Diffusion Approximations for Demographic Inference: DaDi

Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date

Combustion chemistry of solid propellants

Several studies are described of the chemistry of solid propellant combustion which employed a fast-scanning optical spectrometer. Expanded abstracts are presented for four of the studies which were previously reported. One study of the ignition of composite propellants yielded data which suggested early ammonium perchlorate decomposition and reaction. The results of a study of the spatial distribution of molecular species in flames from uncatalyzed and copper or lead catalyzed double-based propellants support previously published conclusions concerning the site of action of these metal catalysts. A study of the ammonium-perchlorate-polymeric-fuel-binder reaction in thin films, made by use of infrared absorption spectrometry, yielded a characterization of a rapid condensed-phase reaction which is likely important during the ignition transient and the burning process

The neck as a keystone structure in avian macroevolution and mosaicism

BACKGROUND: The origin of birds from non-avian theropod dinosaur ancestors required a comprehensive restructuring of the body plan to enable the evolution of powered flight. One of the proposed key mechanisms that allowed birds to acquire flight and modify the associated anatomical structures into diverse forms is mosaic evolution, which describes the parcelization of phenotypic traits into separate modules that evolve with heterogeneous tempo and mode. Avian mosaicism has been investigated with a focus on the cranial and appendicular skeleton, and as such, we do not understand the role of the axial column in avian macroevolution. The long, flexible neck of extant birds lies between the cranial and pectoral modules and represents an opportunity to study the contribution of the axial skeleton to avian mosaicism. RESULTS: Here, we use 3D geometric morphometrics in tandem with phylogenetic comparative methods to provide, to our knowledge, the first integrative analysis of avian neck evolution in context with the head and wing and to interrogate how the interactions between these anatomical systems have influenced macroevolutionary trends across a broad sample of extant birds. We find that the neck is integrated with both the head and the forelimb. These patterns of integration are variable across clades, and only specific ecological groups exhibit either head-neck or neck-forelimb integration. Finally, we find that ecological groups that display head-neck and neck-forelimb integration tend to display significant shifts in the rate of neck morphological evolution. CONCLUSIONS: Combined, these results suggest that the interaction between trophic ecology and head-neck-forelimb mosaicism influences the evolutionary variance of the avian neck. By linking together the biomechanical functions of these distinct anatomical systems, the cervical vertebral column serves as a keystone structure in avian mosaicism and macroevolution

Ammonium-perchlorate diffusion flames - A spectrographic investigation

Spectroscopic analyses on ammonium perchlorate diffusion flames with various fuel

Trends and Variability in Localized Precipitation Around Kibale National Park, Uganda, Africa

Our objective was to understand and describe local spatial and temporal variability in precipitation around Kibale National Park, a tropical forest area of high conservation value. Continental or regional-scale trends are often relied upon to make policy and management decisions, but these analyses are often at too coarse a resolution to capture important variability at a finer scale where management actions operate. Monthly rainfall data derived from ten long-term station records (1941-1975) were used to evaluate local spatiotemporal variability in seasonal and annual rainfall for the area surrounding Kibale National Park. The magnitude, direction and significance of trends in seasonal and annual rainfall within the area surrounding the park were identified using the Mann-Kendall trend test and Sen’s slope estimator. The standardized precipitation index was calculated at 3- and 12-month periods to identify areas of relative wetness or dryness. Analysis of annual trends and precipitation indices indicated that patterns in annual time series do not reflect the direction and magnitude of seasonal trends nor the spatial variability in intra-annual rainfall at the local scale. Significant negative trends in the seasonal long rains, following dry season and short rains were identified at stations west of Kibale, while significant positive trends in the seasonal short rains occurred at stations north of the park. Stations along the western park boundary tended to have more years in which the two dry seasons were abnormally dry than those stations located further from the park

Slow dynamics at the smeared phase transition of randomly layered magnets

We investigate a model for randomly layered magnets, viz. a three-dimensional Ising model with planar defects. The magnetic phase transition in this system is smeared because static long-range order can develop on isolated rare spatial regions. Here, we report large-scale kinetic Monte Carlo simulations of the dynamical behavior close to the smeared phase transition which we characterize by the spin (time) autocorrelation function. In the paramagnetic phase, its behavior is dominated by Griffiths effects similar to those in magnets with point defects. In the tail region of the smeared transition the dynamics is even slower: the autocorrelation function decays like a stretched exponential at intermediate times before approaching the exponentially small asymptotic value following a power law at late times. Our Monte-Carlo results are in good agreement with recent theoretical predictions based on optimal fluctuation theory.Comment: 7 pages, 6 eps figures, final version as publishe

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).</p

SALT Long-slit Spectroscopy of Luminous Obscured Quasars: An Upper Limit on the Size of the Narrow-Line Region?

We present spatially resolved long-slit spectroscopy from the Southern African Large Telescope (SALT) to examine the spatial extent of the narrow-line regions (NLRs) of a sample of 8 luminous obscured quasars at 0.10 < z < 0.43. Our results are consistent with an observed shallow slope in the relationship between NLR size and L_[OIII], which has been interpreted to indicate that NLR size is limited by the density and ionization state of the NLR gas rather than the availability of ionizing photons. We also explore how the NLR size scales with a more direct measure of instantaneous AGN power using mid-IR photometry from WISE, which probes warm to hot dust near the central black hole and so, unlike [OIII], does not depend on the properties of the NLR. Using our results as well as samples from the literature, we obtain a power-law relationship between NLR size and L_8micron that is significantly steeper than that observed for NLR size and L_[OIII]. We find that the size of the NLR goes approximately as L^(1/2)_8micron, as expected from the simple scenario of constant-density clouds illuminated by a central ionizing source. We further see tentative evidence for a flattening of the relationship between NLR size and L_8micron at the high luminosity end, and propose that we are seeing a limiting NLR size of 10 - 20 kpc, beyond which the availability of gas to ionize becomes too low. We find that L_[OIII] ~ L_8micron^(1.4), consistent with a picture in which the L_[OIII] is dependent on the volume of the NLR. These results indicate that high-luminosity quasars have a strong effect in ionizing the available gas in a galaxy.Comment: 9 Pages, 5 figures, accepted to Ap

Identification and cost of adverse events in metastatic breast cancer in taxane and capecitabine based regimens.

PurposeWe sought to compare the economic impact of treatment-related adverse events (AEs) in patients with metastatic breast cancer (mBC) using taxane- or capecitabine-based treatment regimens as either first- or second-line (FL or SL) therapy in the US.MethodsWe used healthcare claims data from the Truven Health Analytics MarketScan® Commercial Databases to conduct a retrospective cohort study comparing the economic impact of AEs amongst taxane- and capecitabine-treated mBC patients in the US. We selected women diagnosed with mBC between 2008-2010 who received a taxane or capecitabine as first- or second-line (FL or SL) chemotherapy. Costs related to hospitalization, outpatient services, emergency department visits, chemotherapy and other medications were tabulated and combined to determine total healthcare costs. The incremental monthly costs associated with the presence of AEs compared to no AEs were estimated using generalized linear models, controlling for age and Charlson Comorbidity Index.ResultsWe identified 15,443 mBC patients meeting inclusion criteria. Adjusted total monthly costs were significantly higher in those who experienced AEs than in those without AEs in both lines of treatment (FL incremental cost: taxanes $1,142, capecitabine$1,817; SL incremental cost: taxanes $1,448, capecitabine$4,437). Total costs increased with the number of AEs and were primarily driven by increased hospitalization amongst those with AEs.ConclusionsAdverse events in taxane- or capecitabine-treated mBC patients are associated with significant increases in costs. Selecting treatment options associated with fewer AEs may reduce costs and improve outcomes in these patients