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WRAP: Warwick Research Archive Portal: No conditions. Results ordered -Date Deposited.

Background:
Following at least 3 months of anticoagulation therapy after a first unprovoked venous thromboembolism (VTE), there is uncertainty about the duration of therapy. Further anticoagulation therapy reduces the risk of having a potentially fatal recurrent VTE but at the expense of a higher risk of bleeding, which can also be fatal.

Objective:
An economic evaluation sought to estimate the long-term cost-effectiveness of using a decision rule for restarting anticoagulation therapy vs. no extension of therapy in patients based on their risk of a further unprovoked VTE.

Methods:A Markov patient-level simulation model was developed, which adopted a lifetime time horizon with monthly time cycles and was from a UK National Health Service (NHS)/Personal Social Services (PSS) perspective.

Results:
Base-case model results suggest that treating patients with a predicted 1 year VTE risk of 17.5% or higher may be cost-effective if decision makers are willing to pay up to £20 000 per quality adjusted life year (QALY) gained. However, probabilistic sensitivity analysis shows that the model was highly sensitive to overall parameter uncertainty and caution is warranted in selecting the optimal decision rule on cost-effectiveness grounds. Univariate sensitivity analyses indicate variables such as anticoagulation therapy disutility and mortality risks were very influential in driving model results.

Conclusion:
This represents the first economic model to consider the use of a decision rule for restarting therapy for unprovoked VTE patients. Better data are required to predict long-term bleeding risks during therapy in this patient group.

Objective: To determine whether patients with paroxysmal atrial fibrillation (AF) are less likely to be treated with anticoagulants than patients with persistent/permanent AF and to investigate trends in treatment between 2000 and 2015. UK and European guidelines recommend that anticoagulants are offered to all patients with AF at increased risk of stroke, irrespective of AF type.

Methods: Sixteen sequential cross-sectional analyses from 2000 to 2015 were carried out with index dates on 1st of May each year. The data source was primary care data from 648 practices across the UK contributing to The Health Improvement Network database. All patients with a diagnosis of AF aged ≥35 years and registered for at least 1 year were included. The main outcome measure was prescription of anticoagulant medication.

Results: The proportion of patients with AF with a diagnosis of paroxysmal AF increased from 7.4% (95% CI 7.0 to 7.8) in 2000 to 14.0% (95% CI 13.7 to 14.3) in 2015. Among patients with a CHADS2 score of ≥1, between 2000 and 2015 the proportion prescribed anticoagulants increased from 18.8% (95% CI 16.4 to 21.4) to 56.2% (95% CI 55.0 to 57.3) and from 34.2% (95% CI 33.3 to 35.0) to 69.4% (95% CI 68.9 to 69.8) in patients with paroxysmal and other (persistent/permanent) AF, respectively; RR for treatment of patients with paroxysmal AF compared with patients with other AF increased from 0.48 (95% CI 0.42 to 0.55) to 0.76 (95% CI 0.74 to 0.77). Adjusting for age, sex, Townsend score and presence or absence of contraindications had little effect on the results.

Conclusions: In 2000, eligible patients with paroxysmal AF were half as likely to be treated with anticoagulants as patients with other AF; this has improved over time, but in 2015, eligible patients with paroxysmal AF were still around 20% less likely to be prescribed anticoagulant medication.

Aim: To evaluate the reliability and performance of the Xprecia Stride coagulometer under the conditions in which it is most likely to be used.

Methods: The performance of the Xprecia Stride coagulometer was compared with a local laboratory and the CoaguChek systems routinely used for international normalised ratio (INR) estimation within one primary and one secondary care based anticoagulation clinic in Birmingham. Anticoagulation clinic personnel were trained to use the Xprecia Stride. Patients attending the clinics were eligible if aged ≥18 years and had received warfarin for at least 3 months. Consenting participants provided capillary blood samples for parallel testing on the Xprecia Stride and CoaguChek systems. At the secondary care clinic, a venous blood sample was also collected for laboratory INR estimation. INR results were compared using linear regression analysis and Bland–Altman plots.

Results: A total of 102 laboratory and 205 parallel coagulometer INR tests were performed. Linear regression revealed strong correlation between the Xprecia Stride and the laboratory (r=0.83) and between the Xprecia Stride and CoaguChek systems (r=0.92). Within the therapeutic range, agreement between the systems was very good with 87% of the Xprecia Stride and laboratory INR results and 93% of the Xprecia Stride and CoaguChek INR results being within 0.5 INR units of each other.

Conclusion: INRs tested using the Xprecia Stride system showed good agreement with the laboratory and CoaguChek systems. Findings indicate that in the hands of the intended users the Xprecia Stride is accurate, reliable and acceptable for use in a routine clinical setting.

Background: Care home residents have venous thromboembolism (VTE) risk profiles similar to medical inpatients; however, the epidemiology of VTE in care homes is unclear.

Aim: To determine the incidence of VTE in care homes.

Design and setting: Observational cohort study of 45 care homes in Birmingham and Oxford, UK.

Method: A consecutive sample of care home residents was enrolled and followed up for 12 months. Data were collected via case note reviews of care home and GP records; mortality information was supplemented with Health and Social Care Information Centre (now called NHS Digital) cause of death data. All potential VTE events were adjudicated by an independent committee according to three measures of diagnostic certainty: definite VTE (radiological evidence), probable VTE (high clinical indication but no radiological evidence), or possible VTE (VTE cannot be ruled out). (Study registration number: ISTCTN80889792.)

Results: There were 1011 participants enrolled, and the mean follow-up period was 312 days (standard deviation 98 days). The incidence rate was 0.71 per 100 person years of observation (95% confidence interval [CI] = 0.26 to 1.54) for definite VTE, 0.83 per 100 person years (95% CI = 0.33 to 1.70) for definite and probable VTE, and 2.48 per 100 person years (95% CI = 1.53 to 3.79) for definite, probable, and possible VTE.

Conclusion: The incidence of VTE in care homes in this study (0.71–2.48 per 100 person years) is substantial compared with that in the community (0.117 per 100 person years) and in people aged ≥70 years (0.44 per 100 person years). Further research regarding risk stratification and VTE prophylaxis in this population is needed.

Background and Purpose: Oral anticoagulants (OAC) substantially reduce risk of stroke in atrial fibrillation, but uptake is suboptimal. Electronic health records enable automated identification of people at risk but not receiving treatment. We investigated the effectiveness of a software tool (AURAS-AF [Automated Risk Assessment for Stroke in Atrial Fibrillation]) designed to identify such individuals during routine care through a cluster-randomized trial.

Methods: Screen reminders appeared each time the electronic health records of an eligible patient was accessed until a decision had been taken over OAC treatment. Where OAC was not started, clinicians were prompted to indicate a reason. Control practices continued usual care. The primary outcome was the proportion of eligible individuals receiving OAC at 6 months. Secondary outcomes included rates of cardiovascular events and reports of adverse effects of the software on clinical decision-making.

Results: Forty-seven practices were randomized. The mean proportion–prescribed OAC at 6 months was 66.3% (SD=9.3) in the intervention arm and 63.9% (9.5) in the control arm (adjusted difference 1.21% [95% confidence interval −0.72 to 3.13]). Incidence of recorded transient ischemic attack was higher in the intervention practices (median 10.0 versus 2.3 per 1000 patients with atrial fibrillation; P=0.027), but at 12 months, we found a lower incidence of both all cause stroke (P=0.06) and hemorrhage (P=0.054). No adverse effects of the software were reported.

Conclusions: No significant change in OAC prescribing occurred. A greater rate of diagnosis of transient ischemic attack (possibly because of improved detection or overdiagnosis) was associated with a reduction (of borderline significance) in stroke and hemorrhage over 12 months.

Reversible addition fragmentation chain transfer (RAFT) polymerization is a very versatile way to generate synthetic polymeric materials. Multiblock copolymers have received enormous scientific interest recently due to the ability to mimic the sequence-regulated microstructure of biopolymers. The objective of this thesis was to investigate RAFT polymerization and explore its potential in the synthesis of sequence-controlled multiblock polymeric chains, and their use to tune the micro-structure of the polymers, engineer single chain polymeric nanoparticles, and fabricate functional polymeric nanomaterials.

This work firstly addresses the investigation of the enormous ability of sequence-controlled multiblock copolymer to tune the physical properties by altering their microstructure. A series of sequence controlled multiblock copolymers were synthesized by RAFT polymerization using ethylene glycol methyl ether acrylate and tert-butyl acrylate as monomers. These block copolymers were synthesized with an alternating order of the two monomers with a similar total degree of polymerization. The number of blocks was varied by decreasing the length of each block while keeping the ratio of monomers constant. Their microphase separation was studied by investigating the glass transition temperature utilizing differential scanning calorimetry analysis. Small angel X-ray scattering analysis was also applied to investigate the transition of the microphase separation with the variation of the segmentations of these multiblock copolymers. The study found the microstructure was significantly affected by the number of segments of the polymer chain whilst keeping the total length constant.

Having demonstrated the enormous potential of sequence controlled multiblock copolymers to access defined microstructures, further studies were focused on mimicking the controlled folding process of the peptide chain to a secondary and tertiary structure using sequence controlled multiblock copolymers. RAFT polymerization was used to produce multiblock copolymers, which are decorated with pendant cross-linkable groups in foldable sections, separated by non-functional spacer blocks in between. An external cross linker was then used to cause the folding of the specific domains. A chain extension-folding sequence was applied to create polymer chains having individual folded subdomains. In order to achieve a further step on the way to copy nature's ability to synthesize highly defined bio-macromolecules with a distinct three dimensional structure, linear diblock copolymer precursors were synthesized by RAFT polymerization. One block of the precursor with pendant functional groups was folded using an external cross-linker to form tadpole-like single chain nanoparticles (SCNPs). These tadpole-like SCNPs could then self-assemble into a more complex stimuli responsive 3D structure by adaptation to environmental pH changes. The stimuli responsive assemblies were found to be able to dissociate responding to low pH or exposure to glucose.

Scanning electrochemical microscopy (SECM) operating as a variable gap ultra-thin layer twin-working electrode cell, has long been recognised as a powerful technique for investigating fast kinetics (heterogeneous electron transfer and homogeneous reactions coupled to electron transfer) as a consequence of high mass transport rates between the working electrodes when biased to promote redox shuttling. Recently, SECM has advanced technically and nanogap cells with dimensions on the 10s of nm scale have been reported. In this paper, we consider double layer effects on voltammetric measurements in this configuration, outlining a comprehensive model that solves the Nernst-Planck equation and Poisson equation with charged interfaces. For supporting electrolyte concentrations that have been used for such measurements (50 mM and 100 mM), it is shown that for typical electrode charges and charge on the glass insulator that encases the ultramicroelectrode (UME) tip used in SECM, there are profound effects on the voltammetric wave-shapes for redox reactions of charged redox couples, in the common modes used to study electron transfer kinetics, namely the tip-voltammetry (feedback) mode and substrate-voltammetry (substrate-generation/tip-collection and competition) modes. Using the reduction and oxidation of a singly charged redox species to a neutral and doubly charged species, respectively, as exemplar systems, it is shown that the charge on the electrodes can greatly distort the voltammetric wave-shape, while charge on the glass that surrounds the UME tip can affect the limiting current. Analysis of SECM voltammograms using methods that do not account for double layer effects will thus result in significant error in the kinetic values derived and tip-substrate distances that have to be estimated from limiting currents in SECM. The model herein provides a framework that could be developed for further studies with nanogap-SECM (e.g. consideration of alternative models for the electrical double layer, other supporting electrolyte concentrations, potential of zero charge on the electrodes and charges on the redox couples). The model results presented are shown to qualitatively match to SECM voltammetric features from experimental data in the literature, and are further supported by experimental data for redox processes of tetrathiafulvalene (TTF), namely the TTF/TTF+ and TTF+/TTF2+ redox couples. This serves to demonstrate the immediate practical application of some of the ideas presented herein. For future applications of SECM, the use of different supporting electrolyte concentrations and a range of tip-substrate separations may allow the determination of both electron transfer kinetics and double layer properties.

Scanning ion conductance microscopy (SICM) is a nanopipette-based scanning probe microscopy technique that utilizes the ionic current flowing between an electrode inserted inside a nanopipette probe containing electrolyte solution and a second electrode placed in a bulk electrolyte bath, to provide information on a substrate of interest. For most applications to date, the composition and concentration of the electrolyte inside and outside the nanopipette is identical, but it is shown herein that it can be very beneficial to lift this restriction. In particular, an ionic concentration gradient at the end of the nanopipette, generates an ionic current with a greatly reduced electric field strength, with particular benefits for live cell imaging. This differential concentration mode of SICM (ΔC-SICM) also enhances surface charge measurements and provides a new way to carry out reaction mapping measurements at surfaces using the tip for simultaneous delivery and sensing of the reaction rate. Comprehensive finite element method (FEM) modeling has been undertaken to enhance understanding of SICM as an electrochemical cell and to enable the interpretation and optimization of experiments. It is shown that electroosmotic flow (EOF) has much more influence on the nanopipette response in the ΔC-SICM configuration compared to standard SICM modes. The general model presented advances previous treatments, and it provides a framework for quantitative SICM studies.

Nanopipettes are used as nanoreactors to study the crystallization of bicalutamide, in a nanoscale antisolvent configuration. Potential controlled ion migration is used to mix an aqueous solution and a dimethyl sulfoxide phase containing bicalutamide, inducing crystallization at the nanopore interface, and generating current blockades due to the nucleation and growth of crystal seeds.

Between July 18th and 24th 2010, 26 leading microbial ecology, computation, bioinformatics and statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how to best characterize the microbial world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" and was sponsored by the Institute for Computing in Science (ICiS) summer 2010 workshop program. The aim of the workshop was to explore the fundamental questions relating to microbial ecology that could be addressed using advances in sequencing potential. Technological advances in next-generation sequencing platforms such as the Illumina HiSeq 2000 can generate in excess of 250 billion base pairs of genetic information in 8 days. Thus, the generation of a trillion base pairs of genetic information is becoming a routine matter. The main outcome from this meeting was the birth of a concept and practical approach to exploring microbial life on earth, the Earth Microbiome Project (EMP). Here we briefly describe the highlights of this meeting and provide an overview of the EMP concept and how it can be applied to exploration of the microbiome of each ecosystem on this planet.

Loss of microbial diversity is considered a major threat because of its importance for ecosystem functions, but there is a lack of conclusive evidence that diversity itself is reduced under anthropogenic stress, and about the consequences of diversity loss. Heavy metals are one of the largest, widespread pollutant types globally, and these represent a significant environmental stressor for terrestrial microbial communities. Using combined metagenomics and functional assays, we show that the compositional and functional response of microbial communities to long-term heavy metal stress results in a significant loss of diversity. Our results indicate that even at a moderate loss of diversity, some key specialized functions (carried out by specific groups) may be compromised. Together with previous work, our data suggest disproportionate impact of contamination on microbes that carry out specialized, but essential, ecosystem functions. Based on these findings, we propose a conceptual framework to explicitly consider diversity of functions and microbial functional groups to test the relationship between biodiversity and soil functions.

Viral haplotype reconstruction from a set of observed reads is one of the most challenging problems in bioinformatics today. Next-generation sequencing technologies enable us to detect single-nucleotide polymorphisms (SNPs) of haplotypes—even if the haplotypes appear at low frequencies. However, there are two major problems. First, we need to distinguish real SNPs from sequencing errors. Second, we need to determine which SNPs occur on the same haplotype, which cannot be inferred from the reads if the distance between SNPs on a haplotype exceeds the read length. We conducted an independent benchmarking study that directly compares the currently available viral haplotype reconstruction programmes. We also present nine in silico data sets that we generated to reflect biologically plausible populations. For these data sets, we simulated 454 and Illumina reads and applied the programmes to test their capacity to reconstruct whole genomes and individual genes. We developed a novel statistical framework to demonstrate the strengths and limitations of the programmes. Our benchmarking demonstrated that all the programmes we tested performed poorly when sequence divergence was low and failed to recover haplotype populations with rare haplotypes.

The templated zeolite-analogue GaPO-34 (CHA structure type) crystallises from a gel precursor Ga2O3:2H3PO4:1HF:1.7SDA:70H2O (where SDA = structure directing agent), treated hydrothermally for 24 hours at 170 °C using either pyridine or 1-methylimizadole as SDA and one of either poorly crystalline ε-Ga2O3 or γ-Ga2O3 as gallium precursor. If the same gels are stirred for periods shorter than 2 hours but treated under identical hydrothermal conditions, then a second phase crystallises, free of GaPO-34. If β-Ga2O3 is used as a reagent only the second phase is found to crystallise, irrespective of gel aging time. The competing phase, which we denote GaPO-34A, has been structurally characterised using synchrotron powder X-ray diffraction for the pyridine material, GaPO-34A(pyr), and using single-crystal X-ray diffraction for the 1-methylimiazole material, GaPO-34A(mim). The structure of GaPO-34A(pyr), P1 @#x0305;, a = 10.22682(6) Å, b = 12.09585(7) Å, c = 13.86713(8) Å, α = 104.6531(4) °, β = 100.8111(6) °, γ = 102.5228(6) °, contains 7 unique gallium sites and 6 phosphorus sites, with empirical formula [Ga7P6O24(OH)2F3(H2O)2].2(C5NH6). GaPO-34A(mim) is isostructural but is modelled as a half volume unit cell, P1 @#x0305;, a = 5.0991(2) Å, b = 12.0631(6) Å, c = 13.8405(9) Å, α = 104.626(5) °, β = 100.346(5) °, γ = 101.936(4) °, with a gallium and a bridging fluoride partially occupied and two partially occupied SDA sites. Solid-state 31P and 71Ga NMR spectroscopy confirms the structural complexity of GaPO-34A with signals resulting from overlapping lineshapes from multiple Ga and P sites, while 1H and 13C solid-state NMR spectra confirm the presence of the protonated SDA and provide evidence for disorder in the SDA. The protonated SDA is located in 14-ring one-dimensional channels with hydrogen bonding deduced from the SDA nitrogens to framework oxygen distances. Upon thermal treatment to investigate SDA removal, structure collapse occurs, which may be due the large number of bridging hydroxides and fluorides in the as-made material, and the unequal amounts of gallium and phosphorus present.

The templated zeolite-analogue GaPO-34 (CHA structure type) crystallises from a gel precursor Ga2O3:2H3PO4:1HF:1.7SDA:70H2O (where SDA = structure directing agent), treated hydrothermally for 24 hours at 170 °C using either pyridine or 1-methylimizadole as SDA and one of either poorly crystalline ε-Ga2O3 or γ-Ga2O3 as gallium precursor. If the same gels are stirred for periods shorter than 2 hours but treated under identical hydrothermal conditions, then a second phase crystallises, free of GaPO-34. If β-Ga2O3 is used as a reagent only the second phase is found to crystallise, irrespective of gel aging time. The competing phase, which we denote GaPO-34A, has been structurally characterised using synchrotron powder X-ray diffraction for the pyridine material, GaPO-34A(pyr), and using single-crystal X-ray diffraction for the 1-methylimiazole material, GaPO-34A(mim). The structure of GaPO-34A(pyr), P1 @#x0305;, a = 10.22682(6) Å, b = 12.09585(7) Å, c = 13.86713(8) Å, α = 104.6531(4) °, β = 100.8111(6) °, γ = 102.5228(6) °, contains 7 unique gallium sites and 6 phosphorus sites, with empirical formula [Ga7P6O24(OH)2F3(H2O)2].2(C5NH6). GaPO-34A(mim) is isostructural but is modelled as a half volume unit cell, P1 @#x0305;, a = 5.0991(2) Å, b = 12.0631(6) Å, c = 13.8405(9) Å, α = 104.626(5) °, β = 100.346(5) °, γ = 101.936(4) °, with a gallium and a bridging fluoride partially occupied and two partially occupied SDA sites. Solid-state 31P and 71Ga NMR spectroscopy confirms the structural complexity of GaPO-34A with signals resulting from overlapping lineshapes from multiple Ga and P sites, while 1H and 13C solid-state NMR spectra confirm the presence of the protonated SDA and provide evidence for disorder in the SDA. The protonated SDA is located in 14-ring one-dimensional channels with hydrogen bonding deduced from the SDA nitrogens to framework oxygen distances. Upon thermal treatment to investigate SDA removal, structure collapse occurs, which may be due the large number of bridging hydroxides and fluorides in the as-made material, and the unequal amounts of gallium and phosphorus present.

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%.

This study shows that an all-thermoplastic (nano- or micro-fibre) polymer can be created using coaxial electrospinning to create fibre mats akin to pre-impregnated fabric, which can be formed into a composite without the addition of other materials. This has not yet been accomplished by using the coaxial electrospinning production process. Experimentation to investigate the maximum fibre volume ratio found that these composites were successfully formed at 0.73 fibre volume fraction, which is higher than the maximum found in traditionally formed composites (0.60 – 0.70). The formation of the composite from the fibre mats was investigated, and found that the composites formed at the lowest temperature and pressure (70 °C and 1 bar) exhibited the higher tensile strength, up to 84 % higher than at other temperatures and pressures. Higher pressure and temperature caused deformation in the reinforcing fibres, resulting in lower tensile strength. The composites were shown to have more consistent Young's modulus and higher tensile strength compared to a composite made from the same materials, but with the fibres and matrix materials produced separately, and combined during the composite forming procedure.

The finalised composite produced in this research exhibited an average Young's Modulus of 2.5 GPa, ultimate tensile strength of 33.2 MPa, and elongation at break of 3.8 %.

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