Contributors: Ladejobi, Olufunmilayo, Elderfield, James, Gardner, Keith A, Gaynor, R Chris, Hickey, John, Hibberd, Julian Michael, Mackay, Ian J, Bentley, Alison R
Contributors: Smith-Unna, Richard, Boursnell, Chris, Patro, Rob, Hibberd, Julian Michael, Kelly, Steven
... TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples.
Research data supporting: Eustachian tube dysfunction: A diagnostic accuracy study and proposed diagnostic pathway.
Contributors: Smith, Matthew Edward, Tysome, James
... Eustachian tube function test data. These data are unprocessed test results from a study to determine the diagnostic accuracy of tests for obstructive and patulous Eustachian tube dysfunction.
Contributors: Tseneklidou, D, Tsagas, CG, Barrow, John David
... We study the linear evolution of magnetised cosmological perturbations in the post-recombination epoch. Using full general relativity and adopting the ideal magnetohydrodynamic approximation, we refine and extend the previous treatments. More specifically, this is the first relativistic study that accounts for the effects of the magnetic tension, in addition to those of the field's pressure. Our solutions show that on sufficiently large scales, larger than the (purely magnetic) Jeans length, the perturbations evolve essentially unaffected by the magnetic presence. The magnetic pressure dominates on small scales, where it forces the perturbations to oscillate and decay. Close to the Jeans length, however, the field's tension takes over and leads to a weak growth of the inhomogeneities. These solutions clearly demonstrate the opposing action of the aforementioned two magnetic agents, namely of the field's pressure and tension, on the linear evolution of cosmological density perturbations.
Contributors: Diaz Anadon, Laura, Verdolini, E, Baker, E, Bosetti, V, Reis, L
... Expert elicitation is a structured approach for obtaining judgments from experts about items of interest to decision makers. This method has been increasingly applied in the energy domain to collect information on the future cost, technical performance, and associated uncertainty of specific energy technologies. This article has two main objectives: (1) to introduce the basics of expert elicitations, including their design and implementation, highlighting their advantages and disadvantages and their potential to inform policymaking and energy system decisions; and (2) to discuss and compare the results of a subset of the most recent expert elicitations on energy technologies, with a focus on future cost trajectories and implied cost reduction rates. We argue that the data on future energy costs provided by expert elicitations allows for more transparent and robust analyses that incorporate technical uncertainty, which can then be used to support the design and assessment of energy and climate change mitigation policies.
Contributors: Delmans, Mihails, Haseloff, Jim
... Scientific instruments often require the integration of mechanics, electronics and optics. While the use of 3D printing techniques and commodity electronics has lowered the cost of instrumentation, the design and prototyping of optical components and light paths can be challenging and expensive. In recent years, attempts have been made to make optical devices more affordable using 3D printing as a method for production of optomechanical components. In this paper we present an assembly standard for the production of 3D printed optical devices. We describe a framework for parametric design of modular mounts, present two modules built using the framework, and demonstrate the potential for generalised design of modular optical devices following the μCube standard.
Contributors: Reeves, Gregory, Grangé-Guermente, Mathieu J, Hibberd, Julian Michael
... C4 photosynthesis is a carbon-concentrating mechanism that increases delivery of carbon dioxide to RuBisCO and as a consequence reduces photorespiration. The C4 pathway is therefore beneficial in environments that promote high photorespiration. This pathway has evolved many times, and involves restricting gene expression to either mesophyll or bundle sheath cells. Here we review the regulatory mechanisms that control cell-preferential expression of genes in the C4 cycle. From this analysis, it is clear that the C4 pathway has a complex regulatory framework, with control operating at epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. Some genes of the C4 pathway are regulated at multiple levels, and we propose that this ensures robust expression in each cell type. Accumulating evidence suggests that multiple genes of the C4 pathway may share the same regulatory mechanism. The control systems for C4 photosynthesis gene expression appear to operate in C3 plants, and so it appears that pre-existing mechanisms form the basis of C4 photosynthesis gene expression.
Correction to: STATAWAARS: a promoter motif associated with spatial expression in the major effector-producing tissues of the plantparasitic nematode Bursaphelenchus xylophilus
Contributors: Espada, Margarida, den Akker, Sebastian E, Maier, Tom, Vijayapalani, Paramasivan, Baum, Thomas, Mota, Manuel, Jones, John T
... Following publication of the original article , the authors reported that one of the authors’ names was erroneously changed during proofing and published incorrectly. In this Correction the incorrect and correct author name are shown. The original publication of this article has been corrected.
Sodium and potassium excretion in an adult Caribbean population of African descent with a high burden of cardiovascular disease
Contributors: Harris, Rachel M, Rose, Angela M C, Hambleton, Ian R, Howitt, Christina, Forouhi, Nita G, Hennis, Anselm J M, Samuels, T. A, Unwin, Nigel
... Abstract Background High sodium diets with inadequate potassium and high sodium-to-potassium ratios are a known determinant of hypertension and cardiovascular disease (CVD). The Caribbean island of Barbados has a high prevalence of hypertension and mortality from CVD. Our objectives were to estimate sodium and potassium excretion, to compare estimated levels with recommended intakes and to identify the main food sources of sodium in Barbadian adults. Methods A sub-sample (n = 364; 25–64 years) was randomly selected from the representative population-based Health of the Nation cross-sectional study (n = 1234), in 2012–13. A single 24-h urine sample was collected from each participant, following a strictly applied protocol designed to reject incomplete samples, for the measurement of sodium and potassium excretion (in mg), which were used as proxy estimates of dietary intake. In addition, sensitivity analyses based on estimated completeness of urine collection from urine creatinine values were undertaken. Multiple linear regression was used to examine differences in sodium and potassium excretion, and the sodium-to-potassium ratio, by age, sex and educational level. Two 24-h recalls were used to identify the main dietary sources of sodium. All analyses were weighted for the survey design. Results Mean sodium excretion was 2656 (2488–2824) mg/day, with 67% (62–73%) exceeding the World Health Organization (WHO) recommended limit of 2000 mg/d. Mean potassium excretion was 1469 (1395–1542) mg/d; < 0.5% met recommended minimum intake levels. Mean sodium-to-potassium ratio was 2.0 (1.9–2.1); not one participant had a ratio that met WHO recommendations. Higher potassium intake and lower sodium-to-potassium ratio were independently associated with age and tertiary education. Sensitivity analyses based on urine creatinine values did not notably alter these findings. Conclusions In this first nationally representative study with objective assessment of sodium and potassium excretion in a Caribbean population in over 20 years, levels of sodium intake were high, and potassium intake was low. Younger age and lower educational level were associated with the highest sodium-to-potassium ratios. These findings provide baseline values for planning future policy interventions for non-communicable disease prevention.
Contributors: Christopher, Peter
... Additional information associated with Peter Christopher's PhD thesis titled: "High Rate Additive Manufacture using Holographic Beam Shaping - An investigation of high power areal holographic projection systems and their effect on light-matter interactions"