Commentary on Robert Riley's article "A personal account of the discovery of hyperbolic structures on some knot complements"

We give some background and biographical commentary on the postumous article that appears in this [journal issue | ArXiv] by Robert Riley on his part of the early history of hyperbolic structures on some compact 3-manifolds. A complete list of Riley's publications appears at the end of the article.Comment: 5 page

Inverse Bremsstrahlung in Shocked Astrophysical Plasmas

There has recently been interest in the role of inverse bremsstrahlung, the emission of photons by fast suprathermal ions in collisions with ambient electrons possessing relatively low velocities, in tenuous plasmas in various astrophysical contexts. This follows a long hiatus in the application of suprathermal ion bremsstrahlung to astrophysical models since the early 1970s. The potential importance of inverse bremsstrahlung relative to normal bremsstrahlung, i.e. where ions are at rest, hinges upon the underlying velocity distributions of the interacting species. In this paper, we identify the conditions under which the inverse bremsstrahlung emissivity is significant relative to that for normal bremsstrahlung in shocked astrophysical plasmas. We determine that, since both observational and theoretical evidence favors electron temperatures almost comparable to, and certainly not very deficient relative to proton temperatures in shocked plasmas, these environments generally render inverse bremsstrahlung at best a minor contributor to the overall emission. Hence inverse bremsstrahlung can be safely neglected in most models invoking shock acceleration in discrete sources such as supernova remnants. However, on scales > 100pc distant from these sources, Coulomb collisional losses can deplete the cosmic ray electrons, rendering inverse bremsstrahlung, and perhaps bremsstrahlung from knock-on electrons, possibly detectable.Comment: 13 pages, including 2 figures, using apjgalley format; to appear in the January 10, 2000 issue, of the Astrophysical Journa

Functional interpretation of single cell similarity maps.

We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration

Global-scale proxy system modeling of oxygen isotopes in lacustrine carbonates: 2 new insights from isotope-enabled-model proxy-data comparison

Proxy System Modelling (PSM) is now recognised as a crucial step in comparing climate model output with proxy records of past environmental change. PSMs filter the climate signal from the model, or from meteorological data, based on the physical, chemical and biological processes of the archive and proxy system under investigation. Here we use a PSM of lake carbonate δ18O to forward model pseudoproxy time-series for every terrestrial grid square in the SPEEDY-IER isotope enabled General Circulation Model (GCM), and compare the results with 31 records of lake δ18O data from the Americas in the NOAA Paleoclimate Database. The model-data comparison shows general patterns of spatial variability in the lake δ18O data are replicated by the combination of SPEEDY-IER and the PSM, with differences largely explained by known biases in the models. The results suggest improved spatial resolution/coverage of climate models and proxy data, respectively, is required for improved data-model comparison, as are increased numbers of higher temporal resolution proxy time series (sub decadal or better) and longer GCM runs. We prove the concept of data-model comparison using isotope enabled GCMs and lake isotope PSMs and outline potential avenues for further work

FDIONIC18 Interactions and stabilisation of acetone, sulfur dioxide and water with 1-octyl-3-methylimidazolium tetrafluoroborate at low temperatures

The interactions between three small molecules, water (H2O) , sulfur dioxide (SO2) and acetone ( (CH3)2CO ) with the ionic liquid (IL) 1-octyl-3-methylimidazolium tetrafluoroborate, [OMIM][BF4], have been determined using line of sight temperature programmed desorption (LOSTPD) from a gold surface. Multilayers of the IL were deposited by physical vapour deposition with multilayers of the small molecular species (adsorbed from the gas phase) at 90 K. LOSTPD was then carried out with the small molecular species desorbing first from the mixed multilayer, followed at higher temperatures by desorption of the IL from the gold surface. The IL had a high activation energy for desorption of 126(6) kJ mol-1 . Pure acetone showed a desorption activation energy of 38(2) kJ mol-1, which increased to 45 - 61 kJ mol-1 when it was pre-adsorbed below an overlying porous layer of the ionic liquid at 90 K. The stabilised acetone is thought to be associated with pores containing ionic moieties. Destabilised acetone was also observed and thought to originate from pores containing octyl chains. The quantity of stabilised acetone scaled with the amount of IL, being ≈ 1.1 molecules per IL ion pair. SO2 and H2O were co-adsorbed with the IL at 90 K leading to an intimate mixture of the two. For pure SO2 the desorption energy was 32(2) kJ mol-1, which increased to 40 - 50 kJ mol-1 for relative concentrations up to 6 SO2 molecules per IL ion pair. For pure water the activation energies were 49(5) kJ mol-1 and 43(1) kJ mol-1 for amorphous and crystalline ice respectively. When co-adsorbed with the IL the stabilisation energies were 42 - 49 kJ mol-1, but up to 505 water molecules per IL ion pair could be stabilised to some degree. The desorption mechanisms and the reasons for these interactions are discussed

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (SPLICEOSOMAL TIMEKEEPER LOCUS1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism. © 2012 American Society of Plant Biologists. All rights reserved

Direct Acceleration of Pickup Ions at The Solar Wind Termination Shock: The Production of Anomalous Cosmic Rays

We have modeled the injection and acceleration of pickup ions at the solar wind termination shock and investigated the parameters needed to produce the observed Anomalous Cosmic Ray (ACR) fluxes. A non-linear Monte Carlo technique was employed, which in effect solves the Boltzmann equation and is not restricted to near-isotropic particle distribution functions. This technique models the injection of thermal and pickup ions, the acceleration of these ions, and the determination of the shock structure under the influence of the accelerated ions. The essential effects of injection are treated in a mostly self-consistent manner, including effects from shock obliquity, cross- field diffusion, and pitch-angle scattering. Using recent determinations of pickup ion densities, we are able to match the absolute flux of hydrogen in the ACRs by assuming that pickup ion scattering mean free paths, at the termination shock, are much less than an AU and that modestly strong cross-field diffusion occurs. Simultaneously, we match the flux ratios He(+)/H(+) or O(+)/H(+) to within a factor approx. 5. If the conditions of strong scattering apply, no pre-termination-shock injection phase is required and the injection and acceleration of pickup ions at the termination shock is totally analogous to the injection and acceleration of ions at highly oblique interplanetary shocks recently observed by the Ulysses spacecraft. The fact that ACR fluxes can be modeled with standard shock assumptions suggests that the much-discussed "injection problem" for highly oblique shocks stems from incomplete (either mathematical or computer) modeling of these shocks rather than from any actual difficulty shocks may have in injecting and accelerating thermal or quasi-thermal particles

Non-linear Particle Acceleration in Oblique Shocks

We have developed a Monte Carlo technique for self-consistently calculating the hydrodynamic structure of oblique, steady-state shocks, together with the first-order Fermi acceleration process and associated non-thermal particle distributions. This is the first internally consistent treatment of modified shocks that includes cross-field diffusion of particles. Our method overcomes the injection problem faced by analytic descriptions of shock acceleration, and the lack of adequate dynamic range and artificial suppression of cross-field diffusion faced by plasma simulations; it currently provides the most broad and versatile description of collisionless shocks undergoing efficient particle acceleration. We present solutions for plasma quantities and particle distributions upstream and downstream of shocks, illustrating the strong differences observed between non-linear and test-particle cases. It is found that there are only marginal differences in the injection efficiency and resultant spectra for two extreme scattering modes, namely large-angle scattering and pitch-angle diffusion, for a wide range of shock parameters, i.e., for subluminal shocks with field obliquities less than or equal to 75 degrees and de Hoffmann-Teller frame speeds much less than the speed of light.Comment: 38 pages, 15 figures, AASTeX format, to appear in the Astrophysical Journal, December 20, 199