Constraining magma storage conditions at a restless volcano in the Main Ethiopian Rift using phase equilibria models

This work is a contribution to the Natural Environment Research Council (NERC) funded RiftVolc project (NE/L013932/1, Rift volcanism: past, present, and future). W.H., T.A.M., and D.M.P. are supported by and contribute to the NERC Centre for the Observation and Modelling of Earthquakes, Volcanoes, and Tectonics (COMET). W.H. M.J.S. were supported by a NERC studentships NE/J5000045/1 and NE/K500811/01 respectively.The Main Ethiopian Rift hosts a number of peralkaline volcanic centres, with many showing signs of recent unrest. Due, in part, to the low number of historical eruptions recorded in the region, volcanism in the Main Ethiopian Rift remains understudied relative to other volcanic settings and conditions of magma storage remain almost entirely unknown. Aluto is one of these restless caldera systems and identifying magma storage conditions is vital for evaluating the risks posed by recent periods of unrest. In this study, we ran ~ 150 fractional crystallisation models, using the Rhyolite-MELTS thermodynamic software, within the range P = 50–300 MPa, starting H2O = 0.5–3 wt% and fO2 = QFM-2 − QFM + 1. This represents a realistic range of potential magma storage conditions at Aluto. We assessed the fractionation trends produced using two different starting compositions, which represent different estimates of the parental melt feeding the system. The predicted liquid lines of descent produced by these models are compared with Aluto whole-rock data from the literature, and are presented along with new observations of the natural phase assemblage and erupted mineral compositions to provide information on the magma storage conditions. Using a new, quantitative statistical approach to compare empirical data and thermodynamic model-outputs, we find that the compositions of evolved peralkaline rhyolites from Aluto are best reproduced by isobaric fractional crystallisation from a rift-related basaltic composition, without the need for significant crustal assimilation. Around 90% protracted fractional crystallisation is required to produce these compositions. This indicates that the magmatic system is likely to exist as a highly crystalline mush. The best agreement between models and natural samples is at low pressures (150 MPa), low initial H2O concentrations (0.5 wt%) and relatively high oxygen fugacity (QFM). The depth of magma storage derived from these results (~ 5.6 ± 1 km) agrees well with the source depths modelled from measured ground deformation at Aluto in 2008. Data from other peralkaline volcanic centres in the Main Ethiopian Rift, such as Boset and Gedemsa, and at other locations globally (e.g. Pantelleria, Italy) suggest that these storage conditions are a common feature of many peralkaline volcanic centres. Our data is consistent with the formation of a Daly Gap at Aluto due to compositional stratification of the magma reservoir beneath the caldera, and the non-linear relationship between temperature and SiO2 concentration during magmatic differentiation.PostprintPeer reviewe

Asthma and gender impact accumulation of T cell subtypes

<p>Abstract</p> <p>Background</p> <p>The "Th2 hypothesis for asthma" asserts that an increased ratio of Th2:Th1 cytokine production plays an important pathogenic role in asthma. Although widely embraced, the hypothesis has been challenged by various empirical observations and has been described as overly simplistic. We sought to establish whether CD3+CD28-mediated and antigen-independent accumulation of type 1 and type 2 T cells differs significantly between nonasthmatic and asthmatic populations.</p> <p>Methods</p> <p>An ex vivo system was used to characterize the regulation of IFN-γ-producing (type 1) and IL-13-producing (type 2) T cell accumulation in response to CD3+CD28 and IL-2 stimulation by flow cytometry.</p> <p>Results</p> <p>IL-13-producing T cells increased in greater numbers in response to antigen-independent stimulation in peripheral blood lymphocytes from female atopic asthmatic subjects compared with male asthmatics and both male and female atopic non-asthmatic subjects. IFN-γ⁺T cells increased in greater numbers in response to either antigen-independent or CD3+CD28-mediated stimulation in peripheral blood lymphocytes from atopic asthmatic subjects compared to non-asthmatic subjects, regardless of gender.</p> <p>Conclusions</p> <p>We demonstrate that T cells from asthmatics are programmed for increased accumulation of both type 2 and type 1 T cells. Gender had a profound effect on the regulation of type 2 T cells, thus providing a mechanism for the higher frequency of adult asthma in females.</p

Towards an Achievable Performance for the Loop Nests

Numerous code optimization techniques, including loop nest optimizations, have been developed over the last four decades. Loop optimization techniques transform loop nests to improve the performance of the code on a target architecture, including exposing parallelism. Finding and evaluating an optimal, semantic-preserving sequence of transformations is a complex problem. The sequence is guided using heuristics and/or analytical models and there is no way of knowing how close it gets to optimal performance or if there is any headroom for improvement. This paper makes two contributions. First, it uses a comparative analysis of loop optimizations/transformations across multiple compilers to determine how much headroom may exist for each compiler. And second, it presents an approach to characterize the loop nests based on their hardware performance counter values and a Machine Learning approach that predicts which compiler will generate the fastest code for a loop nest. The prediction is made for both auto-vectorized, serial compilation and for auto-parallelization. The results show that the headroom for state-of-the-art compilers ranges from 1.10x to 1.42x for the serial code and from 1.30x to 1.71x for the auto-parallelized code. These results are based on the Machine Learning predictions.Comment: Accepted at the 31st International Workshop on Languages and Compilers for Parallel Computing (LCPC 2018

A Minimal Model of Metabolism Based Chemotaxis

Since the pioneering work by Julius Adler in the 1960's, bacterial chemotaxis has been predominantly studied as metabolism-independent. All available simulation models of bacterial chemotaxis endorse this assumption. Recent studies have shown, however, that many metabolism-dependent chemotactic patterns occur in bacteria. We hereby present the simplest artificial protocell model capable of performing metabolism-based chemotaxis. The model serves as a proof of concept to show how even the simplest metabolism can sustain chemotactic patterns of varying sophistication. It also reproduces a set of phenomena that have recently attracted attention on bacterial chemotaxis and provides insights about alternative mechanisms that could instantiate them. We conclude that relaxing the metabolism-independent assumption provides important theoretical advances, forces us to rethink some established pre-conceptions and may help us better understand unexplored and poorly understood aspects of bacterial chemotaxis

Serum insulin level, disease stage, prostate specific antigen (PSA) and Gleason score in prostate cancer

In the present study, we assessed the relationship of serum insulin levels and three surrogate markers of recurrence, T stage, PSA, and Gleason score, in men with localized prostate cancer. Participants in our study were found through urology and radiation oncology clinics, and all eligible patients were asked to take part. All patients were asymptomatic and had been initially diagnosed on the basis of rising PSA or abnormal physical examination. Histological confirmation of diagnosis was obtained for all subjects. Serum insulin levels were determined by chemoluminescent assay with a standard, commercially available instrument. Patients were divided into three previously defined risk groups: Low risk: PSA ⩽10, stage ⩽T2a, or Gleason grade ⩽6. Medium risk: 10 <PSA ⩽15, Gleason 7 or stage T2b. High risk: Gleason >7, tumour in seminal vesicle biopsy, PSA >15 or stage T2c or T3. One hundred and sixty-three men with prostate cancer were studied. There was a significant increase in serum insulin with risk group (P=0.003, one way anova). Tukey's multiple range test showed that the insulin levels of high risk patients were significantly higher than the insulin levels of medium and low risk patients (P=0.05) but the insulin levels of medium and low risk patients were not significantly different from one another. Multivariate linear regression, with insulin as the dependent variable, Gleason score, PSA, and T stage (T1, T2, T3) as the independent variables, was significant overall (P<0.001, r2=0.120). Increased T stage was independently correlated with increased serum insulin levels (P<0.001). Gleason score was negatively, insignificantly correlated with serum insulin level (P=0.059). The positive correlation of PSA and insulin level was not significant (P=0.097). To assure normal distribution of insulin and PSA values, the regression was repeated with log (insulin) as the dependent variable, log (PSA), T stage (T1, T2, T3), and Gleason score as independent variables. The regression was significant overall (P=0.002, r2 =0.095). Increased T stage was independently correlated with increased log (insulin level) (P=0.026). Gleason score was negatively, insignificantly correlated with log (insulin) level (P=0.728). The positive correlation of log (PSA) and log (insulin) levels was significant (P=0.010). The relationship between increased insulin level and advanced tumour stage in prostate cancer we describe here is biologically quite plausible, since insulin is a growth factor. Further studies may document whether serum insulin levels might be a useful biomarker of prostate cancer stage

Condensation of free volume in structures of nematic and hexatic liquid crystals

Eight novel liquid crystalline materials were prepared containing highly branched terminal chains, either 2,4,4-trimethylpentyl or 3,5,5-trimethylhexyl. All materials exhibit nematic mesophases, with additional smectic (Sm) C, hexatic B and SmI phases for certain homologues. Analysis by small- and wide-angle X-ray scattering reveals continual build-up of the correlation length within the nematic phases, where we also observe splitting of the small angle peak into four lobes, indicating pretransitional Sm fluctuations. Connoscopy confirms the nematic phase to be uniaxial and optically positive. We observe that in the solid state, the molecules exist as staggered antiparallel pairs as a consequence of the sterically demanding bulky terminal group, and this would also appear to manifest in the hexatic B phase, where the layer spacing was found to be greater than the molecular length. If true, this is an example of pair formation driven by sterics rather than dipole–dipole interactions and suggests that reentrant systems driven purely by steric frustration may be found

Artificial Neural Network Inference (ANNI): A Study on Gene-Gene Interaction for Biomarkers in Childhood Sarcomas

Objective: To model the potential interaction between previously identified biomarkers in children sarcomas using artificial neural network inference (ANNI). Method: To concisely demonstrate the biological interactions between correlated genes in an interaction network map, only 2 types of sarcomas in the children small round blue cell tumors (SRBCTs) dataset are discussed in this paper. A backpropagation neural network was used to model the potential interaction between genes. The prediction weights and signal directions were used to model the strengths of the interaction signals and the direction of the interaction link between genes. The ANN model was validated using Monte Carlo cross-validation to minimize the risk of over-fitting and to optimize generalization ability of the model. Results: Strong connection links on certain genes (TNNT1 and FNDC5 in rhabdomyosarcoma (RMS); FCGRT and OLFM1 in Ewing’s sarcoma (EWS)) suggested their potency as central hubs in the interconnection of genes with different functionalities. The results showed that the RMS patients in this dataset are likely to be congenital and at low risk of cardiomyopathy development. The EWS patients are likely to be complicated by EWS-FLI fusion and deficiency in various signaling pathways, including Wnt, Fas/Rho and intracellular oxygen. Conclusions: The ANN network inference approach and the examination of identified genes in the published literature within the context of the disease highlights the substantial influence of certain genes in sarcomas

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks premorphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll’s ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths