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  • 1
    Publication Date: 2015-08-11
    Description: Policy makers in the United States often justify agricultural subsidies by stressing that agriculture is the engine of the rural economy. We use the increase in crop prices in the late 2000s to estimate the marginal effect of increased agricultural revenues on local economies in the U.S. Heartland. We find that $1 more in crop revenue generated 64¢ in personal income, with most going to farm proprietors and workers (59%) or nonfarmers who own farm assets (36%). The evidence suggests a weak link between revenues and nonfarm income or employment, or on population. Cuts to agricultural subsidies are therefore likely to have little effect on the broader rural economy in regions like the Heartland.
    Keywords: J43 - Agricultural Labor Markets, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 2
    Publication Date: 2016-07-15
    Description: This is the first of two papers describing the observations and cataloguing of deep 3-GHz observations of the Lockman Hole North using the Karl G. Jansky Very Large Array. The aim of this paper is to investigate, through the use of simulated images, the uncertainties and accuracy of source-finding routines, as well as to quantify systematic effects due to resolution, such as source confusion and source size. While these effects are not new, this work is intended as a particular case study that can be scaled and translated to other surveys. We use the simulations to derive uncertainties in the fitted parameters, as well as bias corrections for the actual catalogue (presented in Paper II). We compare two different source-finding routines, OBIT and AEGEAN, and two different effective resolutions, 8 and 2.75  arcsec. We find that the two routines perform comparably well, with OBIT being slightly better at de-blending sources, but slightly worse at fitting resolved sources. We show that 30–70 per cent of sources are missed or fit inaccurately once the source size becomes larger than the beam, possibly explaining source count errors in high-resolution surveys. We also investigate the effect of blending, finding that any sources with separations smaller than the beam size are fit as single sources. We show that the use of machine-learning techniques can correctly identify blended sources up to 90 per cent of the time, and prior-driven fitting can lead to a 70 per cent improvement in the number of de-blended sources.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2015-02-14
    Description: Although population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole-genome sequences from 14 western lowland gorillas ( Gorilla gorilla gorilla ), 2 eastern lowland gorillas ( G. beringei graueri ), and a single Cross River individual ( G. gorilla diehli ). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor approximately 261 ka, and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage approximately 68 ka. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of 1.4-fold around 970 ka and a recent 5.6-fold contraction in population size 23 ka. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 4
    Publication Date: 2012-03-01
    Description: : Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available. Availability: http://roundup.hms.harvard.edu Contact: dpwall@hms.harvard.edu ; todd_deluca@hms.harvard.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2014-10-04
    Description: : Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Availability and implementation: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu . Contact: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu . Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2015-01-09
    Description: We present a study of diffuse extragalactic radio emission at 1.75 GHz from part of the ELAIS-S1 (European Large Area Infrared Space Observatory Survey – South 1) field using the Australia Telescope Compact Array. The resulting mosaic is 2.46 deg 2 , with a roughly constant noise region of 0.61 deg 2 used for analysis. The image has a beam size of 150 arcsec x 60 arcsec and instrumental 〈 n 〉 = (52 ± 5) μJy beam –1 . Using point-source models from the Australia Telescope Large Area Survey, we subtract the discrete emission in this field for S ≥ 150 μJy beam –1 . Comparison of the source-subtracted probability distribution, or P(D) , with the predicted distribution from unsubtracted discrete emission and noise, yields an excess of (76 ± 23) μJy beam –1 . Taking this as an upper limit on any extended emission, we constrain several models of extended source counts, assuming source ≤ 2 arcmin. The best-fitting models yield temperatures of the radio background from extended emission of T b = (10 ± 7) mK, giving an upper limit on the total temperature at 1.75 GHz of (73 ± 10) mK. Further modelling shows that our data are inconsistent with the reported excess temperature of ARCADE2 to a source-count limit of 1 μJy. Our new data close a loop-hole in the previous constraints, because of the possibility of extended emission being resolved out at higher resolution. Additionally, we look at a model of cluster halo emission and two dark matter particle annihilation source-count models, and discuss general constraints on any predicted counts from such sources. Finally, we report the derived integral count at 1.4 GHz using the deepest discrete count plus our new extended-emission limits, providing numbers that can be used for planning future ultradeep surveys.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2014-04-14
    Description: Radio source counts constrain galaxy populations and evolution, as well as the global star formation history. However, there is considerable disagreement among the published 1.4-GHz source counts below 100 μJy. Here, we present a statistical method for estimating the μJy and even sub-μJy source count using new deep wide-band 3-GHz data in the Lockman Hole from the Karl G. Jansky Very Large Array. We analysed the confusion amplitude distribution P(D) , which provides a fresh approach in the form of a more robust model, with a comprehensive error analysis. We tested this method on a large-scale simulation, incorporating clustering and finite source sizes. We discuss in detail our statistical methods for fitting using Markov chain Monte Carlo, handling correlations, and systematic errors from the use of wide-band radio interferometric data. We demonstrated that the source count can be constrained down to 50 nJy, a factor of 20 below the rms confusion. We found the differential source count near 10 μJy to have a slope of –1.7, decreasing to about –1.4 at fainter flux densities. At 3 GHz, the rms confusion in an 8-arcsec full width at half-maximum beam is ~ 1.2 μJy beam –1 , and a radio background temperature ~14 mK. Our counts are broadly consistent with published evolutionary models. With these results, we were also able to constrain the peak of the Euclidean normalized differential source count of any possible new radio populations that would contribute to the cosmic radio background down to 50 nJy.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2016-04-23
    Description: We observed the spiral galaxies M 51 and M 83 at 20 arscec spatial resolution with the bolometer array Aztronomical Thermal Emission Camera (AzTEC) on the JCMT in the 1.1 mm continuum, recovering the extended emission out to galactocentric radii of more than 12 kpc in both galaxies. The 1.1 mm-continuum fluxes are 5.6 ± 0.7 and 9.9 ± 1.4 Jy, with associated gas masses estimated at 9.4 x 10 9 M and 7.2 x 10 9 M for M 51 and M 83, respectively. In the interarm regions of both galaxies, the N(H 2 )/I(CO) (or X-factor) ratios exceed those in the arms by factors of ~1.5–2. In the inner discs of both galaxies, the X-factor is about 1 x 10 20 cm – 2 (K km s – 1 ) – 1 . In the outer parts, the CO-dark molecular gas becomes more important. While the spiral density wave in M 51 appears to influence the interstellar medium and stars in a similar way, the bar potential in M 83 influences the interstellar medium and the stars differently. We confirm the result of Foyle et al. that the arms merely heighten the star formation rate (SFR) and the gas surface density in the same proportion. Our maps reveal a threshold gas surface density for an SFR increase by two or more orders of magnitude. In both galaxy centres, the molecular gas depletion time is about 1 Gyr climbing to 10–20 Gyr at radii of 6–8 kpc. This is consistent with an inside-out depletion of the molecular gas in the discs of spiral galaxies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2016-04-26
    Description: Fewer than 1% of marine gastropod species live a holoplanktic life. Of these, the shelled heteropods of the family Atlantidae are among the most poorly understood. The atlantids potentially make up an important part of the ocean zooplankton, composing up to 69% of shelled holoplanktic gastropods in the Late Pleistocene to Recent fossil record. They are also likely to be at high risk from current and future global changes, including anthropogenic ocean acidification. However, due to their small size (〈12 mm), difficulty of sampling and complicated morphology, we still lack key information about atlantid taxonomy and ecology. This makes it difficult to understand how important they are in the ocean foodweb and how they will be affected by environmental change. Although many studies have been carried out on the atlantids, these have generally been broad and unconnected. Here, we draw together this previous research, summarizing what is currently known about atlantid taxonomy, palaeontology, ecology and biogeography, and aiming to provide a foundation for future research on this group. The data indicate complex behaviours involving seasonal and vertical migration, and demonstrate extended geographical ranges, with implications for understanding the role of atlantids in the ocean foodweb and their sensitivity to environmental changes. This review highlights the urgent need for further taxonomic research on the atlantids, including molecular analysis, and for improved sampling techniques.
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
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  • 10
    Publication Date: 2016-03-04
    Description: We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10–15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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