FishMark: A Linked Data Application Benchmark

Abstract. FishBase is an important species data collection produced by the FishBase Information and Research Group Inc (FIN), a not-forprofit NGO with the aim of collecting comprehensive information (from the taxonomic to the ecological) about all the world’s finned fish species. FishBase is exposed as a MySQL backed website (supporting a range of canned, although complex queries) and serves over 33 million hits per month. FishDelish is a transformation of FishBase into LinkedData weighing in at 1.38 billion triples. We have ported a substantial number of FishBase SQL queries to FishDelish SPARQL query which form the basis of a new linked data application benchmark (using our derivative of the Berlin SPARQL Benchmark harness). We use this benchmarking framework to compare the performance of the native MySQL application, the Virtuoso RDF triple store, and the Quest OBDA system on a fishbase.org like application.

Remodelling of human atrial K+ currents but not ion channel expression by chronic β-blockade

Chronic β-adrenoceptor antagonist (β-blocker) treatment in patients is associated with a potentially anti-arrhythmic prolongation of the atrial action potential duration (APD), which may involve remodelling of repolarising K+ currents. The aim of this study was to investigate the effects of chronic β-blockade on transient outward, sustained and inward rectifier K+ currents (ITO, IKSUS and IK1) in human atrial myocytes and on the expression of underlying ion channel subunits. Ion currents were recorded from human right atrial isolated myocytes using the whole-cell-patch clamp technique. Tissue mRNA and protein levels were measured using real time RT-PCR and Western blotting. Chronic β-blockade was associated with a 41% reduction in ITO density: 9.3 ± 0.8 (30 myocytes, 15 patients) vs 15.7 ± 1.1 pA/pF (32, 14), p < 0.05; without affecting its voltage-, time- or rate dependence. IK1 was reduced by 34% at −120 mV (p < 0.05). Neither IKSUS, nor its increase by acute β-stimulation with isoprenaline, was affected by chronic β-blockade. Mathematical modelling suggested that the combination of ITO- and IK1-decrease could result in a 28% increase in APD90. Chronic β-blockade did not alter mRNA or protein expression of the ITO pore-forming subunit, Kv4.3, or mRNA expression of the accessory subunits KChIP2, KChAP, Kvβ1, Kvβ2 or frequenin. There was no reduction in mRNA expression of Kir2.1 or TWIK to account for the reduction in IK1. A reduction in atrial ITO and IK1 associated with chronic β-blocker treatment in patients may contribute to the associated action potential prolongation, and this cannot be explained by a reduction in expression of associated ion channel subunits

Containerless, Low-Gravity Undercooling of Ti-Ce Alloys in the MSFC Drop Tube

Previous tests of the classical nucleation theory as applied to liquid-liquid gap miscibility systems found a discrepancy between experiment and theory in the ability to undercool one of the liquids before the L1-L2 separation occurs. To model the initial separation process in a two-phase liquid mixture, different theoretical approaches, such as free-energy gradient and density gradient theories, have been put forth. If there is a large enough interaction between the critical liquid and the crucible, both models predict a wetting temperature (T(sub w)) above which the minority liquid perfectly wets and layers the crucible interface, but only on one side of the immiscibility dome. Materials with compositions on the other side of the dome will have simple surface adsorption by the minority liquid before bulk separation occurs when the coexistence (i.e., binoidal) line in reached. If the interaction between the critical liquid and the crucible were to decrease, T(sub w) would increase, eventually approaching the critical consolute temperature (T(sub cc)). If this situation occurs, then there could be large regions of the miscibility gap where non-perfect wetting conditions prevail resulting in droplets of L1 liquid at the surface having a non-zero contact angle. The resulting bulk structure will then depend on what happens on the surface and the subsequent processing conditions. In the past several decades, many experiments in space have been performed on liquid metal binary immiscible systems for the purpose of determining the effects that different crucibles may have on the wetting and separation process of the liquids. Potard performed experiments that showed different crucible materials could cause the majority phase to preferentially wet the container and thus produce a dispersed microstructure of the minority phase. Several other studies have been performed on immiscibles in a semi-container environment using an emulsion technique. Only one previous study was performed using completely containerless processing of immiscible metals and the results of that investigation are similar to some of the emulsion studies. In all the studies, surface wetting was attributed as the cause for the similar microstructures or the asymmetry in the ability to undercool the liquid below the binoidal on one side of the immiscibility dome. By removing the container completely from the separation process, it was proposed that the loss of the crucible/liquid interaction would produce a large shift in T(sub w) and thus change the wetting characteristics at the surface. By investigating various compositions across the miscibility gap, a change in the type and amount of liquid wetting at the surface of a containerless droplet should change the surface nucleating behavior of the droplet - whether it be the liquid-liquid wetting or the liquid-to-solid transition. Undercooling of the liquid into the metastable region should produce significant differences in the separation process and the microstructure upon solidification. In this study, we attempt to measure these transitions by monitoring the temperature of the sample by optical pyrometry. Microstructural analysis will be made to correlate with the degree of undercooling and the separation mechanisms involved

PD1-Expressing T Cell Subsets Modify the Rejection Risk in Renal Transplant Patients

We tested whether multi-parameter immune phenotyping before or after renal ­transplantation can predict the risk of rejection episodes. Blood samples collected before and weekly for 3 months after transplantation were analyzed by multi-parameter flow cytometry to define 52 T cell and 13 innate lymphocyte subsets in each sample, producing more than 11,000 data points that defined the immune status of the 28 patients included in this study. Principle component analysis suggested that the patients with histologically confirmed rejection episodes segregated from those without rejection. Protein death 1 (PD-1)-expressing subpopulations of regulatory and conventional T cells had the greatest influence on the principal component segregation. We constructed a statistical tool to predict rejection using a support vector machine algorithm. The algorithm correctly identified 7 out of 9 patients with rejection, and 14 out of 17 patients without rejection. The immune profile before transplantation was most accurate in determining the risk of rejection, while changes of immune parameters after transplantation were less accurate in discriminating rejection from non-rejection. The data indicate that pretransplant immune subset analysis has the potential to identify patients at risk of developing rejection episodes, and suggests that the proportion of PD1-expressing T cell subsets may be a key indicator of rejection risk

Precise Measurement of Sigma Beam Asymmetry for Positive Pion Photoproduction on the Proton from 800 to 1500 Mev

The Sigma beam asymmetry for positive pion photoproduction on the proton has been measured over an angular range of 40-170 deg at photon energies from 0.8 to 1.5 GeV. The resulting data set includes 237 accurate points, 136 of these belonging to an almost unexplored domain above 1.05 GeV. Data of such high precision provide severe constraints for partial wave analyses. The influence of this experiment on the GW multipole analysis is demonstrated. Significant changes are found in multipoles connected to the S31(1620) and P13(1720) resonances. Comparisons using the MAID analysis are also presented.Comment: 11 pages, 4 eps figures. to be published in Physics Letters

Constraints on narrow exotic states from K+p and K0_Lp scattering data

We consider the effect of exotic S=+1 resonances Theta+ and Theta++ on K+p elastic scattering data (total cross section) and the process K0_Lp-->K0_Sp. Data near the observed Theta+(1540) are examined for evidence of additional states. The width limit for a Theta++ state is reconsidered and shown to be much less than 1 MeV.Comment: 4 pages, 3 eps figures; minor corrections, one fig adde

Delta isobar masses, large N_c relations, and the quark model

Motivated by recent remarks on the Delta+ mass and comparisons between the quark model and relations based on large-N_c with perturbative flavor breaking, two sets of Delta masses consistent with these constraints are constructed. These two sets, based either on an experimentally determined mass splitting or a quark model of isospin symmetry breaking, are shown to be inconsistent. The model dependence of this inconsistency is examined, and suggestions for improved experiments are made. An explicit quark model calculation and mass relations based on the large-N_c limit with perturbative flavor breaking are compared. The expected level of accuracy of such relations is realized in the quark model, except for mass relations spanning more than one SU(6) representation. It is shown that the Delta0 and Delta++ pole masses and Delta0 - Delta+ = (Delta- - Delta++)/3 about 1.5 MeV are more consistent with model expectations than the analogous Breit-Wigner masses and their splittings.Comment: 10 pages, including 1 eps figure, revte

The GDH Sum Rule and Related Integrals

The spin structure of the nucleon resonance region is analyzed on the basis of our phenomenological model MAID. Predictions are given for the Gerasimov-Drell-Hearn sum rule as well as generalized integrals over spin structure functions. The dependence of these integrals on momentum transfer is studied and rigorous relationships between various definitions of generalized Gerasimov-Drell-Hearn integrals and spin polarizabilities are derived. These results are compared to the predictions of chiral perturbation theory and phenomenological models.Comment: 15 pages LaTeX including 5 figure

Bowel Histology of CVID Patients Reveals Distinct Patterns of Mucosal Inflammation

Diarrhea is the commonest gastrointestinal symptom in patients with common variable immunodeficiency (CVID). Different pathologies in patients’ bowel biopsies have been described and links with infections have been demonstrated. The aim of this study was to analyze the bowel histology of CVID patients in the Royal-Free-Hospital (RFH) London CVID cohort. Ninety-five bowel histology samples from 44 adult CVID patients were reviewed and grouped by histological patterns. Reasons for endoscopy and possible causative infections were recorded. Lymphocyte phenotyping results were compared between patients with different histological features. There was no distinctive feature that occurred in most diarrhea patients. Out of 44 patients (95 biopsies), 38 lacked plasma cells. In 14 of 21 patients with nodular lymphoid hyperplasia (NLH), this was the only visible pathology. In two patients, an infection with Giardia lamblia was associated with NLH. An IBD-like picture was seen in two patients. A coeliac-like picture was found in six patients, four of these had norovirus. NLH as well as inflammation often occurred as single features. There was no difference in blood lymphocyte phenotyping results comparing groups of histological features. We suggest that bowel histology in CVID patients with abdominal symptoms falls into three major histological patterns: (i) a coeliac-like histology, (ii) IBD-like changes, and (iii) NLH. Most patients, but remarkably not all, lacked plasma cells. CVID patients with diarrhea may have an altered bowel histology due to poorly understood and likely diverse immune-mediated mechanisms, occasionally driven by infections