Column ratio mapping: a processing technique for atomic resolution high angle annular dark field(HAADF) images

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [1 1 0]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 Å-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument

Identification of a novel splice variant form of the influenza A virus M2 ion channel with an antigenically distinct ectodomain

Segment 7 of influenza A virus produces up to four mRNAs. Unspliced transcripts encode M1, spliced mRNA2 encodes the M2 ion channel, while protein products from spliced mRNAs 3 and 4 have not previously been identified. The M2 protein plays important roles in virus entry and assembly, and is a target for antiviral drugs and vaccination. Surprisingly, M2 is not essential for virus replication in a laboratory setting, although its loss attenuates the virus. To better understand how IAV might replicate without M2, we studied the reversion mechanism of an M2-null virus. Serial passage of a virus lacking the mRNA2 splice donor site identified a single nucleotide pseudoreverting mutation, which restored growth in cell culture and virulence in mice by upregulating mRNA4 synthesis rather than by reinstating mRNA2 production. We show that mRNA4 encodes a novel M2-related protein (designated M42) with an antigenically distinct ectodomain that can functionally replace M2 despite showing clear differences in intracellular localisation, being largely retained in the Golgi compartment. We also show that the expression of two distinct ion channel proteins is not unique to laboratory-adapted viruses but, most notably, was also a feature of the 1983 North American outbreak of H5N2 highly pathogenic avian influenza virus. In identifying a 14th influenza A polypeptide, our data reinforce the unexpectedly high coding capacity of the viral genome and have implications for virus evolution, as well as for understanding the role of M2 in the virus life cycle

The investigation of III-V semiconductors using SuperSTEM

In recent years, the performance of electron microscopes has been greatly improved through the implementation of practical aberration correction technology. This has allowed the creation of instruments that can form A-scale electron probes at acceleration voltages of only 100kV. As an example, SuperSTEM 1 was the first UK based aberration-corrected 100kV field emission gun scanning transmission electron microscope (FEG-STEM) that was capable of achieving a spatial resolution of 1A. Instruments, such as SuperSTEM 1, permit a wide range of nanostructures to be studied at scales that were not previously possible in commercial microscopes. The introduction of aberration-corrected instruments has been an important development for the characterisation of state of the art semiconductor materials. For instance, some III-V semiconductor structures already incorporate layers that are only a single atom in width. However, due to the limitations of the techniques that have been previously used to characterise such materials, it remains unclear exactly how successful growth methods (such as MBE i.e. molecular beam epitaxy) actually are at producing sharp interfaces. Hence, the ability to study semiconductor materials at the atomic scale has become ever more crucial for technological and economic reasons. In this project, SuperSTEM 1 was used to study several MBE grown III-V semiconductor nanostructures. These materials have applications in present, and possibly future, semiconductor devices. However, in order to improve the performance of such devices, a more in-depth appraisal of the associated growth techniques is necessary. Hence, the aim of this project was to provide atomic scale information on the composition and interfacial sharpness of the various layers that were present in the MBE grown III-V semiconductor nanostructures. This project also required a greater understanding of some aspects of probe scattering and the HAADF (high angle annular dark field) imaging technique due to the exceptional A-scale spatial resolution of SuperSTEM

Business experience and start-up size: buying more lottery tickets next time around?

This paper explores the determinants of start-up size by focusing on a cohort of 6247 businesses that started trading in 2004, using a unique dataset on customer records at Barclays Bank. Quantile regressions show that prior business experience is significantly related with start-up size, as are a number of other variables such as age, education and bank account activity. Quantile treatment effects (QTE) estimates show similar results, with the effect of business experience on (log) start-up size being roughly constant across the quantiles. Prior personal business experience leads to an increase in expected start-up size of about 50%. Instrumental variable QTE estimates are even higher, although there are concerns about the validity of the instrument

Constraining the Jurassic extent of Greater India: Tectonic evolution of the West Australian margin

Alternative reconstructions of the Jurassic northern extent of Greater India differ by up to several thousand kilometers. We present a new model that is constrained by revised seafloor spreading anomalies, fracture zones and crustal ages based on drillsites/dredges from all the abyssal plains along the West Australian margin and the Wharton Basin, where an unexpected sliver of Jurassic seafloor (153 Ma) has been found embedded in Cretaceous (95 My old) seafloor. Based on fracture zone trajectories, this NeoTethyan sliver must have originally formed along a western extension of the spreading center that formed the Argo Abyssal Plain, separating a western extension of West Argoland/West Burma from Greater India as a ribbon terrane. The NeoTethyan sliver, Zenith and Wallaby plateaus moved as part of Greater India until westward ridge jumps isolated them. Following another spreading reorganization, the Jurassic crust resumed migrating with Greater India until it was re-attached to the Australian plate ∼95 Ma. The new Wharton Basin data and kinematic model place strong constraints on the disputed northern Jurassic extent of Greater India. Late Jurassic seafloor spreading must have reached south to the Cuvier Abyssal Plain on the West Australian margin, connected to a spreading ridge wrapping around northern Greater India, but this Jurassic crust is no longer preserved there, having been entirely transferred to the conjugate plate by ridge propagations. This discovery constrains the major portion of Greater India to have been located south of the large-offset Wallaby-Zenith Fracture Zone, excluding much larger previously proposed shapes of Greater India

Refining Our Understanding of the Flow Through Coronary Artery Branches; Revisiting Murray's Law in Human Epicardial Coronary Arteries

Background: Quantification of coronary blood flow is used to evaluate coronary artery disease, but our understanding of flow through branched systems is poor. Murray’s law defines coronary morphometric scaling, the relationship between flow (Q) and vessel diameter (D) and is the basis for minimum lumen area targets when intervening on bifurcation lesions. Murray’s original law (Q α D(P)) dictates that the exponent (P) is 3.0, whilst constant blood velocity throughout the system would suggest an exponent of 2.0. In human coronary arteries, the value of Murray’s exponent remains unknown. Aim: To establish the exponent in Murray’s power law relationship that best reproduces coronary blood flows (Q) and microvascular resistances (Rmicro) in a bifurcating coronary tree. Methods and Results: We screened 48 cases, and were able to evaluate inlet Q and Rmicro in 27 branched coronary arteries, taken from 20 patients, using a novel computational fluid dynamics (CFD) model which reconstructs 3D coronary anatomy from angiography and uses pressure-wire measurements to compute Q and Rmicro distribution in the main- and side-branches. Outputs were validated against invasive measurements using a Rayflow™ catheter. A Murray’s power law exponent of 2.15 produced the strongest correlation and closest agreement with inlet Q (zero bias, r = 0.47, p = 0.006) and an exponent of 2.38 produced the strongest correlation and closest agreement with Rmicro (zero bias, r = 0.66, p = 0.0001). Conclusions: The optimal power law exponents for Q and Rmicro were not 3.0, as dictated by Murray’s Law, but 2.15 and 2.38 respectively. These data will be useful in assessing patient-specific coronary physiology and tailoring revascularisation decisions

Increasing capacity for the treatment of common musculoskeletal problems: A non-inferiority RCT and economic analysis of corticosteroid injection for shoulder pain comparing a physiotherapist and orthopaedic surgeon

Background Role substitution is a strategy employed to assist health services manage the growing demand for musculoskeletal care. Corticosteroid injection is a common treatment in this population but the efficacy of its prescription and delivery by physiotherapists has not been established against orthopaedic standards. This paper investigates whether corticosteroid injection given by a physiotherapist for shoulder pain is as clinically and cost effective as that from an orthopaedic surgeon. Methods A double blind non-inferiority randomized controlled trial was conducted in an Australian public hospital orthopaedic outpatient service, from January 2013 to June 2014. Adults with a General Practitioner referral to Orthopaedics for shoulder pain received subacromial corticosteroid and local anaesthetic injection prescribed and delivered independently by a physiotherapist or a consultant orthopaedic surgeon. The main outcome measure was total Shoulder Pain and Disability Index (SPADI) score at baseline, six and 12 weeks, applying a non-inferiority margin of 15 points. Secondary outcomes tested for superiority included pain, shoulder movement, perceived improvement, adverse events, satisfaction, quality of life and costs. Results 278 participants were independently assessed by the physiotherapist and the orthopaedic surgeon, with 64 randomised (physiotherapist 33, orthopaedic surgeon 31). There were no significant differences in baseline characteristics between groups. Non-inferiority of injection by the physiotherapist was declared from total SPADI scores at 6 and 12 weeks (upper limit of the 95% one-sided confidence interval 13.34 and 7.17 at 6 and 12 weeks, respectively). There were no statistically significant differences between groups on any outcome measures at 6 or 12 weeks. From the perspective of the health funder, the physiotherapist was less expensive. Conclusions Corticosteroid injection for shoulder pain, provided by a suitably qualified physiotherapist is at least as clinically effective, and less expensive, compared with similar care delivered by an orthopaedic surgeon. Policy makers and service providers should consider implementing this model of care

Validation of a novel numerical model to predict regionalized blood flow in the coronary arteries

Aims: Ischaemic heart disease results from insufficient coronary blood flow. Direct measurement of absolute flow (mL/min) is feasible, but has not entered routine clinical practice in most catheterization laboratories. Interventional cardiologists, therefore, rely on surrogate markers of flow. Recently, we described a computational fluid dynamics (CFD) method for predicting flow that differentiates inlet, side branch, and outlet flows during angiography. In the current study, we evaluate a new method that regionalizes flow along the length of the artery. Methods and results: Three-dimensional coronary anatomy was reconstructed from angiograms from 20 patients with chronic coronary syndrome. All flows were computed using CFD by applying the pressure gradient to the reconstructed geometry. Side branch flow was modelled as a porous wall boundary. Side branch flow magnitude was based on morphometric scaling laws with two models: a homogeneous model with flow loss along the entire arterial length; and a regionalized model with flow proportional to local taper. Flow results were validated against invasive measurements of flow by continuous infusion thermodilution (Coroventis™, Abbott). Both methods quantified flow relative to the invasive measures: homogeneous (r 0.47, P 0.006; zero bias; 95% CI -168 to +168 mL/min); regionalized method (r 0.43, P 0.013; zero bias; 95% CI -175 to +175 mL/min). Conclusion: During angiography and pressure wire assessment, coronary flow can now be regionalized and differentiated at the inlet, outlet, and side branches. The effect of epicardial disease on agreement suggests the model may be best targeted at cases with a stenosis close to side branches.</p

Delayed neutrophil apoptosis enhances NET formation in cystic fibrosis

BackgroundCystic fibrosis (CF) lung disease is defined by large numbers of neutrophils and associated damaging products in the airway. Delayed neutrophil apoptosis is described in CF although it is unclear whether this is a primary neutrophil defect or a response to chronic inflammation. Increased levels of neutrophil extracellular traps (NETs) have been measured in CF and we aimed to investigate the causal relationship between these phenomena and their potential to serve as a driver of inflammation. We hypothesised that the delay in apoptosis in CF is a primary defect and preferentially allows CF neutrophils to form NETs, contributing to inflammation.MethodsBlood neutrophils were isolated from patients with CF, CF pigs and appropriate controls. Neutrophils were also obtained from patients with CF before and after commencing ivacaftor. Apoptosis was assessed by morphology and flow cytometry. NET formation was determined by fluorescent microscopy and DNA release assays. NET interaction with macrophages was examined by measuring cytokine generation with ELISA and qRT-PCR.ResultsCF neutrophils live longer due to decreased apoptosis. This was observed in both cystic fibrosis transmembrane conductance regulator (CFTR) null piglets and patients with CF, and furthermore was reversed by ivacaftor (CFTR potentiator) in patients with gating (G551D) mutations. CF neutrophils formed more NETs and this was reversed by cyclin-dependent kinase inhibitor exposure. NETs provided a proinflammatory stimulus to macrophages, which was enhanced in CF.ConclusionsCF neutrophils have a prosurvival phenotype that is associated with an absence of CFTR function and allows increased NET production, which can in turn induce inflammation. Augmenting neutrophil apoptosis in CF may allow more appropriate neutrophil disposal, decreasing NET formation and thus inflammation.</jats:sec