Research Outputs

Examples of research outputs coming from work carried on Viper can be found below.

The HPC Steering Group has agreed that where appropriate, the use of Viper on a research project should be acknowledged in publications with the following statement:

“We acknowledge the Viper High Performance Computing facility of the University of Hull and its support team”

We are always interested to know of any output that features work carried out on Viper, please contact viper@hull.ac.uk

Publications

Donatus O. Onwuli and Sabrina Francesca Samuel and Pagona Sfyri and Kevin Welham and Martin Goddard and Yasir Abu-Omar and Mahmoud Loubani and Francisco Rivero and Antonios Matsakas and David M. Benoit and Mark Wade and John Greenman and Pedro Beltran-Alvarez, 2019-01-31, The inhibitory subunit of cardiac troponin (cTnI) is modified by arginine methylation in the human heart, International Journal of Cardiology, doi: 10.1016/j.ijcard.2019.01.102

Abstract


The inhibitory subunit of cardiac troponin (cTnI) is a gold standard cardiac biomarker and also an essential protein in cardiomyocyte excitation-contraction coupling. The interactions of cTnI with other proteins are fine-tuned by post-translational modification of cTnI. Mutations in cTnI can lead to hypertrophic cardiomyopathy.


Lluis Franch-Gras, Christoph Hahn, Eduardo M. García-Roger, María José Carmona, Manuel Serra & Africa Gómez, 2018-10-30, Genomic signatures of local adaptation to the degree of environmental predictability in rotifers, Scientific reports, doi: 10.1038/s41598-018-34188-y

Abstract


Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.


Deshmukh, Harshal and Papageorgiou, Maria and Kilpatrick, Eric S. and Atkin, Stephen L. and Sathyapalan, Thozhukat, 2018-10, Development of a novel risk prediction and risk stratification score for polycystic ovary syndrome, Clinical Endocrinology, doi: 10.1111/cen.13879

 

Abstract


Summary Objective The aim of this study was to develop a simple phenotypic algorithm that can capture the underlying clinical and hormonal abnormalities to help in the diagnosis and risk stratification of polycystic ovary syndrome (PCOS). Methods The study consisted of 111 women with PCOS fulfilling the Rotterdam diagnostic criteria and 67 women without PCOS. A Firth’s penalized logistic regression model was used for independent variable section. Model optimism, discrimination and calibration were assessed using bootstrapping, area under the curve (AUC) and Hosmer-Lemeshow statistics, respectively. The prognostic index (PI) and risk score for developing PCOS were calculated using independent variables from the regression model. Results Firth penalized logistic regression model with backward selection identified four independent predictors of PCOS namely free androgen index [β 0.30 (0.12), P = 0.008], 17-OHP [β = 0.20 (0.01), P = 0.026], anti-mullerian hormone [AMH; β = 0.04 (0.01) P < 0.0001] and waist circumference [β = 0.08 (0.02), P < 0.0001]. The model estimates indicated high internal validity (minimal optimism on 1000-fold bootstrapping), good discrimination ability (bias corrected c-statistic = 0.90) and good calibration (Hosmer-Lemeshow χ2 = 3.7865). PCOS women with a high-risk score (q1 + q2 + q3 vs q4) presented with a worse metabolic profile characterized by a higher 2-hour glucose (P = 0.01), insulin (P = 0.0003), triglycerides (P = 0.0005), C-reactive protein (P < 0.0001) and low HDL-cholesterol (P = 0.02) as compared to those with lower risk score for PCOS. Conclusions We propose a simple four-variable model, which captures the underlying clinical and hormonal abnormalities in PCOS and can be used for diagnosis and metabolic risk stratification in women with PCOS.


Deshmukh, Harshal and Barker, Emma and Ambarasan, Thineshkrishna and Levin, Daniel and Bell, Samira and Witham, Miles D and George, Jacob, 2018-10, Calcium channel blockers are associated with improved survival and lower cardiovascular mortality in patients with renovascular disease, Cardiovascular Therapeutics, doi: 10.1111/1755-5922.12474

 

Abstract


Background and objective Results of interventional trials in renovascular hypertension have been disappointing and medical therapy is the current recommended gold standard. However, the comparative long-term benefits of different antihypertensive drug classes in atherosclerotic renal artery stenosis are not known. We aim to assess the effect of different antihypertensive drug classes on outcomes in renovascular hypertension Design, setting, participants, and measurements Using Tayside Health Informatics Centre database, anonymised data over a 6-year period was analysed. Biochemistry, prescribing data, morbidity, mortality and demographic data were accessed via hospital medical records and electronic data stored in the Tayside Health Informatics Centre Safe Haven. General Registrar’s Office data was used to identify patients who died from cardiovascular disease. Independent predictors of survival in each group were analyzed using Kaplan-Meier survival curves and Cox proportional hazard models, adjusted for a range of covariates, using Time-Updated Drug Analysis. Blood pressure data was obtained from primary and secondary care clinic blood pressure records for each patient. Adjustments for mean systolic blood pressure over the follow-up period and baseline blood pressure were made. Results 579 patients with Atherosclerotic Renal Artery Stenosis were identified. In the unilateral renal artery stenosis cohort, Calcium Channel Blockers but not ACE inhibitors/ARBs, were associated with a significant reduction in all-cause (HR=0.45, CI= 0.31, 0.65; P=<0.0001) and Cardiovascular ((HR= 0.51, CI =0.29-0.90 P=0.019). This was maintained after adjustment for blood pressure. In the bilateral renal artery stenosis cohort, both classes of drugs reduced all-cause but not cardiovascular mortality. Patients with moderate disease benefitted more than those with mild or severe disease. Conclusions Calcium Channel Blockers are associated with significantly increased survival and lower cardiovascular mortality particularly in patients with moderate RAS disease. This article is protected by copyright. All rights reserved.


Al-Qaissi, Ahmed and Papageorgiou, Maria and Deshmukh, Harshal and Madden, Leigh A. and Rigby, Alan and Kilpatrick, Eric S. and Atkin, Stephen L. and Sathyapalan, Thozhukat, 2018-09, Effects of acute insulin-induced hypoglycaemia on endothelial microparticles in adults with and without type 2 diabetes, Diabetes, Obesity and Metabolism, doi: 10.1111/dom.13548

 

Abstract


Aims To assess whether endothelial microparticles (EMPs), novel surrogate markers of endothelial injury and dysfunction, are differentially produced in response to acute insulin-induced hypoglycaemia in adults with and without type 2 diabetes. Materials and methods A prospective, parallel study was conducted in individuals with type 2 diabetes (n = 23) and controls (n = 22). Hypoglycaemia (<2.2 mmoL/L: <40 mg/dL) was achieved by intravenous infusion of soluble insulin. Blood samples were collected at baseline and at 0, 30, 60, 120, 240 minutes and 24 hours after hypoglycaemia and analysed for CD31+ (platelet endothelial cell adhesion molecule-1), CD54+ (intercellular adhesion molecule 1), CD62-E+ (E-selectin), CD105+ (endoglin), CD106+ (vascular cell adhesion molecule 1) and CD142+ (tissue factor) EMPs by flow cytometry. The peak elevations (\% rise from 0 minutes after hypoglycaemia) in EMP within 240 minutes after insulin-induced hypoglycaemia were modelled using a regression model, with adjustment for relevant covariates. All EMPs were expressed as percentage from 0 minutes hypoglycaemia for each time point and total areas under the curve (AUC0min–24h) were calculated. Results Following insulin-induced hypoglycaemia, levels of circulating EMPs were maximal at 240 minutes (P < 0.001) and returned to baseline values within 24 hours for both groups. The peak elevations (\% rise from 0 minutes following hypoglycaemia) seen in CD31+, CD54+, CD62-E+, CD105+ and CD142+ EMPs within 240 minutes were associated with diabetes status after adjustments for all relevant covariates. Individuals with type 2 diabetes showed increased CD31+ EMPs AUC0min–24h (P = 0.014) and CD105+ EMPs AUC0min–24h (P = 0.006) compared with controls, but there were no differences for CD54+ (P = 0.91), CD62-E+ (P = 0.14), CD106+ (P = 0.36) or CD142+ (P = 0.77) EMPs AUC0min–24h. Conclusions The associations between peak elevations within 240 minutes after insulin-induced hypoglycaemia for CD31+, CD54+, CD62-E+, CD105+ and CD142+ and diabetes status indicate that the assessment of a panel of EMPs within this timeframe would identify a hypoglycaemic event in this population. The greater overall responses over time (AUCs) for apoptosis-induced CD31+ and CD105+ EMPs suggest that hypoglycaemia exerts greater endothelial stress in type 2 diabetes.


Annika M Schoene and Nina Dethlefs, 2018-08-20, Unsupervised suicide note classification, Proceedings of the 7th KDD Workshop on Issues of Sentiment Discovery and Opinion Mining (WISDOM), doi:

Abstract


With the greater availability of linguistic data from public social media platforms and the advancements of natural language processing, a number of opportunities have arisen for researchers to analyse this type of data. Research efforts have mostly focused on detecting the polarity of textual data, evaluating whether there is positive, negative or sometimes neutral content. Especially the use of neural networks has recently yielded significant results in polarity detection experiments. In this paper we present a more fine-grained approach to detecting sentiment in textual data, particularly analysing a corpus of suicide notes, depressive notes and love notes. We achieve a classification accuracy of 71.76% when classifying based on text and sentiment features, and an accuracy of 69.41% when using the words present in the notes alone. We discover that while emotions in all three datasets overlap, each of them has a unique ‘emotion profile’ which allows us to draw conclusions about the potential mental state that is reflects. Using the emotion sequences only, we achieve an accuracy of 75.29%. The results from unannotated data, while worse than the other models, nevertheless represent an encouraging step towards being able to flag potentially harmful social media posts online and in real time. We provide a high-level corpus analysis of the data sets in order to demonstrate the grammatical and emotional differences.


T.L. Lee, J. Mi, S. Ren, S. Zhao, J. Fan, S. Kabra, S. Zhang, and P.S. Grant, 2018-05-26, Modelling and neutron diffraction characterization of the interfacial bonding of spray formed dissimilar steels, Acta Materialia, doi: 10.1016/j.actamat.2018.05.055

 

Abstract


The spray forming of thick, dissimilar steel clad tubes with the objective of achieving a high integrity metallurgical bond across the cladding-substrate interface able to withstand residual stresses and subsequent thermo-mechanical processing was investigated by large scale experiments, modelling and extensive microstructural characterization including microscopy, X-ray tomography, neutron scattering and mechanical testing. The simulated residual stress distributions across the cladding-substrate interface, accounting for any as-sprayed porosity and the distribution of martensitic and retained austenite phases, were compared with neutron diffraction measurements and differences used to infer the load transfer behaviour and thus the mechanical integrity of the interface. The mechanical properties of the interfaces were then also measured directly by shear testing. The link between substrate pre-heating, the spray forming temperature, and the resulting preform temperature, porosity, phase fractions, residual stress, strength and integrity of the interface were established and quantified explicitly.


Chen, Long; Vivier, Elodie; Eling, Charlotte J.; Babra, Tahkur S.; Bouillard, Jean Sebastien G.; Adawi, Ali M.; Benoit, David M.; Hartl, František; Colquhoun, Howard M.; Efremova, Olga A.; Greenland, Barnaby W., 2018-04-07, Conjugated, rod-like viologen oligomers: Correlation of oligomer length with conductivity and photoconductivity, Synthetic Metals, doi: 10.1016/j.synthmet.2018.03.019

 

Abstract


An iterative synthesis has been used to produce conjugated, monodisperse, viologen-based aromatic oligomers containing up to 12 aromatic/heterocyclic rings. The methoxy-substituted oligomers were soluble in common organic solvents and could be processed by spin coating. The conductivities of the resulting films (30–221 nm thick) increased by more than one order of magnitude as the oligomer length increased from unimer (1, 2.20 × 10 −11 S cm- 1 ) through dimer (2) to trimer (3, 6.87 × 10 -10 S cm -1 ). The bandgaps of the materials were estimated from the absorption spectra of these thin films. The longest oligomer, 3, exhibited a noticeably narrower bandgap (2.3 eV) than the shorter oligomers (1 and 2 both 2.7 eV). Oligomer 3 also showed photoconductivity under irradiation across a wide range of wavelengths in the visible spectral region. In conjunction with DFT calculations of these systems our results suggest that structurally related viologen-type oligomers may find use in optoelectronic devices.


Chalupa, David and Hawick, Ken A. and Walker, James A., 2018-04, Hybrid Bridge-Based Memetic Algorithms for Finding Bottlenecks in Complex Networks, Big Data Research, doi: 10.1016/j.bdr.2018.04.001

 

Abstract


We propose a memetic approach to find bottlenecks in complex networks based on searching for a graph partitioning with minimum conductance. Finding the optimum of this problem, also known in statistical mechanics as the Cheeger constant, is one of the most interesting NP-hard network optimisation problems. The existence of low conductance minima indicates bottlenecks in complex networks. However, the problem has not yet been explored in depth in the context of applied discrete optimisation and evolutionary approaches to solve it. In this paper, the use of a memetic framework is explored to solve the minimum conductance problem. The approach combines a hybrid method of initial population generation based on bridge identification and local optima sampling with a steady-state evolutionary process with two local search subroutines. These two local search subroutines have complementary qualities. Efficiency of three crossover operators is explored, namely one-point crossover, uniform crossover, and our own partition crossover. Experimental results are presented for both artificial and real-world complex networks. Results for Barabási–Albert model of scale-free networks are presented, as well as results for samples of social networks and protein–protein interaction networks. These indicate that both well-informed initial population generation and the use of a crossover seem beneficial in solving the problem in large-scale.”


Roggatz, Christina C. and Lorch, Mark and Benoit, David M., 2018-03-22, Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules, Journal of Chemical Theory and Computation, doi: 10.1021/acs.jctc.7b01020

 

Abstract


In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.


Y. Zhao and W. Du and B. Koe and T. Connolley and S. Irvine and P.K. Allan and C.M. Schlepütz and W. Zhang and F. Wang and D.G. Eskin and J. Mi, 2018-03-15, 3D characterisation of the Fe-rich intermetallic phases in recycled Al alloys by synchrotron X-ray microtomography and skeletonisation, Scripta Materialia, doi: 10.1016/j.scriptamat.2017.12.010

 

Abstract


Synchrotron X-ray microtomography and skeletonisation method were used to study the true 3D network structures and morphologies of the Fe-rich intermetallic phases in recycled Al-5.0%Cu-0.6%Mn alloys with 0.5% and 1.0% Fe. It was found that, the Fe-phases in the 1.0%Fe alloy have node lengths of 5–25μm; while those in the 0.5%Fe alloy are of 3–17μm. The Fe-phases in the 1.0%Fe alloy also developed sharper mean curvature with wider distribution than those in the 0.5%Fe alloy. Combining SEM studies of the deeply-etched samples, the true 3D structures of 4 different type Fe phases in both alloys are also revealed and demonstrated.


Bing Wang and Dongyue Tan and Tung Lik Lee and Jia Chuan Khong and Feng Wang and Dmitry Eskin and Thomas Connolley and Kamel Fezzaa and Jiawei Mi, 2018-02-01, Ultrafast synchrotron X-ray imaging studies of microstructure fragmentation in solidification under ultrasound, Acta Materialia, doi: 10.1016/j.actamat.2017.10.067

 

Abstract


Ultrasound processing of metal alloys is an environmental friendly and promising green technology for liquid metal degassing and microstructural refinement. However many fundamental issues in this field are still not fully understood, because of the difficulties in direct observation of the dynamic behaviours caused by ultrasound inside liquid metal and semisolid metals during the solidification processes. In this paper, we report a systematic study using the ultrafast synchrotron X-ray imaging (up to 271,554 frame per second) technique available at the Advanced Photon Source, USA and Diamond Light Source, UK to investigate the dynamic interactions between the ultrasonic bubbles/acoustic flow and the solidifying phases in a Bi-8%Zn alloy. The experimental results were complimented by numerical modelling. The chaotic bubble implosion and dynamic bubble oscillations were revealed in-situ for the first time in liquid metal and semisolid metal. The fragmentation of the solidifying Zn phases and breaking up of the liquid-solid interface by ultrasonic bubbles and enhanced acoustic flow were clearly demonstrated and agreed very well with the theoretical calculations. The research provides unambiguous experimental evidence and robust theoretical interpretation in elucidating the dominant mechanisms of microstructure fragmentation and refinement in solidification under ultrasound.


Hannes C. Gottschalk and Anja Poblotzki and Martin A. Suhm and Muneerah M. Al-Mogren and Jens Antony and Alexander A. Auer and Leonardo Baptista and David M. Benoit and Giovanni Bistoni and Fabian Bohle and Rahma Dahmani and Dzmitry Firaha and Stefan Grimme and Andreas Hansen and Michael E. Harding and Majdi Hochlaf and Christof Holzer and Georg Jansen and Wim Klopper and Wassja A. Kopp and Leif C. Kröger and Kai Leonhard and Halima Mouhib and Frank Neese and Max N. Pereira and Inga S. Ulusoy and Axel Wuttke and Ricardo A. Mata, 2018-01-01, The furan microsolvation blind challenge for quantum chemical methods: First steps, The Journal of Chemical Physics, doi: 10.1063/1.5009011

 

Abstract


Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH–O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.


Vorotnikova, Natalya A. and Vorotnikov, Yuri A. and Novozhilov, Igor N. and Syrokvashin, Mikhail M. and Nadolinny, Vladimir A. and Kuratieva, Natalia V. and Benoit, David M. and Mironov, Yuri V. and Walton, Richard I. and Clarkson, Guy J. and Kitamura, Noboru and Sutherland, Andrew J. and Shestopalov, Michael A. and Efremova, Olga A., 2017-12-22, 23-Electron Octahedral Molybdenum Cluster Complex [{Mo6I8}Cl6]−, Inorganic Chemistry, doi: 10.1021/acs.inorgchem.7b02760

 

Abstract


Photoactive transition metal compounds that are prone to reversible redox reactions are important for myriad applications, including catalysis, optoelectronics, and sensing. This article describes chemical and electrochemical methods to prepare cluster complex (Bu4N)[{Mo6I8}Cl6], a rare example of a 23 e– cluster complex within the family of octahedral clusters of Mo, W, and Re. The low temperature and room temperature crystal structures; electronic structure; and the magnetic, optical, and electrochemical properties of this complex are described.


Ruiz-Lara, T., Few, C. G., Florido, E., Gibson, B. K., Pérez, I., Sánchez-Blázquez, P., 2017-12-15, The role of stellar radial motions in shaping galaxy surface brightness profiles, Astronomy & Astrophysics, doi: 10.1051/0004-6361/201731485

 

Abstract


Aims: The physics driving features such as breaks observed in galaxy surface brightness (SB) profiles remains contentious. Here, we assess the importance of stellar radial motions in shaping their characteristics. Methods: We use the simulated Milky Way-mass cosmological discs from the Ramses Disc Environment Study (RaDES) to characterise the radial redistribution of stars in galaxies displaying type-I (pure exponentials), II (downbending), and III (upbending) SB profiles. We compare radial profiles of the mass fractions and the velocity dispersions of different sub-populations of stars according to their birth and current location. Results: Radial redistribution of stars is important in all galaxies regardless of their light profiles. Type-II breaks seem to be a consequence of the combined effects of outward-moving and accreted stars. The former produce shallower inner profiles (lack of stars in the inner disc) and accumulate material around the break radius and beyond, strengthening the break; the latter can weaken or even convert the break into a pure exponential. Further accretion from satellites can concentrate material in the outermost parts, leading to type-III breaks that can coexist with type-II breaks, but situated further out. Type-III galaxies would be the result of an important radial redistribution of material throughout the entire disc, as well as a concentration of accreted material in the outskirts. In addition, type-III galaxies display the most efficient radial redistribution and the largest number of accreted stars, followed by type-I and II systems, suggesting that type-I galaxies may be an intermediate case between types II and III. In general, the velocity dispersion profiles of all galaxies tend to flatten or even increase around the locations where the breaks are found. The age and metallicity profiles are also affected, exhibiting different inner gradients depending on their SB profile, being steeper in the case of type-II systems (as found observationally). The steep type-II profiles might be inherent to their formation rather than acquired via radial redistribution.


Szitenberg A, Salazar-Jaramillo L, Blok VC, Laetsch DR, Joseph S, Williamson VM, et al., 2017-09-25, Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change., Genome Biology and Evolution, doi: 10.1093/gbe/evx201

 

Abstract


The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the apomictic MIG species are hypotriploids, with a proportion of one genome present in a second copy. The hypotriploid proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.


Thompson, B. B. and Few, C. G. and Bergemann, M. and Gibson, B. K. and MacFarlane, B. A. and Serenelli, A. and Gilmore, G. and Randich, S. and Vallenari, A. and Alfaro, E. J. and Bensby, T. and Francois, P. and Korn, A. J. and Bayo, A. and Carraro, G. and Casey, A. R. and Costado, M. T. and Donati, P. and Franciosini, E. and Frasca, A. and Hourihane, A. and Jofré, P. and Hill, V. and Heiter, U. and Koposov, S. E. and Lanzafame, A. and Lardo, C. and de Laverny, P. and Lewis, J. and Magrini, L. and Marconi, G. and Masseron, T. and Monaco, L. and Morbidelli, L. and Pancino, E. and Prisinzano, L. and Recio-Blanco, A. and Sacco, G. and Sousa, S. G. and Tautvaišienė, G. and Worley, C. C. and Zaggia, S., 2017-09-11, The Gaia-ESO Survey: Matching Chemo-Dynamical Simulations to Observations of the Milky Way, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stx2316

 

Abstract


The typical methodology for comparing simulated galaxies with observational surveys is usually to apply a spatial selection to the simulation to mimic the region of interest covered by a comparable observational survey sample. In this work we compare this approach with a more sophisticated post-processing in which the observational uncertainties and selection effects (photometric, surface gravity and effective temperature) are taken into account. We compare a ‘solar neighbourhood analogue’ region in a model Milky Way-like galaxy simulated with RAMSES-CH with fourth release Gaia-ESO survey data. We find that a simple spatial cut alone is insufficient and that observational uncertainties must be accounted for in the comparison. This is particularly true when the scale of uncertainty is large compared to the dynamic range of the data, e.g. in our comparison, the [Mg/Fe] distribution is affected much more than the more accurately determined [Fe/H] distribution. Despite clear differences in the underlying distributions of elemental abundances between simulation and observation, incorporating scatter to our simulation results to mimic observational uncertainty produces reasonable agreement. The quite complete nature of the Gaia-ESO survey means that the selection function has minimal impact on the distribution of observed age and metal abundances but this would become increasingly more important for surveys with narrower selection functions.


R. J. deBoer, J. Görres, M. Wiescher, R. E. Azuma, A. Best, C. R. Brune, C. E. Fields, S. Jones, M. Pignatari, D. Sayre, K. Smith, F. X. Timmes, and E. Uberseder, 2017-09-07, The 12C(alpha,gamma)16O reaction and its implications for stellar helium burning, Reviews of Modern Physics, doi: 10.1103/RevModPhys.89.035007

 

Abstract


The creation of carbon and oxygen in our Universe is one of the forefront questions in nuclear astrophysics. The determination of the abundance of these elements is key to our understanding of both the formation of life on Earth and to the life cycles of stars. While nearly all models of different nucleosynthesis environments are affected by the production of carbon and oxygen, a key ingredient, the precise determination of the reaction rate of 12C(α,γ)16O, has long remained elusive. This is owed to the reaction’s inaccessibility, both experimentally and theoretically. Nuclear theory has struggled to calculate this reaction rate because the cross section is produced through different underlying nuclear mechanisms. Isospin selection rules suppress the E1 component of the ground state cross section, creating a unique situation where the E1 and E2 contributions are of nearly equal amplitudes. Experimentally there have also been great challenges. Measurements have been pushed to the limits of state-of-the-art techniques, often developed for just these measurements. The data have been plagued by uncharacterized uncertainties, often the result of the novel measurement techniques that have made the different results challenging to reconcile. However, the situation has markedly improved in recent years, and the desired level of uncertainty ≈10% may be in sight. In this review the current understanding of this critical reaction is summarized. The emphasis is placed primarily on the experimental work and interpretation of the reaction data, but discussions of the theory and astrophysics are also pursued. The main goal is to summarize and clarify the current understanding of the reaction and then point the way forward to an improved determination of the reaction rate.


Hahn, Christoph and Genner, Martin J and Turner, George F and Joyce, Domino A, 2017-08-29, The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi, Evolution Letters, doi: 10.1002/evl3.20

 

Abstract


Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population-level RAD-seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome-level specialization for life at depth as an important process in cichlid radiation.


Dethlefs, Nina, 2017-07-18, Domain Transfer for Deep Natural Language Generation from Abstract Meaning Representations, IEEE Computational Intelligence Magazine, doi: 10.1109/MCI.2017.2708558

 

Abstract


Stochastic natural language generation systems that are trained from labelled datasets are often domain-specific in their annotation and in their mapping from semantic input representations to lexical-syntactic outputs. As a result, learnt models fail to generalize across domains, heavily restricting their usability beyond single applications. In this article, we focus on the problem of domain adaptation for natural language generation. We show how linguistic knowledge from a source domain, for which labelled data is available, can be adapted to a target domain by reusing training data across domains. As a key to this, we propose to employ abstract meaning representations as a common semantic representation across domains. We model natural language generation as a long short-term memory recurrent neural network encoder-decoder, in which one recurrent neural network learns a latent representation of a semantic input, and a second recurrent neural network learns to decode it to a sequence of words. We show that the learnt representations can be transferred across domains and can be leveraged effectively to improve training on new unseen domains. Experiments in three different domains and with six datasets demonstrate that the lexical-syntactic constructions learnt in one domain can be transferred to new domains and achieve up to 75-100% of the performance of in-domain training. This is based on objective metrics such as BLEU and semantic error rate and a subjective human rating study. Training a policy from prior knowledge from a different domain is consistently better than pure in-domain training by up to 10%.


Nan Liu and Larry R. Nittler and Marco Pignatari and Conel M. O’D. Alexander and Jianhua WangNan Liu and Larry R. Nittler and Marco Pignatari and Conel M. O’D. Alexander and Jianhua Wang, 2017-06-06, Stellar Origin of 15 N-rich Presolar SiC Grains of Type AB: Supernovae with Explosive Hydrogen Burning, The Astrophysical Journal Letters, doi: 10.3847/2041-8213/aa74e5

 

Abstract


We report C, N, and Si isotopic data for 59 highly 13 C-enriched presolar submicron- to micron-sized SiC grains from the Murchison meteorite, including eight putative nova grains (PNGs) and 29 15 N-rich ( 14 N/ 15 N ≤ solar) AB grains, and their Mg–Al, S, and Ca–Ti isotope data when available. These 37 grains are enriched in 13 C, 15 N, and 26 Al with the PNGs showing more extreme enhancements. The 15 N-rich AB grains show systematically higher 26 Al and 30 Si excesses than the 14 N-rich AB grains. Thus, we propose to divide the AB grains into groups 1 ( 14 N/ 15 N < solar) and 2 ( 14 N/ 15 N ≥ solar). For the first time, we have obtained both S and Ti isotopic data for five AB1 grains and one PNG and found 32 S and/or 50 Ti enhancements. Interestingly, one AB1 grain had the largest 32 S and 50 Ti excesses, strongly suggesting a neutron-capture nucleosynthetic origin of the 32 S excess and thus the initial presence of radiogenic 32 Si ( t 1/2 = 153 years). More importantly, we found that the 15 N and 26 Al excesses of AB1 grains form a trend that extends to the region in the N–Al isotope plot occupied by C2 grains, strongly indicating a common stellar origin for both AB1 and C2 grains. Comparison of supernova models with the AB1 and C2 grain data indicates that these grains came from supernovae that experienced H ingestion into the He/C zones of their progenitors.


Dethlefs, Nina and Turner, Alexander, 2017-05-27, Deep Text Generation — Using Hierarchical Decomposition to Mitigate the Effect of Rare Data Points, Language, Data, and Knowledge: First International Conference, LDK 2017, Galway, Ireland, June 19-20, 2017, Proceedings, doi: 10.1007/978-3-319-59888-8_25

 

Abstract


The generation of in situ sp2–sp3 diboron adducts has revolutionised the synthesis of organoboranes. Organocatalytic diboration reactions have represented a milestone in terms of unpredictable reactivity of these adducts. However, current methodologies have limitations in terms of substrate scope, selectivity and functional group tolerance. Here a new methodology based on the use of simple amines as catalyst is reported. This methodology provides a completely selective transformation overcoming current substrate scope and functional/protecting group limitations. Mechanistic studies have been included in this report.


Mishenina, T. and Pignatari, M. and Côté, B. and Thielemann, F.-K. and Soubiran, C. and Basak, N. and Gorbaneva, T. and Korotin, S. A. and Kovtyukh, V. V. and Wehmeyer, B. and Bisterzo, S. and Travaglio, C. and Gibson, B. K. and Jordan, C. and Paul, A. and Ritter, C. and Herwig, F., 2017-05-11, Observing the metal-poor solar neighbourhood: a comparison of galactic chemical evolution predictions, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stx1145

 

Abstract


Atmospheric parameters and chemical compositions for 10 stars with metallicities in the region of −2.2 < [Fe/H] < −0.6 were precisely determined using high-resolution, high signal-to-noise, spectra. For each star, the abundances, for 14–27 elements, were derived using both local thermodynamic equilibrium (LTE) and non-LTE (NLTE) approaches. In particular, differences by assuming LTE or NLTE are about 0.10 dex; depending on [Fe/H], Teff, gravity and element lines used in the analysis. We find that the O abundance has the largest error, ranging from 0.10 and 0.2 dex. The best measured elements are Cr, Fe, and Mn; with errors between 0.03 and 0.11 dex. The stars in our sample were included in previous different observational work. We provide a consistent data analysis. The data dispersion introduced in the literature by different techniques and assumptions used by the different authors is within the observational errors, excepting for HD103095. We compare these results with stellar observations from different data sets and a number of theoretical galactic chemical evolution (GCE) simulations. We find a large scatter in the GCE results, used to study the origin of the elements. Within this scatter as found in previous GCE simulations, we cannot reproduce the evolution of the elemental ratios [Sc/Fe], [Ti/Fe], and [V/Fe] at different metallicities. The stellar yields from core-collapse supernovae are likely primarily responsible for this discrepancy. Possible solutions and open problems are discussed.


Makina, Y. and Mahjoubi, K. and Benoit, D. M. and Jaidane, N.-E. and Al-Mogren, M. Mogren and Hochlaf, M., 2017-05-09, Periodic Dispersion-Corrected Approach for Isolation Spectroscopy of N2 in an Argon Environment: Clusters, Surfaces, and Matrices, The Journal of Physical Chemistry A, doi: 10.1021/acs.jpca.7b00093

 

Abstract


Ab initio and Perdew, Burke, and Ernzerhof (PBE) density functional theory with dispersion correction (PBE-D3) calculations are performed to study N2–Arn (n ≤ 3) complexes and N2 trapped in Ar matrix (i.e., N2@Ar). For cluster computations, we used both Møller–Plesset (MP2) and PBE-D3 methods. For N2@Ar, we used a periodic-dispersion corrected model for Ar matrix, which consists on a slab of four layers of Ar atoms. We determined the equilibrium structures and binding energies of N2 interacting with these entities. We also deduced the N2 vibrational frequency shifts caused by clustering or embedding compared to an isolated N2 molecule. Upon complexation or embedding, the vibrational frequency of N2 is slightly shifted, while its equilibrium distance remains unchanged. This is due to the weak interactions between N2 and Ar within these compounds. Our calculations show the importance of inclusion of dispersion effects for the accurate description of geometrical and spectroscopic parameters of N2 isolated, in interaction with Ar surfaces, or trapped in Ar matrices.


Siri Chongchitnan and Matthew Hunt, 2017-03-27, On the abundance of extreme voids II: a survey of void mass functions, Journal of Cosmology and Astroparticle Physics, doi: 10.1088/1475-7516/2017/03/049

 

Abstract


The abundance of cosmic voids can be described by an analogue of halo mass functions for galaxy clusters. In this work, we explore a number of void mass functions: from those based on excursion-set theory to new mass functions obtained by modifying halo mass functions. We show how different void mass functions vary in their predictions for the largest void expected in an observational volume, and compare those predictions to observational data. Our extreme-value formalism is shown to be a new practical tool for testing void theories against simulation and observation.


Dethlefs, Nina and Hawick, Ken, 2017-02-04, DEFIne: A Fluent Interface DSL for Deep Learning Applications, Proceedings of the 2nd International Workshop on Real World Domain Specific Languages, doi: 10.1145/3039895.3039898

 

Abstract


Recent years have seen a surge of interest in deep learning models that outperform other machine learning algorithms on benchmarks across many disciplines. Most existing deep learning libraries facilitate the development of neural nets by providing a mathematical framework that helps users implement their models more efficiently. This still represents a substantial investment of time and effort, however, when the intention is to compare a range of competing models quickly for a specific task. We present DEFIne, a fluent interface DSL for the specification, optimisation and evaluation of deep learning models. The fluent interface is implemented through method chaining. DEFIne is embedded in Python and is build on top of its most popular deep learning libraries, Keras and Theano. It extends these with common operations for data pre-processing and representation as well as visualisation of datasets and results. We test our framework on three benchmark tasks from different domains: heart disease diagnosis, hand-written digit recognition and weather forecast generation. Results in terms of accuracy, runtime and lines of code show that our DSL achieves equivalent accuracy and runtime to state-of-the-art models, while requiring only about 10 lines of code per application.


Uberseder, E.; Heil, M.; Kaeppeler, F.; Lederer, C.; Mengoni, A.; Bisterzo, S.; Pignatari, M.; Wiescher, M.;, 2017-02-02, Stellar (n ,gamma) cross sections of 23Na, Physical Review C, doi: 10.1103/PhysRevC.95.025803

 

Abstract


The cross section of the 23Na(n ,γ )24Na reaction was measured via the activation method at the Karlsruhe 3.7 MV Van de Graaff accelerator. NaCl samples were exposed to quasistellar neutron spectra at k T =5.1 and 25 keV produced via the 18O(p,n )18F and 7Li(p ,n )7Be reactions, respectively. The derived capture cross sections <σ> kT=5 keV=9.1 ±0.3 mb and <σ> kT =25keV=2.03 ±0.05 mb are significantly lower than reported in literature. These results were used to substantially revise the radiative width of the first 23Na resonance and to establish an improved set of Maxwellian average cross sections. The implications of the lower capture cross section for current models of s-process nucleosynthesis are discussed.


Farre, Albert and Soares, Kaline and Briggs, Rachel A. and Balanta, Angelica and Benoit, David M. and Bonet, Amadeu, 2016-10-26, Amine Catalysis for the Organocatalytic Diboration of Challenging Alkenes, Chemistry – A European Journal, doi: 10.1002/chem.201603979

 

Abstract


The generation of in situ sp2–sp3 diboron adducts has revolutionised the synthesis of organoboranes. Organocatalytic diboration reactions have represented a milestone in terms of unpredictable reactivity of these adducts. However, current methodologies have limitations in terms of substrate scope, selectivity and functional group tolerance. Here a new methodology based on the use of simple amines as catalyst is reported. This methodology provides a completely selective transformation overcoming current substrate scope and functional/protecting group limitations. Mechanistic studies have been included in this report


Conferences

Elke Roediger presented on Fluid dynamics in the ICM Presentation at Physics of the Intracluster Medium: Theory and Computation 2016 workshop at University of Minnesota in 2016-08

Nina Dethlefs presented on Deep natural language learning on Viper at Network on Computational Statistics and Machine Learning Workshop at Edinburgh University in 2016-08

Angela Dyson presented on The effects of non-equilibrium phonons on electron transport in GaN & AlN at High Efficiency Materials for Photovoltaics (HEMP) workshop at Imperial College London in 2016-09

Angela Dyson presented on Monte-Carlo simulation of a GaN Gunn diode at International Workshop on Nitride Semiconductors at Orlando Florida in 2016-10

Christina Roggatz presented on How quantum chemical methods help to unravel the effects of pH on marine communication at Molecular Graphics and Modelling Society Young Modellers Forum 2016 at The Old Naval College London in 2016-11

Nina Dethlefs presented on Domain Adaptation using Linguistic Knowledge at Lets discuss: Learning methods for dialogue NIPS 2016 workshop at ​Centre Convencions Internacional Barcelona in 2016-12

Matthew Bennett presented at the Meeting of the materials chemistry young scientists sub committee at Aston University in 2017

Daniel Naylor presented on Prospects for THz Emission in Gunn Diodes at UK Nitrides Consortium Winter Conference 2017 at University of Oxford in 2017-01

Wenjia Du presented on Four Dimensional Real-time Studies of Metal Solidification under External Fields at The Minerals, Metals & Materials Society 146th Annual Meeting and Exhibition at California in 2017-02

James Keegans presented on Production of iron-group elements in core-collapse supernovae at Rußbach School on Nuclear Astrophysics at Austria in 2017-03

David Benoit presented on Accurate adsorbate vibrations from first principles at Computational Molecular Science 2017 at Warwick in 2017-03