Induction of IL 2 receptor expression and cytotoxicity of thymocytes by stimulation with TCF1

We investigated the role of T cell cytotoxicity inducing factor 1 (TCF1) in the induction of a cytotoxic T cell response. We found that help-deficient thymocyte cultures supplied with saturating amounts of purified IL 2 did not develop CTL in a 5-day culture. The expression of cytotoxicity was dependent on the addition of TCF1 derived from the T cell hybridoma K15. TCF1 also induced proliferation of thymocytes in the presence of IL 2. Only the PNA- thymocyte subpopulation responded to TCF1 with proliferation and cytotoxicity in the presence of IL 2. The monokine IL 1 also induced proliferation in this subpopulation but failed to induce cytotoxicity. IL 1 was further distinguished from TCF1 by inhibition of IL 1-induced but not TCF1-induced proliferation by anti-IL 1 antibodies. In addition, using anti-IL 2 receptor antibodies (AMT 13), we showed that TCF1 in the presence of IL 2 substantially increased IL 2 receptor expression in thymocytes. IL 1 had the same effect on induction of IL 2 receptor expression as TCF1. Because some effects of IL 1 and TCF1 are distinct and some overlap, we discuss whether IL 1 and TCF1 induce different subsets of PNA- thymocytes

Physical Organization of DNA by Multiple Non-Specific DNA-Binding Modes of Integration Host Factor (IHF)

10.1371/journal.pone.0049885PLoS ONE711

Drift-induced deceleration of Solar Energetic Particles

We investigate the deceleration of Solar Energetic Particles (SEPs) during their propagation from the Sun through interplanetary space, in the presence of weak to strong scattering in a Parker spiral configuration, using relativistic full orbit test particle simulations. The calculations retain all three spatial variables describing particles’ trajectories, allowing to model any transport across the magnetic field. Large energy change is shown to occur for protons, due to the combined effect of standard adiabatic deceleration and a significant contribution from particle drift in the direction opposite to that of the solar wind electric field. The latter drift-induced deceleration is found to have a stronger effect for SEP energies than for galactic cosmic rays. The kinetic energy of protons injected at 1 MeV is found to be reduced by between 35 and 90% after four days, and for protons injected at 100 MeV by between 20 and 55%. The overall degree of deceleration is a weak function of the scattering mean free path, showing that, although adiabatic deceleration plays a role, a large contribution is due to particle drift. Current SEP transport models are found to account for drift-induced deceleration in an approximate way and their accuracy will need to be assessed in future work

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a "Biodiversity Data Archive". A wide variety of use cases were assembled and discussed in order to inform further developments

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a "Biodiversity Data Archive". A wide variety of use cases were assembled and discussed in order to inform further developments

CAMISIM: Simulating metagenomes and microbial communities

© 2019 The Author(s). Background: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Results: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. Conclusions: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation

Heliospheric Transport of Neutron-Decay Protons

We report on new simulations of the transport of energetic protons originating from the decay of energetic neutrons produced in solar flares. Because the neutrons are fast-moving but insensitive to the solar wind magnetic field, the decay protons are produced over a wide region of space, and they should be detectable by current instruments over a broad range of longitudes for many hours after a sufficiently large gamma-ray flare. Spacecraft closer to the Sun are expected to see orders-of magnitude higher intensities than those at the Earth-Sun distance. The current solar cycle should present an excellent opportunity to observe neutron-decay protons with multiple spacecraft over different heliographic longitudes and distances from the Sun.Comment: 12 pages, 4 figures, to be published in special issue of Solar Physic

The band structure of BeTe - a combined experimental and theoretical study

Using angle-resolved synchrotron-radiation photoemission spectroscopy we have determined the dispersion of the valence bands of BeTe(100) along $\Gamma X$, i.e. the [100] direction. The measurements are analyzed with the aid of a first-principles calculation of the BeTe bulk band structure as well as of the photoemission peaks as given by the momentum conserving bulk transitions. Taking the calculated unoccupied bands as final states of the photoemission process, we obtain an excellent agreement between experimental and calculated spectra and a clear interpretation of almost all measured bands. In contrast, the free electron approximation for the final states fails to describe the BeTe bulk band structure along $\Gamma X$ properly.Comment: 21 pages plus 4 figure

Observations of Electrons from the Decay of Solar Flare Neutrons

We have found evidence for fluxes of energetic electrons in interplanetary space on board the ISEE-3 spacecraft which we interpret as the decay products of neutrons generated in a solar flare on 1980 June 21. The decay electrons arrived at the s/c shortly before the electrons from the flare and can be distinguished from the latter by their distinctive energy spectrum. The time profile of the decay electrons is in good agreement with the results from a simulation based on a scattering mean free path derived from a fit to the flare electron data. The comparison with simultaneously observed decay protons and a published direct measurement of high-energy neutrons places important constraints on the parent neutron spectrum.Comment: 4 pages (postscript), accepted by Astrophysical Journal Letter