Functional Tolerance is Maintained Despite Proliferation of CD4 T Cells after Encounter with Tissue-derived Antigen

Since negative selection in the thymus is incomplete, some self-reactive T cells are able to mature and seed the periphery. To study how these T cells interact following encounter with the self-protein they recognize in the periphery, we have developed an adoptive transfer system in which HEL-specific TCR transgenic CD4 T cells are transferred to mice expressing HEL protein in the pancreas under the control of the rat insulin promoter. Here we show that after adoptive transfer of HEL-specific T cells functional tolerance is maintained despite evidence that the T cells encounter and respond to pancreas-expressed antigen. Even the provision of an additional activation stimulus by peripheral immunization with HEL protein is insufficient to induce the T cells to cause autoimmune tissue injury. However, in the presence of blocking anti-CTLA-4-mAb, immunized adoptive transfer recipients rapidly developed diabetes. These data suggest that the CTLA-4 pathway regulates the pathogenicity of antigen-specific T cells following a peripheral activation stimulus

A practical guide to pre-trial simulations for Bayesian adaptive trials using SAS and BUGS

It is often unclear what specific adaptive trial design features lead to an efficient design which is also feasible to implement. Before deciding on a particular design, it is generally advisable to carry out a simulation study to characterise the properties of candidate designs under a range of plausible assumptions. The implementation of such pre-trial simulation studies presents many challenges and requires considerable statistical programming effort and time. Despite the scale and complexity, there is little existing literature to guide the implementation of such projects using commonly available software. This Teacher's Corner article provides a practical step-by-step guide to implementing such simulation studies including how to specify and fit a Bayesian model in WinBUGS or OpenBUGS using SAS, and how results from the Bayesian analysis may be pulled back into SAS and used for adaptation of allocation probabilities before simulating subsequent stages of the trial. The interface between the two software platforms is described in detail along with useful tips and tricks. A key strength of our approach is that the entire exercise can be defined and controlled from within a single SAS program

Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms

The diversity of arbuscular mycorrhizal (AM) fungi was investigated in an unfertilized limestone grassland soil supporting different synthesized vascular plant assemblages that had developed for 3 yr. The experimental treatments comprised: bare soil; monocultures of the nonmycotrophic sedge Carex flacca; monocultures of the mycotrophic grass Festuca ovina; and a species-rich mixture of four forbs, four grasses and four sedges. The diversity of AM fungi was analysed in roots of Plantago lanceolata bioassay seedlings using terminal-restriction fragment length polymorphism (T-RFLP). The extent of AM colonization, shoot biomass and nitrogen and phosphorus concentrations were also measured. The AM diversity was affected significantly by the floristic composition of the microcosms and shoot phosphorus concentration was positively correlated with AM diversity. The diversity of AM fungi in P. lanceolata decreased in the order: bare soil > C. flacca > 12 species > F. ovina. The unexpectedly high diversity in the bare soil and sedge monoculture likely reflects differences in the modes of colonization and sources of inoculum in these treatments compared with the assemblages containing established AM-compatible plants

Elevated levels of inflammatory cytokines predict survival in idiopathic and familial pulmonary arterial hypertension

BACKGROUND: Inflammation is a feature of pulmonary arterial hypertension (PAH), and increased circulating levels of cytokines are reported in patients with PAH. However, to date, no information exists on the significance of elevated cytokines or their potential as biomarkers. We sought to determine the levels of a range of cytokines in PAH and to examine their impact on survival and relationship to hemodynamic indexes. METHODS AND RESULTS: We measured levels of serum cytokines (tumor necrosis factor-alpha, interferon-gamma and interleukin-1beta, -2, -4, -5, -6, -8, -10, -12p70, and -13) using ELISAs in idiopathic and heritable PAH patients (n=60). Concurrent clinical data included hemodynamics, 6-minute walk distance, and survival time from sampling to death or transplantation. Healthy volunteers served as control subjects (n=21). PAH patients had significantly higher levels of interleukin-1beta, -2, -4, -6, -8, -10, and -12p70 and tumor necrosis factor-alpha compared with healthy control subjects. Kaplan-Meier analysis showed that levels of interleukin-6, 8, 10, and 12p70 predicted survival in patients. For example, 5-year survival with interleukin-6 levels of >9 pg/mL was 30% compared with 63% for patients with levels < or = 9 pg/mL (P=0.008). In this PAH cohort, cytokine levels were superior to traditional markers of prognosis such as 6-minute walk distance and hemodynamics. CONCLUSIONS: This study illustrates dysregulation of a broad range of inflammatory mediators in idiopathic and familial PAH and demonstrates that cytokine levels have a previously unrecognized impact on patient survival. They may prove to be useful biomarkers and provide insight into the contribution of inflammation in PAH

Structures of mixed manganese ruthenium oxides (Mn1−xRux)O2(Mn_{1−x}Ru_x)O_2 crystallised under acidic hydrothermal conditions

A synthesis method for the preparation of mixed manganese–ruthenium oxides is presented along with a detailed characterisation of the solids produced. The use of 1 M aqueous sulfuric acid mediates the redox reaction between KRuO$_4$, KMnO$_4$ and Mn$^{2+}$ to form ternary oxides. At reaction temperature of 100°C the products are mixtures of α-MnO$_2$ (hollandite-type) and β-MnO$_2$ (rutile-type), with some evidence of Ru incorporation in each from their expanded unit cell volumes. At reaction temperature of 200°C solid-solutions β-Mn$_{1−x}$Ru$_x$O$_2$ are formed and materials with x ≤ 0.6 have been studied. The amount of Ru included in the oxide is greater than expected from the ratio of metals used in the synthesis, as determined by elemental analysis, implying that some Mn remains unreacted in solution. Powder X-ray diffraction (XRD) shows that while the unit cell volume expands in a linear manner, following Vegard's law, the tetragonal lattice parameters, and the a/c ratio, do not follow the extrapolated trends: this anisotropic behaviour is consistent with the different local coordination of the metals in the end members. Powder XRD patterns show increased peak broadening with increasing ruthenium content, which is corroborated by electron microscopy that shows nanocrystalline material. X-ray absorption near-edge spectra show that the average oxidation state of Mn in the solid solutions is reduced below +4 while that of Ru is increased above +4, suggesting some redistribution of charge. Analysis of the extended X-ray absorption fine structure provides complementary local structural information, confirming the formation of a solid solution, while X-ray photoelectron spectroscopy shows that the surface oxidation states of both Ru and Mn are on average lower than +4, suggesting a disordered surface layer may be present in the materials

Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae

OBJECTIVES: The objective of this study was to determine the distribution and genetic basis of trimethoprim resistance in Actinobacillus pleuropneumoniae isolates from pigs in England. METHODS: Clinical isolates collected between 1998 and 2011 were tested for resistance to trimethoprim and sulphonamide. The genetic basis of trimethoprim resistance was determined by shotgun WGS analysis and the subsequent isolation and sequencing of plasmids. RESULTS: A total of 16 (out of 106) A. pleuropneumoniae isolates were resistant to both trimethoprim (MIC >32 mg/L) and sulfisoxazole (MIC ≥256 mg/L), and a further 32 were resistant only to sulfisoxazole (MIC ≥256 mg/L). Genome sequence data for the trimethoprim-resistant isolates revealed the presence of the dfrA14 dihydrofolate reductase gene. The distribution of plasmid sequences in multiple contigs suggested the presence of two distinct dfrA14-containing plasmids in different isolates, which was confirmed by plasmid isolation and sequencing. Both plasmids encoded mobilization genes, the sulphonamide resistance gene sul2, as well as dfrA14 inserted into strA, a streptomycin-resistance-associated gene, although the gene order differed between the two plasmids. One of the plasmids further encoded the strB streptomycin-resistance-associated gene. CONCLUSIONS: This is the first description of mobilizable plasmids conferring trimethoprim resistance in A. pleuropneumoniae and, to our knowledge, the first report of dfrA14 in any member of the Pasteurellaceae. The identification of dfrA14 conferring trimethoprim resistance in A. pleuropneumoniae isolates will facilitate PCR screens for resistance to this important antimicrobial

Benchmark problems for continuum radiative transfer. High optical depths, anisotropic scattering, and polarisation

Solving the continuum radiative transfer equation in high opacity media requires sophisticated numerical tools. In order to test the reliability of such tools, we present a benchmark of radiative transfer codes in a 2D disc configuration. We test the accuracy of seven independently developed radiative transfer codes by comparing the temperature structures, spectral energy distributions, scattered light images, and linear polarisation maps that each model predicts for a variety of disc opacities and viewing angles. The test cases have been chosen to be numerically challenging, with midplane optical depths up 10^6, a sharp density transition at the inner edge and complex scattering matrices. We also review recent progress in the implementation of the Monte Carlo method that allow an efficient solution to these kinds of problems and discuss the advantages and limitations of Monte Carlo codes compared to those of discrete ordinate codes. For each of the test cases, the predicted results from the radiative transfer codes are within good agreement. The results indicate that these codes can be confidently used to interpret present and future observations of protoplanetary discs.Comment: 15 pages, 10 figures, accepted for publication in A&

Fate of Pharmaceutical and Personal Care Products in Irrigated Wastewater Effluent

The potential human and environmental health risks posed by pharmaceuticals and personal care products (PPCPs) have been identified as a research priority at both the federal and state level. It has been well documented that municipal wastewater treatment plants with surface discharge fail to remove many of these emerging contaminants; however, little research has been conducted to determine the capability of lagoon treatment systems to remove PPCPs or of organic-matter-rich clay loam soils to filter PPCPs and reduce surface water pollution. The objective of this study was to determine the fate and transport of selected pharmaceuticals in lagoon-treated wastewater effluent applied as cropland irrigation in Illinois. In this study, we were able to determine the presence of six of the seven priority PPCPs in lagoon-treated wastewater effluent; verify the absence of studied PPCPs in soil and well water prior to treatment; determine characteristics of cropland soil that may impact PPCP transport when wastewater irrigation begins; and conduct sorption isotherm studies to understand the sorption and desorption capabilities of field soils in Lexington, Illinois.Illinois Sustainable Technology Center, Prairie Research Institute, University of Illinois at Urbana-Champaign; Grant Number HWR12223Ope

The evolution of ultraviolet emission lines from the circumstellar material surrounding SN 1987A

The presence of narrow high-temperature emission lines from nitrogen-rich gas close to SN 1987A has been the principal observational constraint on the evolu- tionary status of the supernova's progenitor. A new analysis of the complete five-year set of low and high resolution IUE ultraviolet spectra of SN 1987A (1987.2--1992.3) provide fluxes for the N V 1240, N IV] 1486, He II 1640, OIII] 1665, NIII] 1751, and CIII] 1908 lines with significantly reduced random and systematic errors and reveals significant short-term fluctuations in the light curves. The N V, N IV] and N III] lines turn on sequentially over 15 to 20 days and show a progression from high to low ionization potential, implying an ioni- zation gradient in the emitting region. The line emission turns on suddenly at 83+/-4 days after the explosion, as defined by N IV]. The N III] line reaches peak luminosity at 399+/-15 days. A ring radius of (6.24+/-0.20)E{17} cm and inclination of 41.0+/-3.9 is derived from these times, assuming a circular ring. The probable role of resonant scattering in the N V light curve introduces systematic errors that leads us to exclude this line from the timing analysis. A new nebular analysis yields improved CNO abundance ratios N/C=6.1+/-1.1 and N/O=1.7+/-0.5, confirming the nitrogen enrichment found in our previous paper. From the late-time behavior of the light curves we find that the emission origi- nates from progressively lower density gas. We estimate the emitting mass near maximum (roughly 400 days) to be roughly 4.7E{-2} solar masses, assuming a filling factor of unity and an electron density of 2.6E4 cm^{-3}. These results are discussed in the context of current models for the emission and hydrodynamics of the ring.Comment: 38 pages, AASTeX v.4.0, 13 Postscript figures; ApJ, in pres