Jumble Java Byte Code to Measure the Effectiveness of Unit Tests

Jumble is a byte code level mutation testing tool for Java which inter-operates with JUnit. It has been designed to operate in an industrial setting with large projects. Heuristics have been included to speed the checking of mutations, for example, noting which test fails for each mutation and running this first in subsequent mutation checks. Significant effort has been put into ensuring that it can test code which uses custom class loading and reflection. This requires careful attention to class path handling and coexistence with foreign class-loaders. Jumble is currently used on a continuous basis within an agile programming environment with approximately 370,000 lines of Java code under source control. This checks out project code every fifteen minutes and runs an incremental set of unit tests and mutation tests for modified classes. Jumble is being made available as open source

Evidence that hematopoietic stem cell function is preserved during aging in long-lived S6K1 mutant mice

The mechanistic target of rapamycin (mTOR) signalling pathway plays a highly conserved role in aging; mice lacking ribosomal protein S6 kinase 1 (S6K1-/-) have extended lifespan and healthspan relative to wild type (WT) controls. Exactly how reduced mTOR signalling induces such effects is unclear, although preservation of stem cell function may be important. We show, using gene expression analyses, that there was a reduction in expression of cell cycle genes in young (12 week) and aged (80 week) S6K1-/- BM-derived c-Kit+ cells when compared to age-matched WT mice, suggesting that these cells are more quiescent in S6K1-/- mice. In addition, we investigated hematopoietic stem cell (HSC) frequency and function in young and aged S6K1-/- and WT mice. Young, but not aged, S6K1-/- mice had more LSK (lineage-, c-Kit+, Sca-1+) cells (% of bone marrow (BM)), including the most primitive long-term repopulating HSC (LT-HSC) relative to WT controls. Donor-derived engraftment of LT-HSCs in recipient mice was unaffected by genotype in young mice, but was enhanced in transplants using LT-HSCs derived from aged S6K1-/- mice. Our results are the first to provide evidence that age-associated HSC functional decline is ameliorated in a long-lived mTOR mutant mouse

A Lagrangian analysis of ice-supersaturated air over the North Atlantic

Understanding the nature of air parcels that exhibit ice-supersaturation is important because they are the regions of potential formation of both cirrus and aircraft contrails, which affect the radiation balance. Ice-supersaturated air parcels in the upper troposphere and lower stratosphere over the North Atlantic are investigated using Lagrangian trajectories. The trajectory calculations use ERA-Interim data for three winter and three summer seasons, resulting in approximately 200,000 trajectories with ice-supersaturation for each season. For both summer and winter, the median duration of ice-supersaturation along a trajectory is less than 6 hours. 5% of air which becomes ice-supersaturated in the troposphere, and 23% of air which becomes ice-supersaturated in the stratosphere will remain ice-supersaturated for at least 24 hours. Weighting the ice-supersaturation duration with the observed frequency indicates the likely overall importance of the longer duration ice-supersaturated trajectories. Ice-supersaturated air parcels typically experience a decrease in moisture content while ice-supersaturated, suggesting that cirrus clouds eventually form in the majority of such air. A comparison is made between short-lived (less than 24 h) and long-lived (greater than 24 h) ice-supersaturated air flows. For both air flows, ice-supersaturation occurs around the northernmost part of the trajectory. Short-lived ice-supersaturated air flows show no significant differences in speed or direction of movement to subsaturated air parcels. However, long-lived ice-supersaturated air occurs in slower moving air flows, which implies that they are not associated with the fastest moving air through a jet stream

Projected free energies for polydisperse phase equilibria

A `polydisperse' system has an infinite number of conserved densities. We give a rational procedure for projecting its infinite-dimensional free energy surface onto a subspace comprising a finite number of linear combinations of densities (`moments'), in which the phase behavior is then found as usual. If the excess free energy of the system depends only on the moments used, exact cloud, shadow and spinodal curves result; two- and multi-phase regions are approximate, but refinable indefinitely by adding extra moments. The approach is computationally robust and gives new geometrical insights into the thermodynamics of polydispersity.Comment: 4 pages, REVTeX, uses multicol.sty and epsf.sty, 1 postscript figure include

Fractal measures of spatial pattern as a heuristic for return rate in vegetative systems

Measurement of population persistence is a long-standing problem in ecology; in particular, whether it is possible to gain insights into persistence without long time-series. Fractal measurements of spatial patterns, such as the Korcak exponent or boundary dimension, have been proposed as indicators of the persistence of underlying dynamics. Here we explore under what conditions a predictive relationship between fractal measures and persistence exists. We combine theoretical arguments with an aerial snapshot and time series from a long-term study of seagrass. For this form of vegetative growth, we find that the expected relationship between the Korcak exponent and persistence is evident at survey sites where the population return rate can be measured. This highlights a limitation of the use of power-law patch-size distributions and other indicators based on spatial snapshots. Moreover, our numeric simulations show that for a single species and a range of environmental conditions that the Korcak–persistence relationship provides a link between temporal dynamics and spatial pattern; however, this relationship is specific to demographic factors, so we cannot use this methodology to compare between species

Biomaterial Strategies for Immunomodulation

Strategies to enhance, suppress, or qualitatively shape the immune response are of importance for diverse biomedical applications, such as the development of new vaccines, treatments for autoimmune diseases and allergies, strategies for regenerative medicine, and immunotherapies for cancer. However, the intricate cellular and molecular signals regulating the immune system are major hurdles to predictably manipulating the immune response and developing safe and effective therapies. To meet this challenge, biomaterials are being developed that control how, where, and when immune cells are stimulated in vivo, and that can finely control their differentiation in vitro. We review recent advances in the field of biomaterials for immunomodulation, focusing particularly on designing biomaterials to provide controlled immunostimulation, targeting drugs and vaccines to lymphoid organs, and serving as scaffolds to organize immune cells and emulate lymphoid tissues. These ongoing efforts highlight the many ways in which biomaterials can be brought to bear to engineer the immune system.Bill & Melinda Gates FoundationUnited States. Army Research Office. Institute for Soldier Nanotechnologies (Contract W911NF-13-D-0001)Ragon Institute of MGH, MIT and HarvardCancer Research Institute (New York, N.Y.) (Irvington Postdoctoral Fellowship)National Institutes of Health (U.S.) (Awards AI104715, CA172164, CA174795, and AI095109

Separable approximation to two-body matrix elements

Two-body matrix elements of arbitrary local interactions are written as the sum of separable terms in a way that is well suited for the exchange and pairing channels present in mean-field calculations. The expansion relies on the transformation to center of mass and relative coordinate (in the spirit of Talmi's method) and therefore it is only useful (finite number of expansion terms) for harmonic oscillator single particle states. The converge of the expansion with the number of terms retained is studied for a Gaussian two body interaction. The limit of a contact (delta) force is also considered. Ways to handle the general case are also discussed.Comment: 10 pages, 5 figures (for high resolution versions of some of the figures contact the author

Integral-Field Spectroscopy of the Post Red Supergiant IRC +10420: evidence for an axi-symmetric wind

We present NAOMI/OASIS adaptive-optics assisted integral-field spectroscopy of the transitional massive hypergiant IRC +10420, an extreme mass-losing star apparently in the process of evolving from a Red Supergiant toward the Wolf-Rayet phase. To investigate the present-day mass-loss geometry of the star, we study the appearance of the line-emission from the inner wind as viewed when reflected off the surrounding nebula. We find that, contrary to previous work, there is strong evidence for wind axi-symmetry, based on the equivalent-width and velocity variations of H$\alpha$ and Fe {\sc ii} $\lambda$6516. We attribute this behaviour to the appearance of the complex line-profiles when viewed from different angles. We also speculate that the Ti {\sc ii} emission originates in the outer nebula in a region analogous to the Strontium Filament of $\eta$ Carinae, based on the morphology of the line-emission. Finally, we suggest that the present-day axisymmetric wind of IRC +10420, combined with its continued blueward evolution, is evidence that the star is evolving toward the B[e] supergiant phase.Comment: 22 pages, 9 figures, accepted for publication in ApJ. B&W-optimized version can be downloaded from http://www.cis.rit.edu/~bxdpci/pubs.htm