Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae

DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both non-coding and non-synonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50KB windows across the genomes of humans and non-human homininae. Interestingly, we find that while non-coding diversity is equally affected by these three genomic variables, non-synonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggests that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of non-synonymous to non-coding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes

Preservation and analytical procedures for the analysis of chloro-\u3ci\u3es\u3c/i\u3e-triazines and their chlorodegradate products in drinking waters using direct injection liquid chromatography tandem mass spectrometry

A direct injection, liquid chromatography tandemmass spectrometry (LC–MS/MS)method has been developed for the analysis of the chloro-s-triazine herbicides and their degradates in finished drinking water. The target compounds in the method were selected based on their inclusion in a common mechanism group (CMG) because of their ability to induce a similar toxic effect through a common mechanism of toxicity. The target list includes the chloro-s-triazines (atrazine, simazine, cyanazine, and propazine) and their dealkylated degradates (desethylatrazine, desisopropylatrazine, and diaminochlorotriazine). Potential matrix effects are minimized by the use of individual isotopically enriched internal standards. Analyte stability in finished chlorinated drinking water samples is ensured through careful selection of proper dechlorinating and antimicrobial reagents and through buffering sample pH. In the absence of proper dechlorination, the target analytes were found to degrade over a short period of time, even under refrigerated storage conditions. The final method has adequate sensitivity to accurately detect all target analytes at or below0.1µg/L and displays sufficient precision and robustness towarrant publication as EPA Method 536

Cryogenic, high power, near diffraction limited, Yb:YAG slab laser

A cryogenic slab laser that is suitable for scaling to high power, while taking full advantage of the improved thermo-optical and thermo-mechanical properties of Yb:YAG at cryogenic temperatures is described. The laser uses a conduction cooled, end pumped, zigzag slab geometry resulting in a near diffraction limited, robust, power scalable design. The design and the initial characterization of the laser up to 200W are presented.Miftar Ganija, David Ottaway, Peter Veitch and Jesper Munc

The Wage Effects of Offshoring: Evidence from Danish Matched Worker-Firm Data

We estimate how offshoring and exporting affect wages by skill type. Our data match the population of Danish workers to the universe of private-sector Danish firms, whose trade flows are broken down by product and origin and destination countries. Our data reveal new stylized facts about offshoring activities at the firm level, and allow us to both condition our identification on within-job-spell changes and construct instruments for offshoring and exporting that are time varying and uncorrelated with the wage setting of the firm. We find that within job spells, (1) offshoring tends to increase the high-skilled wage and decrease the low-skilled wage; (2) exporting tends to increase the wages of all skill types; (3) the net wage effect of trade varies substantially across workers of the same skill type; and (4) conditional on skill, the wage effect of offshoring exhibits additional variation depending on task characteristics. We then track the outcomes for workers after a job spell and find that those displaced from offshoring firms suffer greater earnings losses than other displaced workers, and that low-skilled workers suffer greater and more persistent earnings losses than high-skilled workers.

Constraining nonlinear time series modeling with the metabolic theory of ecology

Forecasting the response of ecological systems to environmental change is a critical challenge for sustainable management. The metabolic theory of ecology (MTE) posits scaling of biological rates with temperature, but it has had limited application to population dynamic forecasting. Here we use the temperature dependence of the MTE to constrain empirical dynamic modeling (EDM), an equation-free nonlinear machine learning approach for forecasting. By rescaling time with temperature and modeling dynamics on a “metabolic time step,” our method (MTE-EDM) improved forecast accuracy in 18 of 19 empirical ectotherm time series (by 19% on average), with the largest gains in more seasonal environments. MTE-EDM assumes that temperature affects only the rate, rather than the form, of population dynamics, and that interacting species have approximately similar temperature dependence. A review of laboratory studies suggests these assumptions are reasonable, at least approximately, though not for all ecological systems. Our approach highlights how to combine modern data-driven forecasting techniques with ecological theory and mechanistic understanding to predict the response of complex ecosystems to temperature variability and trends

Overview of Advanced LIGO Adaptive Optics

This is an overview of the adaptive optics used in Advanced LIGO (aLIGO), known as the thermal compensation system (TCS). The thermal compensation system was designed to minimize thermally-induced spatial distortions in the interferometer optical modes and to provide some correction for static curvature errors in the core optics of aLIGO. The TCS is comprised of ring heater actuators, spatially tunable CO$_{2}$ laser projectors and Hartmann wavefront sensors. The system meets the requirements of correcting for nominal distortion in Advanced LIGO to a maximum residual error of 5.4nm, weighted across the laser beam, for up to 125W of laser input power into the interferometer