structure and sparsity of the standard pooling problem in its p-formulation. We show that the sparse patterns of active topological structure are associated with a piecewise objective function. Finally, the presentation explains the conditions under which sparsity vanishes and where the combinatorial complexity emerges to cross over the P/NP boundary. We formally present the results obtained and their derivations for various specialised instances

Experiments and Simulations of short-pulse laser-pumped extreme ultraviolet lasers

Recent experimental work on the development of extreme ultraviolet lasers undertaken using as the pumping source the VULCAN laser at the Rutherford Appleton Laboratory is compared to detailed simulations. It is shown that short duration (similar topicosecond) pumping can produce X-ray laser pulses of a few picosecond duration and that measurement of the emission from the plasma can give an estimate of the duration of the gain coefficient. The Ehybrid fluid and atomic physics code developed at the University of York is used to simulate X-ray laser gain and plasma emission. Two postprocessors to the Ehybrid code are utilized: 1) to raytrace the X-ray laser beam amplification and refraction and 2) to calculate the radiation emission in the kiloelectronvolt photon energy range. The raytracing and spectral simulations are compared, respectively, to measured X-ray laser output and the output of two diagnostics recording transverse X-ray emission. The pumping laser energy absorbed in the plasma is examined by comparing the simulations to experimental results. It is shown that at high pumping irradiance (>10(15) Wcm(-2)), fast electrons are produced by parametric processes in the preformed long scale-length plasmas. These fast electrons do not pump the population inversion and so pumping efficiency is reduced at high irradiance

Initial Results of a Silicon Sensor Irradiation Study for ILC Extreme Forward Calorimetry

Detectors proposed for the International Linear Collider (ILC) incorporate a tungsten sampling calorimeter (`BeamCal') intended to reconstruct showers of electrons, positrons and photons that emerge from the interaction point of the collider with angles between 5 and 50 milliradians. For the innermost radius of this calorimeter, radiation doses at shower-max are expected to reach 100 MRad per year, primarily due to minimum-ionizing electrons and positrons that arise in the induced electromagnetic showers of e+e- `beamstrahlung' pairs produced in the ILC beam-beam interaction. However, radiation damage to calorimeter sensors may be dominated by hadrons induced by nuclear interactions of shower photons, which are much more likely to contribute to the non-ionizing energy loss that has been observed to damage sensors exposed to hadronic radiation. We report here on the results of SLAC Experiment T-506, for which several different types of silicon diode sensors were exposed to doses of radiation induced by showering electrons of energy 3.5-10.6 GeV. By embedding the sensor under irradiation within a tungsten radiator, the exposure incorporated hadronic species that would potentially contribute to the degradation of a sensor mounted in a precision sampling calorimeter. Depending on sensor technology, efficient charge collection was observed for doses as large as 220 MRad.Comment: Talk presented at the International Workshop on Future Linear Colliders (LCWS13), Tokyo, Japan, 11-15 November 201

Transition towards health promoting hospitals: adapting a global framework to Pakistan.

The World Health Organization encourages hospitals to become Health Promoting Hospitals (HPH) but adapting this concept to Pakistan has not been investigated. We explore perceptions of healthcare stakeholders about strategies and a priority action-plan to encourage HPHs in Pakistan. We conducted a qualitative study in 2007 where key-informant interviews and focus group discussions were held with healthcare stakeholders in Karachi. Thematic analysis was done and emerging themes were categorized. The HPH core components were perceived as the standard framework , however more emphasis was placed on priority actions as to satisfy basic needs of Patients, staff and the community. This included basic facilities of comfort, health, hygiene, safety, security and emotional support. A change in the traditional mindset from cure to care and identification of key personnel, awareness-raising and cooperation would strengthen advocacy efforts for HPH in Pakistan

Autoimmune-autoinflammatory rheumatoid arthritis overlaps: a rare but potentially important subgroup of diseases

At the population level, rheumatoid arthritis (RA) is generally viewed as autoimmune in nature with a small subgroup of cases having a palindromic form or systemic autoinflammatory disorder (SAID) phenotype. Herein, we describe resistant cases of classical autoantibody associated RA that had clinical, genetic and therapeutic responses indicative of coexistent autoinflammatory disease. Five patients with clinically overlapping features between RA and SAID including polysynovitis and autoantibody/shared epitope positivity, and who had abrupt severe self-limiting attacks including fevers and serositis, are described. Mutations or single nucleotide polymorphisms in recognised autoinflammatory pathways were evident. Generally, these cases responded poorly to conventional Disease-modifying anti-rheumatic drugs (DMARD) treatment with some excellent responses to colchicine or interleukin 1 pathway blockade. A subgroup of RA cases have a mixed autoimmune-autoinflammatory phenotype and genotype with therapeutic implications