Summary Visualizations of Gene Ontology Terms With GO-Figure!

The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large-scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualizations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualization tools and resources there is a lack of standalone open-source software solutions that facilitate explorations of key features of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualizations of lists of GO terms, designed to support exploratory data analyses and dataset comparisons

Constraining the properties of neutron star crusts with the transient low-mass X-ray binary Aql X-1

Aql X-1 is a prolific transient neutron star low-mass X-ray binary that exhibits an accretion outburst approximately once every year. Whether the thermal X-rays detected in intervening quiescent episodes are the result of cooling of the neutron star or due to continued low-level accretion remains unclear. In this work we use Swift data obtained after the long and bright 2011 and 2013 outbursts, as well as the short and faint 2015 outburst, to investigate the hypothesis that cooling of the accretion-heated neutron star crust dominates the quiescent thermal emission in Aql X-1. We demonstrate that the X-ray light curves and measured neutron star surface temperatures are consistent with the expectations of the crust cooling paradigm. By using a thermal evolution code, we find that ~1.2-3.2 MeV/nucleon of shallow heat release describes the observational data well, depending on the assumed mass-accretion rate and temperature of the stellar core. We find no evidence for varying strengths of this shallow heating after different outbursts, but this could be due to limitations of the data. We argue that monitoring Aql X-1 for up to ~1 year after future outbursts can be a powerful tool to break model degeneracies and solve open questions about the magnitude, depth and origin of shallow heating in neutron star crusts.Comment: 14 pages, 5 figures, 3 tables, accepted to MNRA

Tannakian approach to linear differential algebraic groups

Tannaka's Theorem states that a linear algebraic group G is determined by the category of finite dimensional G-modules and the forgetful functor. We extend this result to linear differential algebraic groups by introducing a category corresponding to their representations and show how this category determines such a group.Comment: 31 pages; corrected misprint

Arboreal forage lichen response to partial cutting of high elevation mountain caribou range in the Quesnel Higland of east-central British Columbia

Group selection silvicultural systems have been recommended for managing mountain caribou (Rangifer tarandus caribou) habitat in high elevation Engelmann spruce – subalpine fir forests in east-central British Columbia. We measured the response of arboreal lichen (a key winter forage) to harvesting of 30% of the forested area using three partial cutting treatments, which created small (0.03 ha), medium (0.13 ha), and large (1.0 ha) openings, and a no-harvest treatment. Treatments were replicated on four sites, and monitored over a ten year post-harvest period. The short-term loss of lichen associated with removal of approximately one third of the trees was partially offset by a significant (P=0.01) increase in lichen abundance on trees in the caribou feeding zone (up to 4.5 m) in the three partial cutting treatments relative to trees in the uncut forest. Differences among treatments in the change in lichen composition, as measured by the percentage of Alectoria sarmentosa and Bryoria spp., were marginally significant (P=0.10). The partial cutting treatments showing a greater likelihood of shifting towards more Bryoria spp. than no-harvest treatment (P=0.04). In the year of harvest (1993), larger trees were found to hold more lichen than smaller trees (P=0.04), and live trees supported more lichen than dead trees (P=0.01), but lichen loading was similar among tree species (P=0.51). Tree fall rates were similar among treatments, based on the ten year average (0.6–0.8% of sample trees per year). The results indicate that caribou foraging habitat is maintained in the residual forest when group selection systems that remove only 30% of the trees are applied. Information on the distribution of lichen is useful for developing stand level prescriptions. Providing lichen bearing habitat meets just one of the needs of caribou. A comprehensive approach that considers all factors and their interactions is essential to maintain and recover the threatened mountain caribou

Terrestrial lichen response to partial cutting in lodgepole pine forests on caribou winter range in west-central British Columbia

In west-central British Columbia, terrestrial lichens located in older, lodgepole pine (Pinus contorta) forests are important winter forage for woodland caribou (Rangifer tarandus caribou). Clearcut harvesting effectively removes winter forage habitat for decades, so management approaches based on partial cutting were designed to maintain continuous lichen-bearing habitat for caribou. This study tested a group selection system, based on removal of 33% of the forest every 80 years in small openings (15 m diameter), and two irregular shelterwood treatments (whole-tree and stem-only harvesting methods) where 50% of the stand area is cut every 70 years in 20 to 30 m diameter openings. The abundance of common terrestrial lichens among the partial cutting and no-harvest treatments was compared across five replicate blocks, pre-harvest (1995) and post-harvest (1998, 2000 and 2004). The initial loss of preferred forage lichens (Cladonia, Cladina, Cetraria and Stereocaulon) was similar among harvesting treatments, but there was greater reduction in these lichens in the openings than in the residual forest. After eight years, forage lichens in the group selection treatment recovered to pre-harvest amounts, while lichen in the shelterwood treatments steadily increased from 49 to 57% in 1998 to about 70% of pre-harvest amounts in 2004. Although not part of the randomized block design, there was substantially less lichen in three adjacent clearcut blocks than in the partial cuts. Regression analysis pre- and post-harvest indicated that increased cover of trees, shrubs, herbs, woody debris and logging slash corresponded with decreased forage lichen abundance. In the short-term, forestry activities that minimize inputs of woody debris, control herb and shrub development, and moderate the changes in light and temperatures associated with canopy removal will lessen the impact on lichen. Implementation of stand level prescriptions is only one aspect of caribou habitat management. A comprehensive approach should consider all factors and their interactions to maintain a viable population of woodland caribou in west-central British Columbia

Tidally Driven Processes Leading to Near-Field Turbulence in a Channel at the Crest of the Mendocino Escarpment*

In situ observations of tidally driven turbulence were obtained in a small channel that transects the crest of the Mendocino Ridge, a site of mixed (diurnal and semidiurnal) tides. Diurnal tides are subinertial at this latitude, and once per day a trapped tide leads to large flows through the channel giving rise to tidal excursion lengths comparable to the width of the ridge crest. During these times, energetic turbulence is observed in the channel, with overturns spanning almost half of the full water depth. A high-resolution, nonhydrostatic, 2.5-dimensional simulation is used to interpret the observations in terms of the advection of a breaking tidal lee wave that extends from the ridge crest to the surface and the subsequent development of a hydraulic jump on the flanks of the ridge. Modeled dissipation rates show that turbulence is strongest on the flanks of the ridge and that local dissipation accounts for 28% of the energy converted from the barotropic tide into baroclinic motion.United States. Office of Naval Research (Grant ONR N00014- 12-1-0943)National Science Foundation (U.S.). (Grant NSF OCE 1129763

On representations of super coalgebras

The general structure of the representation theory of a $Z_2$-graded coalgebra is discussed. The result contains the structure of Fourier analysis on compact supergroups and quantisations thereof as a special case. The general linear supergroups serve as an explicit illustration and the simplest example is carried out in detail.Comment: 18 pages, LaTeX, KCL-TH-94-

Extention of Finite Solvable Torsors over a Curve

Let $R$ be a discrete valuation ring with fraction field $K$ and with algebraically closed residue field of positive characteristic $p$. Let $X$ be a smooth fibered surface over $R$ with geometrically connected fibers endowed with a section $x\in X(R)$. Let $G$ be a finite solvable $K$-group scheme and assume that either $|G|=p^n$ or $G$ has a normal series of length 2. We prove that every quotient pointed $G$-torsor over the generic fiber $X_{\eta}$ of $X$ can be extended to a torsor over $X$ after eventually extending scalars and after eventually blowing up $X$ at a closed subscheme of its special fiber $X_s$.Comment: 16 page

Cubic Curves, Finite Geometry and Cryptography

Some geometry on non-singular cubic curves, mainly over finite fields, is surveyed. Such a curve has 9,3,1 or 0 points of inflexion, and cubic curves are classified accordingly. The group structure and the possible numbers of rational points are also surveyed. A possible strengthening of the security of elliptic curve cryptography is proposed using a `shared secret' related to the group law. Cubic curves are also used in a new way to construct sets of points having various combinatorial and geometric properties that are of particular interest in finite Desarguesian planes.Comment: This is a version of our article to appear in Acta Applicandae Mathematicae. In this version, we have corrected a sentence in the third paragraph. The final publication is available at springerlink.com at http://www.springerlink.com/content/xh85647871215644