Conley: Computing connection matrices in Maple

In this work we announce the Maple package conley to compute connection and C-connection matrices. conley is based on our abstract homological algebra package homalg. We emphasize that the notion of braids is irrelevant for the definition and for the computation of such matrices. We introduce the notion of triangles that suffices to state the definition of (C)-connection matrices. The notion of octahedra, which is equivalent to that of braids is also introduced.Comment: conley is based on the package homalg: math.AC/0701146, corrected the false "counter example

Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures

Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus. We present a structural comparison of several members of the Caliciviridae, showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures. Furthermore, at intermediate resolutions we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera, such as sapovirus and rabbit haemorrhagic disease virus. Phylogenetic analysis confirms vesivirus 2117 as a vesivirus closely related to canine vesiviruses. We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage

Measuring Ejecta Velocity Improves Type Ia Supernova Distances

We use a sample of 121 spectroscopically normal Type Ia supernovae (SNe Ia) to show that their intrinsic color is correlated with their ejecta velocity, as measured from the blueshift of the Si II 6355 feature near maximum brightness, v_Si. The SN Ia sample was originally used by Wang et al. (2009) to show that the relationship between color excess and peak magnitude, which in the absence of intrinsic color differences describes a reddening law, was different for two subsamples split by v_Si (defined as "Normal" and "High-Velocity"). We verify this result, but find that the two subsamples have the same reddening law when extremely reddened events (E(B-V) > 0.35 mag) are excluded. We also show that (1) the High-Velocity subsample is offset by ~0.06 mag to the red from the Normal subsample in the (B_max - V_max) - M_V plane, (2) the B_max - V_max cumulative distribution functions of the two subsamples have nearly identical shapes, but the High-Velocity subsample is offset by ~0.07 mag to the red in B_max - V_max, and (3) the bluest High-Velocity SNe Ia are ~0.10 mag redder than the bluest Normal SNe Ia. Together, this evidence indicates a difference in intrinsic color for the subsamples. Accounting for this intrinsic color difference reduces the scatter in Hubble residuals from 0.190 mag to 0.130 mag for SNe Ia with A_V < 0.7 mag. The scatter can be further reduced to 0.109 mag by exclusively using SNe Ia from the Normal subsample. Additionally, this result can at least partially explain the anomalously low values of R_V found in large SN Ia samples. We explain the correlation between ejecta velocity and color as increased line blanketing in the High-Velocity SNe Ia, causing them to become redder. We discuss some implications of this result, and stress the importance of spectroscopy for future SN Ia cosmology surveys, with particular focus on the design of WFIRST.Comment: 9 pages, 8 figures, submitted to Ap

Local and Remote Mean and Extreme Temperature Response to Regional Aerosol Emissions Reductions

The climatic implications of regional aerosol and precursor emissions reductions implemented to protect human health are poorly understood. We investigate the mean and extreme temperature response to regional changes in aerosol emissions using three coupled chemistryclimate models: NOAA GFDL CM3, NCAR CESM1, and NASA GISS-E2. Our approach contrasts a long present-day control simulation from each model (up to 400 years with perpetual year 2000 or 2005 emissions) with 14 individual aerosol emissions perturbation simulations (160240 years each). We perturb emissions of sulfur dioxide (SO2) and/or carbonaceous aerosol within six world regions and assess the statistical significance of mean and extreme temperature responses relative to internal variability determined by the control simulation and across the models. In all models, the global mean surface temperature response (perturbation minus control) to SO2 and/or carbonaceous aerosol is mostly positive (warming) and statistically significant and ranges from +0.17 K (Europe SO2) to -0.06 K (US BC). The warming response to SO2 reductions is strongest in the US and Europe perturbation simulations, both globally and regionally, with Arctic warming up to 1 K due to a removal of European anthropogenic SO2 emissions alone; however, even emissions from regions remote to the Arctic, such as SO2 from India, significantly warm the Arctic by up to 0.5 K. Arctic warming is the most robust response across each model and several aerosol emissions perturbations. The temperature response in the Northern Hemisphere midlatitudes is most sensitive to emissions perturbations within that region. In the tropics, however, the temperature response to emissions perturbations is roughly the same in magnitude as emissions perturbations either within or outside of the tropics. We find that climate sensitivity to regional aerosol perturbations ranges from 0.5 to 1.0 K (W m(exp -2))(exp -1) depending on the region and aerosol composition and is larger than the climate sensitivity to a doubling of CO2 in two of three models. We update previous estimates of regional temperature potential (RTP), a metric for estimating the regional temperature responses to a regional emissions perturbation that can facilitate assessment of climate impacts with integrated assessment models without requiring computationally demanding coupled climate model simulations. These calculations indicate a robust regional response to aerosol forcing within the Northern Hemisphere midlatitudes, regardless of where the aerosol forcing is located longitudinally. We show that regional aerosol perturbations can significantly increase extreme temperatures on the regional scale. Except in the Arctic in the summer, extreme temperature responses largely mirror mean temperature responses to regional aerosol perturbations through a shift of the temperature distributions and are mostly dominated by local rather than remote aerosol forcing

Endophenotypes for Age-Related Macular Degeneration: Extending Our Reach into the Preclinical Stages of Disease.

The key to reducing the individual and societal burden of age-related macular degeneration (AMD)-related vision loss, is to be able to initiate therapies that slow or halt the progression at a point that will yield the maximum benefit while minimizing personal risk and cost. There is a critical need to find clinical markers that, when combined with the specificity of genetic testing, will identify individuals at the earliest stages of AMD who would benefit from preventive therapies. These clinical markers are endophenotypes for AMD, present in those who are likely to develop AMD, as well as in those who have clinical evidence of AMD. Clinical characteristics associated with AMD may also be possible endophenotypes if they can be detected before or at the earliest stages of the condition, but we and others have shown that this may not always be valid. Several studies have suggested that dynamic changes in rhodopsin regeneration (dark adaptation kinetics and/or critical flicker fusion frequencies) may be more subtle indicators of AMD-associated early retinal dysfunction. One can test for the relevance of these measures using genetic risk profiles based on known genetic risk variants. These functional measures may improve the sensitivity and specificity of predictive models for AMD and may also serve to delineate clinical subtypes of AMD that may differ with respect to prognosis and treatment

Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

The Baltic Sea is the world's largest area suffering from eutrophication-driven hypoxia. Low oxygen levels are threatening its biodiversity and ecosystem functioning. The main causes for eutrophication-driven hypoxia are high nutrient loadings and global warming. Wastewater treatment plants (WWTP) contribute to eutrophication as they are important sources of nitrogen to coastal areas. Here, we evaluated the effects of wastewater treatment plant effluent inputs on Baltic Sea planktonic communities in four experiments. We tested for effects of effluent inputs on chlorophyll <i>a</i> content, bacterial community composition, and metabolic rates: gross primary production (GPP), net community production (NCP), community respiration (CR) and bacterial production (BP). Nitrogen-rich dissolved organic matter (DOM) inputs from effluents increased bacterial production and decreased primary production and community respiration. Nutrient amendments and seasonally variable environmental conditions lead to lower alpha-diversity and shifts in bacterial community composition (e.g. increased abundance of a few cyanobacterial populations in the summer experiment), concomitant with changes in metabolic rates. An increase in BP and decrease in CR could be caused by high lability of the DOM that can support secondary bacterial production, without an increase in respiration. Increases in bacterial production and simultaneous decreases of primary production lead to more carbon being consumed in the microbial loop, and may shift the ecosystem towards heterotrophy

Oxy-functionalization of nucleophilic rhenium(I) metal carbon bonds catalyzed by selenium(IV)

We report that SeO_2 catalyzes the facile oxy-functionalization of (CO)_5Re(I)-Me^(δ−) with IO_4− to generate methanol. Mechanistic studies and DFT calculations reveal that catalysis involves methyl group transfer from Re to the electrophilic Se center followed by oxidation and subsequent reductive functionalization of the resulting CH_3Se(VI) species. Furthermore, (CO)_3Re(I)(Bpy)-R (R = ethyl, n-propyl, and aryl) complexes show analogous transfer to SeO_2 to generate the primary alcohols. This represents a new strategy for the oxy-functionalization of M−R^(δ−) polarized bonds

Stratospheric ozone chemistry feedbacks are not critical for the determination of climate sensitivity in CESM1(WACCM)

The Community Earth System Model‐Whole Atmosphere Community Climate Model (CESM1‐WACCM) is used to assess the importance of including chemistry feedbacks in determining the equilibrium climate sensitivity (ECS). Two 4×CO2 model experiments were conducted: one with interactive chemistry and one with chemical constituents other than CO2 held fixed at their preindustrial values. The ECS determined from these two experiments agrees to within 0.01 K. Similarly, the net feedback parameter agrees to within 0.01 W m−2 K−1. This agreement occurs in spite of large changes in stratospheric ozone found in the simulation with interactive chemistry: a 30% decrease in the tropical lower stratosphere and a 40% increase in the upper stratosphere, broadly consistent with other published estimates. Off‐line radiative transfer calculations show that ozone changes alone account for the difference in radiative forcing. We conclude that at least for determining global climate sensitivity metrics, the exclusion of chemistry feedbacks is not a critical source of error in CESM