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  • American Chemical Society (ACS)  (35)
  • Oxford University Press  (20)
  • Nature Publishing Group (NPG)  (12)
  • BioMed Central  (11)
  • 2010-2014  (78)
  • 1
    Publication Date: 2012-02-01
    Print ISSN: 0015-749X
    Electronic ISSN: 1938-3738
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 2
    Publication Date: 2014-07-15
    Print ISSN: 1542-4766
    Electronic ISSN: 1542-4774
    Topics: Economics
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  • 3
    Publication Date: 2014-02-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Porter, John R -- Wratten, Steve -- England -- Nature. 2014 Feb 20;506(7488):295. doi: 10.1038/506295a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Copenhagen, Denmark. ; Lincoln University, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24553231" target="_blank"〉PubMed〈/a〉
    Keywords: Gross Domestic Product/*trends ; Humans ; *Quality of Life ; Sociology/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-08-01
    Description: The solar neighbourhood is the closest and most easily studied sample of the Galactic interstellar medium, an understanding of which is essential for models of star formation and galaxy evolution. Observations of an unexpectedly intense diffuse flux of easily absorbed 1/4-kiloelectronvolt X-rays, coupled with the discovery that interstellar space within about a hundred parsecs of the Sun is almost completely devoid of cool absorbing gas, led to a picture of a 'local cavity' filled with X-ray-emitting hot gas, dubbed the local hot bubble. This model was recently challenged by suggestions that the emission could instead be readily produced within the Solar System by heavy solar-wind ions exchanging electrons with neutral H and He in interplanetary space, potentially removing the major piece of evidence for the local existence of million-degree gas within the Galactic disk. Here we report observations showing that the total solar-wind charge-exchange contribution is approximately 40 per cent of the 1/4-keV flux in the Galactic plane. The fact that the measured flux is not dominated by charge exchange supports the notion of a million-degree hot bubble extending about a hundred parsecs from the Sun.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galeazzi, M -- Chiao, M -- Collier, M R -- Cravens, T -- Koutroumpa, D -- Kuntz, K D -- Lallement, R -- Lepri, S T -- McCammon, D -- Morgan, K -- Porter, F S -- Robertson, I P -- Snowden, S L -- Thomas, N E -- Uprety, Y -- Ursino, E -- Walsh, B M -- England -- Nature. 2014 Aug 14;512(7513):171-3. doi: 10.1038/nature13525. Epub 2014 Jul 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, University of Miami, Coral Gables, Florida 33124, USA. ; NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA. ; Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045, USA. ; Universite Versailles St Quentin; Sorbonne Universites, UPMC Universite Paris 06; CNRS/INSU, LATMOS-IPSL, Guyancourt 78280, France. ; The Henry A. Rowland Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA. ; GEPI Observatoire de Paris, CNRS UMR 8111, Universite Paris Diderot, 92190, Meudon, France. ; Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA. ; Department of Physics, University of Wisconsin, Madison, Wisconsin 53706, USA. ; 1] NASA Goddard Space Flight Center, Greenbelt, Maryland 20771, USA [2] Space Sciences Laboratory, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25079321" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-12-23
    Description: Background: As our world becomes warmer, agriculture is increasingly impacted by rising soil salinity and understanding plant adaptation to salt stress can help enable effective crop breeding. Salt tolerance is a complex plant phenotype and we know little about the pathways utilized by naturally tolerant plants. Legumes are important species in agricultural and natural ecosystems, since they engage in symbiotic nitrogen-fixation, but are especially vulnerable to salinity stress. Results: Our studies of the model legume Medicago truncatula in field and greenhouse settings demonstrate that Tunisian populations are locally adapted to saline soils at the metapopulation level and that saline origin genotypes are less impacted by salt than non-saline origin genotypes; these populations thus likely contain adaptively diverged alleles. Whole genome resequencing of 39 wild accessions reveals ongoing migration and candidate genomic regions that assort non-randomly with soil salinity. Consistent with natural selection acting at these sites, saline alleles are typically rare in the range-wide species' gene pool and are also typically derived relative to the sister species M. littoralis. Candidate regions for adaptation contain genes that regulate physiological acclimation to salt stress, such as abscisic acid and jasmonic acid signaling, including a novel salt-tolerance candidate orthologous to the uncharacterized gene AtCIPK21. Unexpectedly, these regions also contain biotic stress genes and flowering time pathway genes. We show that flowering time is differentiated between saline and non-saline populations and may allow salt stress escape. Conclusions: This work nominates multiple potential pathways of adaptation to naturally stressful environments in a model legume. These candidates point to the importance of both tolerance and avoidance in natural legume populations. We have uncovered several promising targets that could be used to breed for enhanced salt tolerance in crop legumes to enhance food security in an era of increasing soil salinization.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 6
    Publication Date: 2014-11-16
    Description: The long and complex history of southern Africa makes it a geological nexus for understanding how crust forms, evolves and survives plate tectonic processes over billions of years. The goal of this study is to characterize the crustal thickness, composition, and Moho impedance contrasts across the Kaapvaal and Zimbabwe Cratons and surrounding mobile belts, which range in age from Archean to Palaeozoic. We use data gathered from the 1997–1999 Southern Africa Seismic Experiment, the Africa Array (2006–2007) and the Global Seismographic Network (1993–2009) to generate P -wave receiver function Gaussian-weighted common conversion point stacks across the region in order to provide a continuous 3-D image of crustal variations throughout southern Africa. We observe thickened crust associated with mobile belts and the intrusion of the Bushveld Complex relative to the less-deformed cratons. The southern Kaapvaal and eastern Zimbabwe Cratons have a well-defined Moho with an average depth of ~34 km and Vp / Vs of ~1.73, indicative of felsic average crustal composition. We explain the felsic composition observed in the Kaapvaal Craton in the context of significant crustal modification related to the deposition of the Ventersdorp lavas. We find that the Bushveld Province, the site of the world's largest layered mafic intrusion, has a thick (〉40 km) crust with a Vp / Vs 〉 1.8, indicative of a mafic average crustal composition. The magnitude of Moho conversions beneath the Bushveld Province is variable, with the lowest amplitude conversion appearing between the eastern and western limbs of the Bushveld Complex, indicative of mafic underplating beneath the region. In the Limpopo Belt and western Zimbabwe Craton, we observe low amplitude Moho conversions beneath the Okavango Dyke Swarm, and attribute this to the reworking of the crust by mafic underplating and intrusion during the Jurassic rifting of Gondwanaland. The Namaqua-Natal event thickened the crust and created a gradational transition from crust to mantle as seen by low amplitude Ps arrivals from receiver functions. Evidence for the presence of a mafic lower crust beneath the Namaqua-Natal Belt is observed in high Vp / Vs values (~1.8) and a high concentration of granulite xenoliths in kimberlite intrusions. In contrast to past interpretations for craton formation that suggest sharp Moho boundaries and low Vp / Vs ratios are characteristic of undisturbed cratons, we propose that these crustal properties are more controlled by tectonic events that later modify the existing cratonic crust. We cannot rule out secular crustal formation variations in the early Earth, but we propose that the southern African cratonic crust has been too heavily modified by later tectonic events to be used in arguments for secular variation, as may be the case for other cratons as well. Thus, it is important to consider the regional geological history of cratons to ensure that secular variation is not confused with the effects of later tectonic deformation and crustal modification.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
    Publication Date: 2014-12-14
    Description: Background: Most PCR-based diagnostics are still considered time- and labor-intensive due to disparate purification, amplification, and detection steps. Advancements in PCR enzymes and buffer chemistry have increased inhibitor tolerance, facilitating PCR directly from crude samples. Obviating the need for DNA purification, while lacking a concentration step, these direct sample methods are particularly apt for human genetic testing. However, direct PCR protocols have traditionally employed thermal cyclers with slow ramp rates and conservative hold times that significantly increase an assay?s time-to-result. For this proof-of-principle study, our objective was to significantly reduce sample preparation and assay time for a PCR-based genetic test, for myotonic dystrophy type 1 (DM1), by pairing an inhibitor-resistant enzyme mix with a rapid thermal cycler to analyze samples directly in whole blood. Methods: DM1 genetic screening was done with an adapted conventional PCR approach that employed the Streck Philisa? Thermal Cycler, the inhibitor-resistant NEBNext? High-Fidelity 2X PCR Master Mix, and agarose gel electrophoresis or an Agilent 2100 Bioanalyzer for detection. The Gene Link? Myotonic Dystrophy Genemer? Kit was used as a reference assay kit to evaluate the rapid assay. Results: In this work, a rapid and direct PCR assay testing 10% whole blood as template has been developed as an exclusionary screening assay for DM1, a triple-repeat genetic disorder. PCR amplification was completed in 15 minutes using 30 cycles, including in situ hot-start/cell lysis. Out of the 40 donors screened, this assay identified 23 (57.5%) as DM1 negative suggesting no need for further testing. These data are 100% concordant with data collected using the commercially available Gene Link Genemer? Kit per the kit-specific PCR protocol. Conclusions: The PCR assay described in this study amplified DM1 short tandem repeats in 15 minutes. By eliminating sample purification and slower conventional PCR protocols, we demonstrated how adaptation of current PCR technology and chemistries can produce a simple-to-use exclusionary screening assay that is independent of up-front sample prep, improving a clinical lab technician?s time-to-result. We envision this direct and rapid methodology could be applied to other conventional PCR-based genetic tests and sample matrices where genomic DNA is targeted for analysis within a given molecular diagnostic platform.
    Electronic ISSN: 1471-2350
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 8
    Publication Date: 2014-11-21
    Description: Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results: We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 30 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions: Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 9
    Publication Date: 2014-11-21
    Description: We announce a new facility in the spectral code cloudy that enables tracking the evolution of a cooling parcel of gas with time. For gas cooling from temperatures relevant to galaxy clusters, earlier calculations estimated the [Fe  xiv ] 5303/[Fe  x ] 6375 luminosity ratio, a critical diagnostic of a cooling plasma, to slightly less than unity. By contrast, our calculations predict a ratio of ~3. We revisit recent optical coronal line observations along the X-ray cool arc around NGC 4696 by Canning et al., which detected [Fe  x ] 6375, but not [Fe  xiv ] 5303. We show that these observations are not consistent with predictions of cooling flow models. Differential extinction could in principle account for the observations, but it requires extinction levels ( A V  〉 3.625) incompatible with previous observations. The non-detection of [Fe  xiv ] implies a temperature ceiling of 2.1 million K. Assuming cylindrical geometry and transonic turbulent pressure support, we estimate the gas mass at ~1 million M . The coronal gas is cooling isochorically. We propose that the coronal gas has not condensed out of the intracluster medium, but instead is the conductive or mixing interface between the X-ray plume and the optical filaments. We present a number of emission lines that may be pursued to test this hypothesis and constrain the amount of intermediate-temperature gas in the system.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 10
    Publication Date: 2014-01-10
    Description: Journal of the American Chemical Society DOI: 10.1021/ja410569g
    Print ISSN: 0002-7863
    Electronic ISSN: 1520-5126
    Topics: Chemistry and Pharmacology
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