Data Analysis WorkbeNch (DAWN) Basham, Mark; Filik, Jacob; Wharmby, Michael T. ...
Journal of synchrotron radiation,
20/May , Volume:
22, Issue:
3
Journal Article
Peer reviewed
Open access
Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed ...to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single‐crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientific area.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Identification of vectors is of prime importance in the field of medical entomology for both operational and research purposes. An external quality assessment of mosquito identification capacities ...was carried out within the MediLabSecure Network, which is composed of laboratories located in 19 countries close to the European Union around the Mediterranean and Black seas.
A set of blind samples consisting of 7 or 8 adult mosquitoes and 4 larvae was given to each participant laboratory. In all, 138 adult mosquitoes and 76 larvae of different species were distributed for genus and species identification.
All identifications were exclusively morphology based. Overall, 81% of identifications were correct at the genus level, 64% at the species level. The results were highly varied among the 19 participating laboratories. The levels of correct identifications were: 100% (three laboratories), 90-95% (four laboratories), 50-75% (six laboratories) and < 50% (six laboratories).
This evaluation showed the need to maintain efforts in capacity building and quality control in the field of medical entomology and, more specifically, in the morphological identification of the Culicidae.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The dynamics of the layer-displacement fluctuations in smectic membranes have been studied by x-ray photon correlation spectroscopy (XPCS). We report transitions from an oscillatory damping regime to ...simple exponential decay of the fluctuations, both as a function of membrane thickness and upon changing from specular to off-specular scattering. This behavior is in agreement with recent theories. Employing avalanche photodiode detectors and the uniform filling mode of the synchrotron storage ring, the fast limits of XPCS have been explored down to 50 ns.
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CMK, CTK, FMFMET, IJS, NUK, PNG, UM
We report combined x-ray photon correlation spectroscopy (XPCS) and neutron spin echo (NSE) measurements of the layer-displacement fluctuations in smectic liquid-crystal membranes in the range from ...10 ns to 10 micros. NSE reveals a new regime, determined by bulk elasticity, in which relaxation times decrease with the wave vector of the fluctuations. XPCS probes slower surface-tension-dominated relaxation times, independent of the wave vector. XPCS gives a difference in correlation times at specular and off-specular positions that can be related to different detection schemes.
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CMK, CTK, FMFMET, IJS, NUK, PNG, UM
We discuss heterodyne and homodyne detection in photon correlation spectroscopy (PCS) performed at X-ray and visible wavelengths. Fluctuating smectic membranes in a reflection geometry have been used ...as model systems. At X-ray wavelength (XPCS), under specular conditions a strong elastic signal is present that acts as a time-independent internal reference source. This leads to a transition from heterodyne detection at the specular ridge to homodyne detection off-specular giving rise to a difference in relaxation time of a factor 2. In addition by comparing similar propagating modes at the specular ridge (XPCS) and at off-specular positions (PCS with visible light), cos-like and
cos
2
-like oscillations have been observed as expected for heterodyne and homodyne mixing, respectively.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
In 2013, a novel orthopoxvirus was detected in skin lesions of two cattle herders from the Kakheti region of Georgia (country); this virus was named Akhmeta virus. Subsequent investigation of these ...cases revealed that small mammals in the area had serological evidence of orthopoxvirus infections, suggesting their involvement in the maintenance of these viruses in nature. In October 2015, we began a longitudinal study assessing the natural history of orthopoxviruses in Georgia. As part of this effort, we trapped small mammals near Akhmeta (
= 176) and Gudauri (
= 110). Here, we describe the isolation and molecular characterization of
from lesion material and pooled heart and lung samples collected from five wood mice (
and
) in these two locations. The genomes of Akhmeta virus obtained from rodents group into 2 clades: one clade represented by viruses isolated from
samples, and one clade represented by viruses isolated from
samples. These genomes also display several presumptive recombination events for which gene truncation and identity have been examined.
Akhmeta virus is a unique
that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia;
spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species.
In X-ray photon correlation spectroscopy (XPCS) the degree of coherence of the X-ray beam determines the contrast of the observed intensity correlation function. In this article, we present XPCS ...measurements of smectic liquid crystal membranes in a reflectivity geometry showing that both coherence and resolution can influence the time dependence of the correlation function. Variation of the pre-detector slits as well as of the projected coherence length on the membrane induce a time dependence of the intensity correlation function. We also treat several practical aspects and limitations we encountered during our XPCS studies. Finally the conditions for heterodyne detection at the specular ridge and homodyne detection at off-specular conditions are discussed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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