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  • 2015-2019  (158)
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Year
  • 1
    Publication Date: 2015-10-28
    Description: In this work, acoustic scattering cancellation is expanded to cases of acoustic waves interacting with non-spherical elastic objects and collections of closely packed objects. The proposed method for achieving this is by using spherical fluid layers to represent the objects as effective spherical targets, with multiple fluid layers and an elastic core, for which scattering cancellation is used to determine the necessary layer properties. Three representative objects are considered here to illustrate this approach: a sphere with dimples, a sphere with bumps, and a bicone. Theoretical results are presented for each of the non-spherical objects in water, which indicate a reduction of 30–40 dB in scattering strength when coated with a two-layer fluid cancellation shell. This cancellation is achieved for objects in the resonant scattering regime, which is characterized by constructive and destructive interference patterns that arise from higher scattering modes. The analytical results are verified using three-dimensional finite element simulations.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 2
    Publication Date: 2015-05-19
    Description: Annually-resolved and millennium-long reconstructions of large-scale temperature variability are primarily composed of tree-ring width (TRW) chronologies. Changes in ring width, however, have recently been shown to bias the ratio between low- and high-frequency signals. To overcome limitations in capturing the full spectrum of past temperature variability we present a network of 15 maximum-latewood-density (MXD) chronologies distributed across the Northern Hemisphere extra-tropics. Independent subsets of continental-scale records consistently reveal high MXD before 1580 and after 1910, with below average values between these periods. Reconstructed extra-tropical summer-temperatures not only reflect these long-term trends, but also distinct cooling pulses after large volcanic eruptions. In contrast to TRW-dominated reconstructions, this MXD-based record indicates a delayed onset of the Little Ice Age (LIA) by almost two centuries. The reduced memory inherent in MXD is likely responsible for the rapid recovery from volcanic-induced cooling in the 14 th century and the continuation of warmer temperatures until ~1600.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
    Publication Date: 2016-07-13
    Description: Organic Letters DOI: 10.1021/acs.orglett.6b01309
    Print ISSN: 1523-7060
    Electronic ISSN: 1523-7052
    Topics: Chemistry and Pharmacology
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  • 4
    Publication Date: 2015-12-12
    Description: We describe recent upgrades to a 3D tracking microscope to include simultaneous Nipkow spinning disk imaging and time-gated single-particle tracking (SPT). Simultaneous 3D molecular tracking and spinning disk imaging enable the visualization of cellular structures and proteins around a given fluorescently labeled target molecule. The addition of photon time-gating to the SPT hardware improves signal to noise by discriminating against Raman scattering and short-lived fluorescence. In contrast to camera-based SPT, single-photon arrival times are recorded, enabling time-resolved spectroscopy (e.g., measurement of fluorescence lifetimes and photon correlations) to be performed during single molecule/particle tracking experiments.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 5
    Publication Date: 2015-07-18
    Description: Scintillation noise due to the Earth's turbulent atmosphere can be a dominant noise source in high-precision astronomical photometry when observing bright targets from the ground. Here we describe the phenomenon of scintillation from its physical origins to its effect on photometry. We show that Young's scintillation-noise approximation used by many astronomers tends to underestimate the median scintillation noise at several major observatories around the world. We show that using median atmospheric optical turbulence profiles, which are now available for most sites, provides a better estimate of the expected scintillation noise and that real-time turbulence profiles can be used to precisely characterize the scintillation-noise component of contemporaneous photometric measurements. This will enable a better understanding and calibration of photometric noise sources and the effectiveness of scintillation correction techniques. We also provide new equations for calculating scintillation noise, including for extremely large telescopes where the scintillation noise will actually be lower than previously thought. These equations highlight the fact that scintillation noise and shot noise have the same dependence on exposure time and so if an observation is scintillation limited, it will be scintillation limited for all exposure times. The ratio of scintillation noise to shot noise is also only weakly dependent on telescope diameter and so a bigger telescope may not yield a reduction in fractional scintillation noise.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2016-08-12
    Description: Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a 〉300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 7
    Publication Date: 2015-12-16
    Description: Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2015-05-22
    Description: Ancient human mobility at the individual level is conventionally studied by the diverse application of suitable techniques (e.g. aDNA, radiogenic strontium isotopes, as well as oxygen and lead isotopes) to either hard and/or soft tissues. However, the limited preservation of coexisting hard and soft human tissues hampers the possibilities of investigating high-resolution diachronic mobility periods in the life of a single individual. Here, we present the results of a multidisciplinary study of an exceptionally well preserved circa 3.400-year old Danish Bronze Age female find, known as the Egtved Girl. We applied biomolecular, biochemical and geochemical analyses to reconstruct her mobility and diet. We demonstrate that she originated from a place outside present day Denmark (the island of Bornholm excluded), and that she travelled back and forth over large distances during the final months of her life, while consuming a terrestrial diet with intervals of reduced protein intake. We also provide evidence that all her garments were made of non-locally produced wool. Our study advocates the huge potential of combining biomolecular and biogeochemical provenance tracer analyses to hard and soft tissues of a single ancient individual for the reconstruction of high-resolution human mobility. Scientific Reports 5 doi: 10.1038/srep10431
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 9
    Publication Date: 2015-02-08
    Description: Study of proteins located at the host–parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack. Micro-exon gene (MEG) protein products and venom allergen-like (VAL) proteins have been shown to be present in schistosome secretions or associated with glands, which led to the hypothesis that they are important components in the molecular interaction of the parasite with the host. Phylogenetic and structural analysis of genes and their transcripts in these two classes shows that recent species-specific expansion of gene number for these families occurred separately in three different species of schistosomes. Enrichment of transposable elements in MEG and VAL genes in Schistosoma mansoni provides a credible mechanism for preferential expansion of gene numbers for these families. Analysis of the ratio between synonymous and nonsynonymous substitution rates (d N /d S ) in the comparison between schistosome orthologs for the two classes of genes reveals significantly higher values when compared with a set of a control genes coding for secreted proteins, and for proteins previously localized in the tegument. Additional analyses of paralog genes indicate that exposure of the protein to the definitive host immune system is a determining factor leading to the higher than usual d N /d S values in those genes. The observation that two genes encoding S. mansoni vaccine candidate proteins, known to be exposed at the parasite surface, also display similar evolutionary dynamics suggests a broad response of the parasite to evolutionary pressure imposed by the definitive host immune system.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 10
    Publication Date: 2015-04-28
    Description: Motivation: The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate. Results: Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes. Availability and implementation: Data used to generate models are available as Supplementary Material . Contact: julie.wilson@york.ac.uk 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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