Using Wmatrix to classify open response survey data in the social sciences: observations and recommendations

We report here on our use of Wmatrix (Rayson 2009) and the USAS tagger (Rayson et al. 2004) as an alternative to more commonly used content analysis methods for sorting and coding open response survey data in the social sciences

Jointly reconstructing ground motion and resistivity for ERT-based slope stability monitoring

Electrical resistivity tomography (ERT) is increasingly being used to investigate unstable slopes and monitor the hydrogeological processes within. But movement of electrodes or incorrect placement of electrodes with respect to an assumed model can introduce significant resistivity artefacts into the reconstruction. In this work, we demonstrate a joint resistivity and electrode movement reconstruction algorithm within an iterative Gauss–Newton framework. We apply this to ERT monitoring data from an active slow-moving landslide in the UK. Results show fewer resistivity artefacts and suggest that electrode movement and resistivity can be reconstructed at the same time under certain conditions. A new 2.5-D formulation for the electrode position Jacobian is developed and is shown to give accurate numerical solutions when compared to the adjoint method on 3-D models. On large finite element meshes, the calculation time of the newly developed approach was also proven to be orders of magnitude faster than the 3-D adjoint method and addressed modelling errors in the 2-D perturbation and adjoint electrode position Jacobian

OpenSep: A generalizable open source pipeline for SOFA score calculation and Sepsis-3 classification

EHR-based sepsis research often uses heterogeneous definitions of sepsis leading to poor generalizability and difficulty in comparing studies to each other. We have developed OpenSep, an open-source pipeline for sepsis phenotyping according to the Sepsis-3 definition, as well as determination of time of sepsis onset and SOFA scores. The Minimal Sepsis Data Model was developed alongside the pipeline to enable the execution of the pipeline to diverse sources of electronic health record data. The pipeline\u27s accuracy was validated by applying it to the MIMIC-IV version 1.0 data and comparing sepsis onset and SOFA scores to those produced by the pipeline developed by the curators of MIMIC. We demonstrated high reliability between both the sepsis onsets and SOFA scores, however the use of the Minimal Sepsis Data model developed for this work allows our pipeline to be applied to more broadly to data sources beyond MIMIC

Microstructural characterisation and mechanical properties of Ti-5Al-5V-5Mo-3Cr built by wire and arc additive manufacture

The as-deposited microstructure and mechanical properties of the near-β titanium alloy Ti-5Al-5V-5Mo-3Cr (Ti-5553) produced by wire-arc additive manufacture (WAAM) were investigated, to understand its microstructural evolution under WAAM deposition conditions and to establish correlations between the microstructure features formed and the thermal cycles experienced during deposition. The ‘as-deposited’ Ti-5553 WAAM material exhibited higher tensile strengths than other as-deposited additively manufactured Ti-5553 deposits previously reported in the literature, but had significant anisotropy in elongation, as a consequence of the coarse and columnar β-grain structure that formed on solidification, which exhibited a strong {001}β⟨001⟩β cube texture. The multiple reheating cycles, inherent to the WAAM process, were recorded using a novel ‘harpoon’ thermocouple technique, and the α precipitation evolution was related to the thermal history. Electron probe microanalysis chemical maps revealed significant solute microsegregation during solidification, which influenced the subsequent precipitation due to its effect on the local β-phase stability. As each layer experienced more reheating cycles, the microstructure evolution could be ‘time resolved’ and the α laths were found to precipitate in a specific sequence of nucleation sites, starting at the β-grain boundaries and then inter-dendritically, where there was lower matrix β stability. However, after the reheating peak temperature was insufficiently high to have any further effect, the microstructure consisted of a relatively uniform distribution of α laths

Finance & Stochastic

The study analyses quantitative models for financial markets by starting from geometric Brown process and Wiener process by analyzing Ito’s lemma and first passage model. Furthermore, it is analyzed the prices of the options, Vanilla & Exotic, by using the expected value and numerical model with geometric applications. From contingent claim approach ALM strategies are also analyzed so to get the effective duration measure of liabilities by assuming that clients buy options for protection and liquidity by assuming defaults protection barrier as well. Furthermore, the study analyses interest rate models by showing that the yields curve is given by the average of the expected short rates & variation of GDP with the liquidity risk, but in the case we have crisis it is possible to have risk premium as well, the study is based on simulated modelisation by using the drift condition in combination with the inflation models as expectation of the markets. Moreover, the CIR process is considered as well by getting with modification of the diffusion process the same result of the simulated modelisation but we have to consider that the CIR process is considered in the simulated environment as well. The credit risk model is considered as well in intensity model & structural model by getting the liquidity and risk premium and the PD probability from the Rating Matrix as well by using the diagonal. Furthermore, the systemic risk is considered as well by using a deco relation concept by copula approaches. Moreover, along the equilibrium condition between financial markets is achieved the equity pricing with implications for the portfolio construction in simulated environment with Bayesian applications for smart beta. Finally, Value at Risk is also analyzed both static and dynamic with implications for the percentile of daily return and the tails risks by using a simulated approach

Clinical risk prediction for pre-eclampsia in nulliparous women: development of model in international prospective cohort

Objectives To develop a predictive model for pre-eclampsia based on clinical risk factors for nulliparous women and to identify a subgroup at increased risk, in whom specialist referral might be indicated

Development of an invasively monitored porcine model of acetaminophen-induced acute liver failure

Background: The development of effective therapies for acute liver failure (ALF) is limited by our knowledge of the pathophysiology of this condition, and the lack of suitable large animal models of acetaminophen toxicity. Our aim was to develop a reproducible invasively-monitored porcine model of acetaminophen-induced ALF. Method: 35kg pigs were maintained under general anaesthesia and invasively monitored. Control pigs received a saline infusion, whereas ALF pigs received acetaminophen intravenously for 12 hours to maintain blood concentrations between 200-300 mg/l. Animals surviving 28 hours were euthanased. Results: Cytochrome p450 levels in phenobarbital pre-treated animals were significantly higher than non pre-treated animals (300 vs 100 pmol/mg protein). Control pigs (n=4) survived 28-hour anaesthesia without incident. Of nine pigs that received acetaminophen, four survived 20 hours and two survived 28 hours. Injured animals developed hypotension (mean arterial pressure; 40.8+/-5.9 vs 59+/-2.0 mmHg), increased cardiac output (7.26+/-1.86 vs 3.30+/-0.40 l/min) and decreased systemic vascular resistance (8.48+/-2.75 vs 16.2+/-1.76 mPa/s/m3). Dyspnoea developed as liver injury progressed and the increased pulmonary vascular resistance (636+/-95 vs 301+/-26.9 mPa/s/m3) observed may reflect the development of respiratory distress syndrome. Liver damage was confirmed by deterioration in pH (7.23+/-0.05 vs 7.45+/-0.02) and prothrombin time (36+/-2 vs 8.9+/-0.3 seconds) compared with controls. Factor V and VII levels were reduced to 9.3 and 15.5% of starting values in injured animals. A marked increase in serum AST (471.5+/-210 vs 42+/-8.14) coincided with a marked reduction in serum albumin (11.5+/-1.71 vs 25+/-1 g/dL) in injured animals. Animals displayed evidence of renal impairment; mean creatinine levels 280.2+/-36.5 vs 131.6+/-9.33 mumol/l. Liver histology revealed evidence of severe centrilobular necrosis with coagulative necrosis. Marked renal tubular necrosis was also seen. Methaemoglobin levels did not rise >5%. Intracranial hypertension was not seen (ICP monitoring), but there was biochemical evidence of encephalopathy by the reduction of Fischer's ratio from 5.6 +/- 1.1 to 0.45 +/- 0.06. Conclusion: We have developed a reproducible large animal model of acetaminophen-induced liver failure, which allows in-depth investigation of the pathophysiological basis of this condition. Furthermore, this represents an important large animal model for testing artificial liver support systems

IL2RA Genetic Heterogeneity in Multiple Sclerosis and Type 1 Diabetes Susceptibility and Soluble Interleukin-2 Receptor Production

Multiple sclerosis (MS) and type 1 diabetes (T1D) are organ-specific autoimmune disorders with significant heritability, part of which is conferred by shared alleles. For decades, the Human Leukocyte Antigen (HLA) complex was the only known susceptibility locus for both T1D and MS, but loci outside the HLA complex harboring risk alleles have been discovered and fully replicated. A genome-wide association scan for MS risk genes and candidate gene association studies have previously described the IL2RA gene region as a shared autoimmune locus. In order to investigate whether autoimmunity risk at IL2RA was due to distinct or shared alleles, we performed a genetic association study of three IL2RA variants in a DNA collection of up to 9,407 healthy controls, 2,420 MS, and 6,425 T1D subjects as well as 1,303 MS parent/child trios. Here, we report “allelic heterogeneity” at the IL2RA region between MS and T1D. We observe an allele associated with susceptibility to one disease and risk to the other, an allele that confers susceptibility to both diseases, and an allele that may only confer susceptibility to T1D. In addition, we tested the levels of soluble interleukin-2 receptor (sIL-2RA) in the serum from up to 69 healthy control subjects, 285 MS, and 1,317 T1D subjects. We demonstrate that multiple variants independently correlate with sIL-2RA levels

Recreation of in-host acquired single nucleotide polymorphisms by CRISPR-Cas9 reveals an uncharacterised gene playing a role in Aspergillus fumigatus azole resistance via a non-cyp51A mediated resistance mechanism

EB, AB and AW are supported by the Wellcome Trust Strategic Award (grant 097377) and the MRC Centre for Medical Mycology (grant MR/N006364/1) at the University of Aberdeen. AB was also supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/K017365/1) and the Medical Research Council (MR/M026663/1). JW and AAB were supported by the BMBF-funded project DrugBioTune in the frame of InfectControl2020 and the excellence graduate school Jena School of Microbial Communication. ST and PW acknowledge the support of the European Regional Development Fund, Scottish Funding Council and Highlands and Islands Enterprise. The work in this paper is funded by a BBSRC EASTBIO grant (BB/M010996/1) awarded to AW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Parsimony and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history:A response to Brown et al.

Our recent study evaluated the performance of parsimony and probabilistic models of phylogenetic inference based on categorical data [1]. We found that a Bayesian implementation of a probabilistic Markov model produced more accurate results than either of the competing parsimony approaches (the main method currently employed), and the maximum-likelihood implementation of the same model. This occurs principally because the results of Bayesian analyses are less resolved (less precise) as a measure of topological uncertainty is intrinsically recovered in this MCMC-based approach and can be used to construct a majority-rule consensus tree that reflects this. Of the three main methods, maximum likelihood performed theworst of all as a single exclusively bifurcating tree is estimated in this framework which does not integrate an intrinsic measure of support.N