Hearing the grass grow. Emotional and epistemological challenges of practice-near research

This paper discusses the concept of practice-near research in terms of the emotional and epistemological challenges that arise from the researcher coming 'near' enough to other people for psychological processes to ensue. These may give rise in the researcher to confusion, anxiety and doubt about who is who and what is what; but also to the possibility of real emotional and relational depth in the research process. Using illustrations from three social work doctoral research projects undertaken by students at the Tavistock Clinic and the University of East London the paper examines four themes that seem to the author to be central to meaningful practice-near research undertaken in a spirit of true emotional and epistemological open-mindedness: the smell of the real; losing our minds; the inevitability of personal change; and the discovery of complex particulars

Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

How To Model Supernovae in Simulations of Star and Galaxy Formation

We study the implementation of mechanical feedback from supernovae (SNe) and stellar mass loss in galaxy simulations, within the Feedback In Realistic Environments (FIRE) project. We present the FIRE-2 algorithm for coupling mechanical feedback, which can be applied to any hydrodynamics method (e.g. fixed-grid, moving-mesh, and mesh-less methods), and black hole as well as stellar feedback. This algorithm ensures manifest conservation of mass, energy, and momentum, and avoids imprinting 'preferred directions' on the ejecta. We show that it is critical to incorporate both momentum and thermal energy of mechanical ejecta in a self-consistent manner, accounting for SNe cooling radii when they are not resolved. Using idealized simulations of single SN explosions, we show that the FIRE-2 algorithm, independent of resolution, reproduces converged solutions in both energy and momentum. In contrast, common 'fully-thermal' (energy-dump) or 'fully-kinetic' (particle-kicking) schemes in the literature depend strongly on resolution: when applied at mass resolution >100 solar masses, they diverge by orders-of-magnitude from the converged solution. In galaxy-formation simulations, this divergence leads to orders-of-magnitude differences in galaxy properties, unless those models are adjusted in a resolution-dependent way. We show that all models that individually time-resolve SNe converge to the FIRE-2 solution at sufficiently high resolution. However, in both idealized single-SN simulations and cosmological galaxy-formation simulations, the FIRE-2 algorithm converges much faster than other sub-grid models without re-tuning parameters.Comment: 18 pages, 9 figures (+8 pages, 6 figures in appendices). MNRAS (updated to match published version

A Predicted Correlation Between Age Gradient and Star Formation History in FIRE Dwarf Galaxies

We explore the radial variation of star formation histories in dwarf galaxies simulated with Feedback In Realistic Environments (FIRE) physics. The sample contains 9 low-mass field dwarfs with M_ star = 10^5 - 10^7 M_sun from previous FIRE results, and a new suite of 17 higher mass field dwarfs with M_star = 10^7 - 10^9 M_sun introduced here. We find that age gradients are common in our dwarfs, with older stars dominant at large radii. The strength of the gradient correlates with overall galaxy age such that earlier star formation produces a more pronounced gradient. The relation between formation time and strength of the gradient is driven by both mergers and star-formation feedback. Mergers can both steepen and flatten the age gradient depending on the timing of the merger and star formation history of the merging galaxy. In galaxies without significant mergers, early feedback pushes stars to the outskirts at early times. Interestingly, among galaxies without mergers, those with large dark matter cores have flatter age gradients because these galaxies have more late-time feedback. If real galaxies have age gradients as we predict, stellar population studies that rely on sampling a limited fraction of a galaxy can give a biased view of its global star formation history. We show that central fields can be biased young by a few Gyrs while outer fields are biased old. Fields positioned near the 2D half-light radius will provide the least biased measure of a dwarf galaxy's global star formation history.Comment: 13 pages, 8 figures. Submitted to MNRAS, comments welcom

Simulating galaxies in the reionization era with FIRE-2: morphologies and sizes

We study the morphologies and sizes of galaxies at z>5 using high-resolution cosmological zoom-in simulations from the Feedback In Realistic Environments project. The galaxies show a variety of morphologies, from compact to clumpy to irregular. The simulated galaxies have more extended morphologies and larger sizes when measured using rest-frame optical B-band light than rest-frame UV light; sizes measured from stellar mass surface density are even larger. The UV morphologies are usually dominated by several small, bright young stellar clumps that are not always associated with significant stellar mass. The B-band light traces stellar mass better than the UV, but it can also be biased by the bright clumps. At all redshifts, galaxy size correlates with stellar mass/luminosity with large scatter. The half-light radii range from 0.01 to 0.2 arcsec (0.05-1 kpc physical) at fixed magnitude. At z>5, the size of galaxies at fixed stellar mass/luminosity evolves as (1+z)^{-m}, with m~1-2. For galaxies less massive than M_star~10^8 M_sun, the ratio of the half-mass radius to the halo virial radius is ~10% and does not evolve significantly at z=5-10; this ratio is typically 1-5% for more massive galaxies. A galaxy's "observed" size decreases dramatically at shallower surface brightness limits. This effect may account for the extremely small sizes of z>5 galaxies measured in the Hubble Frontier Fields. We provide predictions for the cumulative light distribution as a function of surface brightness for typical galaxies at z=6.Comment: 11 pages, 11 figures, resubmitted to MNRAS after revision for referee's comment

Molecular Cloning and Heterologous Expression of the Dehydrophos Biosynthetic Gene Cluster

SummaryDehydrophos is a vinyl phosphonate tripeptide produced by Streptomyces luridus with demonstrated broad-spectrum antibiotic activity. To identify genes necessary for biosynthesis of this unusual compound we screened a fosmid library of S. luridus for the presence of the phosphoenolpyruvate mutase gene, which is required for biosynthesis of most phosphonates. Integration of one such fosmid clone into the chromosome of S. lividans led to heterologous production of dehydrophos. Deletion analysis of this clone allowed identification of the minimal contiguous dehydrophos cluster, which contained 17 open reading frames (ORFs). Bioinformatic analyses of these ORFs are consistent with a proposed biosynthetic pathway that generates dehydrophos from phosphoenolpyruvate. The early steps of this pathway are supported by analysis of intermediates accumulated by blocked mutants and in vitro biochemical experiments

Using Automated Health Plan Data to Assess Infection Risk from Coronary Artery Bypass Surgery

We determined if infection indicators were sufficiently consistent across health plans to allow comparison of hospitals’ risks of infection after coronary artery bypass surgery. Three managed care organizations accounted for 90% of managed care in eastern Massachusetts, from October 1996 through March 1999. We searched automated inpatient and outpatient claims and outpatient pharmacy dispensing files for indicator codes suggestive of postoperative surgical site infection. We reviewed full text medical records of patients with indicator codes to confirm infection status. We compared the hospital-specific proportions of cases with an indicator code, adjusting for health plan, age, sex, and chronic disease score. A total of 536 (27%) of 1,953 patients had infection indicators. Infection was confirmed in 79 (53%) of 149 reviewed records with adequate documentation. The proportion of patients with an indicator of infection varied significantly (p<0.001) between hospitals (19% to 36%) and health plans (22% to 33%). The difference between hospitals persisted after adjustment for health plan and patients’ age and sex. Similar relationships were observed when postoperative antibiotic information was ignored. Automated claims and pharmacy data from different health plans can be used together to allow inexpensive, routine monitoring of indicators of postoperative infection, with the goal of identifying institutions that can be further evaluated to determine if risks for infection can be reduced