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  • American Society of Hematology  (35,109)
  • International Union of Crystallography  (32,939)
  • BioMed Central  (14,128)
  • Espoo : Geologian Tutkimuskeskus
  • Essen : Verl. Glückauf
  • 2020-2024  (181)
  • 2005-2009  (82,006)
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  • 1
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    Insights on long-term ecosystem changes from stable isotopes in historical squid beaks (2024)
    BioMed Central | Springer
    Details
    Publication Date: 2024-07-08
    Description: Background: Assessing the historical dynamics of key food web components is crucial to understand how climate change impacts the structure of Arctic marine ecosystems. Most retrospective stable isotopic studies to date assessed potential ecosystem shifts in the Arctic using vertebrate top predators and filter-feeding invertebrates as proxies. However, due to long life histories and specific ecologies, ecosystem shifts are not always detectable when using these taxa. Moreover, there are currently no retrospective stable isotopic studies on various other ecological and taxonomic groups of Arctic biota. To test whether climate-driven shifts in marine ecosystems are reflected in the ecology of short-living mesopredators, ontogenetic changes in stable isotope signatures in chitinous hard body structures were analysed in two abundant squids (Gonatus fabricii and Todarodes sagittatus) from the low latitude Arctic and adjacent waters, collected between 1844 and 2023. Results: We detected a temporal increase in diet and habitat-use generalism (= opportunistic choice rather than specialization), trophic position and niche width in G. fabricii from the low latitude Arctic waters. These shifts in trophic ecology matched with the Atlantification of the Arctic ecosystems, which includes increased generalization of food webs and higher primary production, and the influx of boreal species from the North Atlantic as a result of climate change. The Atlantification is especially marked since the late 1990s/early 2000s. The temporal patterns we found in G. fabricii’s trophic ecology were largely unreported in previous Arctic retrospective isotopic ecology studies. Accordingly, T. sagittatus that occur nowadays in the high latitude North Atlantic have a more generalist diet than in the XIXth century. :Conclusions Our results suggest that abundant opportunistic mesopredators with short life cycles (such as squids) are good candidates for retrospective ecology studies in the marine ecosystems, and to identify ecosystem shifts driven by climate change. Enhanced generalization of Arctic food webs is reflected in increased diet generalism and niche width in squids, while increased abundance of boreal piscivorous fishes is reflected in squids’ increased trophic position. These findings support opportunism and adaptability in squids, which renders them as potential winners of short-term shifts in Arctic ecosystems.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 2
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    INSIGHT: in situ heuristic tool for the efficient reduction of grazing‐incidence X‐ray scattering data (2024)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-04-25
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉INSIGHT〈/italic〉 is a Python‐based software tool for processing and reducing 2D grazing‐incidence wide‐ and small‐angle X‐ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel‐wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time‐resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one‐step solution to reduce, process, analyze and export findings of large 〈italic〉in situ〈/italic〉 and 〈italic〉operando〈/italic〉 data sets.〈/p〉
    Keywords: ddc:548 ; grazing‐incidence X‐ray scattering ; time‐resolved studies ; in situ studies ; operando studies ; computer programs
    Language: English
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  • 3
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    The effect of calcium supplementation on calcium and bone metabolism during load carriage in women: protocol for a randomised controlled crossover trial (2023)
    Springer | BioMed Central
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    Publication Date: 2024-02-07
    Description: Military field exercises are characterised by high volumes of exercise and prolonged periods of load carriage. Exercise can decrease circulating serum calcium and increase parathyroid hormone and bone resorption. These disturbances to calcium and bone metabolism can be attenuated with calcium supplementation immediately before exercise. This randomised crossover trial will investigate the effect of calcium supplementation on calcium and bone metabolism, and bone mineral balance, during load carriage exercise in women. Methods Thirty women (eumenorrheic or using the combined oral contraceptive pill, intrauterine system, or intrauterine device) will complete two experimental testing sessions either with, or without, a calcium supplement (1000 mg). Each experimental testing session will involve one 120 min session of load carriage exercise carrying 20 kg. Venous blood samples will be taken and analysed for biochemical markers of bone resorption and formation, calcium metabolism, and endocrine function. Urine will be collected pre- and post-load carriage to measure calcium isotopes for the calculation of bone calcium balance. Discussion The results from this study will help identify whether supplementing women with calcium during load carriage is protective of bone and calcium homeostasis.
    Type: Article , PeerReviewed
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  • 4
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    Rhythm of relationships in a social fish over the course of a full year in the wild (2023)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background: Animals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. Little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of a dynamic social network. Methods: To that end, we tracked the behaviour of 36 adult common carp, Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups over time. Results: The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Therefore, smaller, characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks. Conclusions: We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.
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  • 5
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    Energy‐dispersive X‐ray stress analysis under geometric constraints: exploiting the material's inherent anisotropy (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-09-12
    Description: Two data evaluation concepts for X‐ray stress analysis based on energy‐dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single‐crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard‐to‐reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near‐surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain‐free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in‐plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.
    Description: The single‐crystal elastic anisotropy and the anisotropy of the near‐surface (residual) stress state of polycrystalline materials with random texture are exploited in energy‐dispersive X‐ray stress analysis to study samples under constrained measurement conditions.
    Keywords: ddc:548 ; X‐ray stress analysis ; energy‐dispersive diffraction ; polycrystalline materials ; single‐crystal elastic anisotropy
    Language: English
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  • 6
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    Mapping the 3D position of battery cathode particles in Bragg coherent diffractive imaging (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-14
    Description: In Bragg coherent diffractive imaging, the precise location of the measured crystals in the interior of the sample is usually missing. Obtaining this information would help the study of the spatially dependent behavior of particles in the bulk of inhomogeneous samples, such as extra‐thick battery cathodes. This work presents an approach to determine the 3D position of particles by precisely aligning them at the instrument axis of rotation. In the test experiment reported here, with a 60 µm‐thick LiNi0.5Mn1.5O4 battery cathode, the particles were located with a precision of 20 µm in the out‐of‐plane direction, and the in‐plane coordinates were determined with a precision of 1 µm.
    Description: A method to determine the 3D position of particles in Bragg coherent diffractive imaging experiments is proposed. Test measurements demonstrate depth‐resolution with a precision of 20 µm along the beam. image
    Keywords: ddc:548 ; extra‐thick battery cathodes ; Bragg coherent X‐ray diffractive imaging ; battery cathodes ; Bragg diffraction ; sphere of confusion ; 3D mapping
    Language: English
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  • 7
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    The soft X‐ray and XUV split‐and‐delay unit at beamlines FL23/24 at FLASH2 (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-01-12
    Description: A split‐and‐delay unit for the extreme ultraviolet and soft X‐ray spectral regions has been built which enables time‐resolved experiments at beamlines FL23 and FL24 at the Free‐electron LASer in Hamburg (FLASH). Geometric wavefront splitting at a sharp edge of a beam splitting mirror is applied to split the incoming soft X‐ray pulse into two beams. Ni and Pt coatings at grazing incidence angles have been chosen in order to cover the whole spectral range of FLASH2 and beyond, up to hν = 1800 eV. In the variable beam path with a grazing incidence angle of ϑd = 1.8°, the total transmission (T) ranges are of the order of 0.48 〈 T 〈 0.84 for hν 〈 100 eV and T 〉 0.50 for 100 eV 〈 hν 〈 650 eV with the Ni coating, and T 〉 0.06 for hν 〈 1800 eV for the Pt coating. For a fixed beam path with a grazing incidence angle of ϑf = 1.3°, a transmission of T 〉 0.61 with the Ni coating and T 〉 0.23 with a Pt coating is achieved. Soft X‐ray pump/soft X‐ray probe experiments are possible within a delay range of −5 ps 〈 Δt 〈 +18 ps with a nominal time resolution of tr = 66 as and a measured timing jitter of tj = 121 ± 2 as. First experiments with the split‐and‐delay unit determined the averaged coherence time of FLASH2 to be τc = 1.75 fs at λ = 8 nm, measured at a purposely reduced coherence of the free‐electron laser.
    Description: The properties of the recently installed split‐and‐delay unit at beamlines FL23 and FL24 at FLASH2 are presented. Its operational range, performance parameters and results of a first experiment are described. image
    Keywords: ddc:550.724 ; time‐resolved pump–probe ; XUV ; soft X‐rays ; free‐electron laser
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  • 8
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    XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2024-01-12
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉XDSGUI〈/italic〉 is a lightweight graphical user interface (GUI) for the 〈italic〉XDS〈/italic〉, 〈italic〉SHELX〈/italic〉 and 〈italic〉ARCIMBOLDO〈/italic〉 program packages that serves both novice and experienced users in obtaining optimal processing and phasing results for X‐ray, neutron and electron diffraction data. The design of the program enables data processing and phasing without command line usage, and supports advanced command flows in a simple user‐modifiable and user‐extensible way. The GUI supplies graphical information based on the tabular log output of the programs, which is more intuitive, comprehensible and efficient than text output can be.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A customizable stateless graphical user interface simplifies the processing, analysis and phasing of diffraction data.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2yr5110:jcr2yr5110-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray diffraction ; neutron diffraction ; electron diffraction ; data processing ; graphical user interfaces ; phasing ; XDS ; ARCIMBOLDO ; SHELX
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  • 9
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 3. Pseudosymmetry (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-20
    Description: A pseudosymmetric description of the crystal lattice derived from a single wide‐angle Kikuchi pattern can have several causes. The small size (〈15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst.54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non‐equivalent positions are too similar and reciprocal‐lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.
    Description: Distinguishing between actual and apparent pseudosymmetry in electron backscatter diffraction patterns is nearly impossible, even for simulated patterns. However, the resulting lattice is always a superlattice as long as the signal is not a superposition of multiple patterns.
    Keywords: ddc:548 ; Bravais lattices ; pseudosymmetry ; lattice point density ; ordered/disordered structures ; lattice distortion ; electron backscatter diffraction ; backscattered Kikuchi diffraction patterns ; lattice parameters ; Funk transform
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  • 10
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    Crystal diffraction prediction and partiality estimation using Gaussian basis functions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-04
    Description: The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
    Description: Reflection position, size and shape prediction and partiality estimation of crystal diffraction by integrating using a Gaussian basis are described.
    Keywords: ddc:548 ; partiality estimation ; diffraction prediction ; merging ; serial snapshot crystallography
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  • 11
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 2. Offset corrections (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-21
    Description: A band width determination using the first derivative of the band profile systematically underestimates the true Bragg angle. Corrections are proposed to compensate for the resulting offset Δa/a of the mean lattice parameters derived from as many Kikuchi band widths as possible. For dynamically simulated Kikuchi patterns, Δa/a can reach up to 8% for phases with a high mean atomic number Z, whereas for much more common low‐Z materials the offset decreases linearly. A predicted offset Δa/a = f(Z) is therefore proposed, which also includes the unit‐cell volume and thus takes into account the packing density of the scatterers in the material. Since Z is not always available for unknown phases, its substitution by Zmax, i.e. the atomic number of the heaviest element in the compound, is still acceptable for an approximate correction. For simulated Kikuchi patterns the offset‐corrected lattice parameter deviation is Δa/a 〈 1.5%. The lattice parameter ratios, and the angles α, β and γ between the basis vectors, are not affected at all.
    Description: Automatically determined band widths in simulated backscatter Kikuchi patterns exhibit differences from the double Bragg angles that correlate with the scatterer density. Corrections are proposed to compensate for this.
    Keywords: ddc:548 ; mean atomic number ; Kikuchi patterns ; lattice parameters ; automated Bragg angle determination ; lattice parameter determination ; dynamical theory of electron diffraction ; electron backscatter diffraction ; Funk transform
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  • 12
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    POWTEX visits POWGEN (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The high‐intensity time‐of‐flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world‐wide 〈sup〉3〈/sup〉He crisis in 2009, the authors promptly initiated the development of 〈sup〉3〈/sup〉He‐free detector alternatives that are tailor‐made for the requirements of large‐area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular‐ and wavelength‐dependent data from the POWTEX detector, unfortunately damaged by a 50〈italic〉g〈/italic〉 shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the 〈italic〉PowderReduceP2D〈/italic〉 algorithm implemented in 〈italic〉Mantid〈/italic〉 [Arnold 〈italic〉et al.〈/italic〉 (2014). 〈italic〉Nucl. Instrum. Methods Phys. Res. A〈/italic〉, 〈bold〉764〈/bold〉, 156–166]. The final part of the data treatment chain, namely a novel multi‐dimensional refinement using a modified version of the 〈italic〉GSAS‐II〈/italic〉 software suite [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?aj5212"〉Toby & Von Dreele (2013). 〈italic〉J. Appl. Cryst.〈/italic〉〈bold〉46〈/bold〉, 544–549〈/ext-link〉], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of 〈italic〉GSAS‐II〈/italic〉. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly‐user sample, BaZn(NCN)〈sub〉2〈/sub〉. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi‐dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the 〈italic〉a〈/italic〉 and 〈italic〉b〈/italic〉 lattice parameters of BaZn(NCN)〈sub〉2〈/sub〉 crystallizing in 〈italic〉Pbca〈/italic〉 as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, 〈italic〉e.g.〈/italic〉 the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large‐area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The first real‐world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular‐ and wavelength‐dispersive Rietveld refinement using a modified version of 〈italic〉GSAS‐II〈/italic〉.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2tu5033:jcr2tu5033-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; neutron detectors ; POWGEN beamline ; POWTEX detector ; DREAM beamline ; time‐of‐flight diffraction ; angular‐dispersive refinement ; wavelength‐dispersive refinement ; powder diffraction ; Rietveld refinement ; multi‐dimensional refinement
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  • 13
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    A note on the wedge reversion antisymmetry operation and 51 types of physical quantities in arbitrary dimensions (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The paper by Gopalan [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327〈/ext-link〉] presented an enumeration of the 41 physical quantity types in non‐relativistic physics, in arbitrary dimensions, based on the formalism of Clifford algebra. Gopalan considered three antisymmetries: spatial inversion, 〈overline〉1〈/overline〉, time reversal, 1′, and wedge reversion, 1〈sup〉†〈/sup〉. A consideration of the set of all seven antisymmetries (〈overline〉1〈/overline〉, 1′, 1〈sup〉†〈/sup〉, 1′〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉′, 〈overline〉1〈/overline〉′〈sup〉†〈/sup〉) leads to an extension of the results obtained by Gopalan. It is shown that there are 51 types of physical quantities with distinct symmetry properties in total.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉It is shown that there are 51 types of physical quantities in arbitrary dimensions with distinct transformations by wedge reversion symmetry. In the paper by 〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉Gopalan [(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327]〈/ext-link〉 only 41 types were enumerated.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:20532733:aya2ib5117:aya2ib5117-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; multivectors ; wedge reversion ; antisymmetry ; Clifford algebra
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  • 14
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    Use of electron backscatter diffraction patterns to determine the crystal lattice. Part 1. Where is the Bragg angle? (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2023-07-19
    Description: The derivation of a crystal structure and its phase‐specific parameters from a single wide‐angle backscattered Kikuchi diffraction pattern requires reliable extraction of the Bragg angles. By means of the first derivative of the lattice profile, an attempt is made to determine fully automatically and reproducibly the band widths in simulated Kikuchi patterns. Even under such ideal conditions (projection centre, wavelength and lattice plane traces are perfectly known), this leads to a lattice parameter distribution whose mean shows a linear offset that correlates with the mean atomic number Z of the pattern‐forming phase. The consideration of as many Kikuchi bands as possible reduces the errors that typically occur if only a single band is analysed. On the other hand, the width of the resulting distribution is such that higher image resolution of diffraction patterns, employing longer wavelengths to produce wider bands or the use of higher interference orders is less advantageous than commonly assumed.
    Description: The lattice parameters of more than 350 phases have been determined from simulated backscatter Kikuchi patterns. The deviations correlating with the mean atomic number correspond to those observed previously for experimental electron backscatter diffraction patterns.
    Keywords: ddc:548 ; Bragg angles ; Kikuchi bands ; Kikuchi patterns ; first derivative ; lattice parameters ; lattice parameter determination ; Bravais lattice type ; electron backscatter diffraction ; Radon transform
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  • 15
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    Data reduction for X‐ray serial crystallography using machine learning (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-19
    Description: Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large‐scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
    Description: A machine learning method for distinguishing good and bad images in serial crystallography is presented. To reduce the computational cost, this uses the oriented FAST and rotated BRIEF feature extraction method from computer vision to detect image features, followed by a multilayer perceptron (neural network) to classify the images.
    Keywords: ddc:548 ; serial crystallography ; data reduction ; machine learning ; feature extraction
    Language: English
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    Towards joint in situ determination of pressure and temperature in the large volume press exclusively from X‐ray diffraction (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-19
    Description: Since high‐pressure devices have been used at synchrotron facilities, accurate determination of pressure and temperature in the sample has been a crucial objective, particularly for experiments that simulate the Earth's interior. However, in some cases using a thermocouple may have a high likelihood of failure or is incompatible with a high‐pressure assembly. To address these challenges and similar issues, we aim to expand a previously proposed solution: to jointly estimate pressure and temperature (〈italic〉PT〈/italic〉) through 〈italic〉in situ〈/italic〉 X‐ray diffraction, to cover a wider range of internal 〈italic〉PT〈/italic〉 calibrants tested over larger 〈italic〉PT〈/italic〉 ranges. A modifiable Python‐based software is offered to quickly obtain results. To achieve these aims, 〈italic〉in situ〈/italic〉 large volume press experiments are performed on pellets of intimately mixed powders of a halide (NaCl, KCl, KBr, CsCl) or MgO and a metal (Pt, Re, Mo, W, Ni) in the pressure range 3–11 GPa and temperature range 300–1800 K. Although the pressure range was chosen for practical reasons, it also covers an equally important depth range in the Earth (down to 350 km) for geoscience studies. A thermocouple was used to validate the 〈italic〉PT〈/italic〉 conditions in the cell assemblies. The key results show that choosing the appropriate calibrant materials and using a joint 〈italic〉PT〈/italic〉 estimation can yield surprisingly small uncertainties (〈italic〉i.e.〈/italic〉 〈±0.1 GPa and 〈±50 K). This development is expected to benefit current and future research at extreme conditions, as other materials with high compressibility or high thermal pressure, stable over large 〈italic〉PT〈/italic〉 ranges, may be discovered and used as 〈italic〉PT〈/italic〉 calibrants.〈/p〉
    Description: Research in high‐pressure devices, such as the diamond anvil cell and the large volume press, requires knowledge of the pressure and temperature in the sample. Here, a large volume press and an internal resistive heater were used to generate high load and heat to various combinations of intimately mixed powders of materials. X‐ray diffraction and custom software were used to jointly estimate the pressures and temperatures in the samples and establish calibrants for 〈italic〉in situ〈/italic〉 experiments at extreme conditions.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2vl5008:jsy2vl5008-fig-0001"〉
    Description: https://gitlab.desy.de/robert.farla/eoscross
    Keywords: ddc:548 ; equations of state ; X‐ray diffraction ; large volume press ; high pressure ; resistive heating
    Language: English
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    In situ neutron diffraction for analysing complex coarse‐grained functional materials (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-10-24
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Complex functional materials play a crucial role in a broad range of energy‐related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for 〈italic〉in situ〈/italic〉 or 〈italic〉operando〈/italic〉 investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under 〈italic〉in situ〈/italic〉 conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of 〈italic〉in situ〈/italic〉 experiments on barium titanate with an applied electric field, details of the electric‐field‐induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain‐wall densities and mobilities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉This work reports 〈italic〉in situ〈/italic〉 neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain‐size‐dependent strain mechanisms and shows the competitiveness of neutron diffraction with high‐resolution synchrotron diffraction.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2vb5054:jcr2vb5054-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; ddc:548 ; neutron diffraction ; in situ ; applied electric fields ; barium titanate ; strain mechanisms ; grain sizes ; complex functional materials ; microstructures ; coexisting phases
    Language: English
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    Beam‐induced redox chemistry in iron oxide nanoparticle dispersions at ESRF–EBS (2023)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-21
    Description: The storage ring upgrade of the European Synchrotron Radiation Facility makes ESRF–EBS the most brilliant high‐energy fourth‐generation light source, enabling in situ studies with unprecedented time resolution. While radiation damage is commonly associated with degradation of organic matter such as ionic liquids or polymers in the synchrotron beam, this study clearly shows that highly brilliant X‐ray beams readily induce structural changes and beam damage in inorganic matter, too. Here, the reduction of Fe3+ to Fe2+ in iron oxide nanoparticles by radicals in the brilliant ESRF–EBS beam, not observed before the upgrade, is reported. Radicals are created due to radiolysis of an EtOH–H2O mixture with low EtOH concentration (∼6 vol%). In light of extended irradiation times during insitu experiments in, for example, battery and catalysis research, beam‐induced redox chemistry needs to be understood for proper interpretation of insitu data.
    Description: With the increased brilliance at the European Research Facility–Extremely Brilliant Source (ESRF–EBS), a beam‐induced reduction of non‐stochiometric iron oxide nanoparticles (almost maghemite composition) to magnetite was observed in a mixture of ethanol and water with low ethanol concentration.
    Keywords: ddc:548 ; beam‐induced radiolysis ; radiation damage on inorganic materials ; ESRF–EBS
    Language: English
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    Machine learning for scattering data: strategies, perspectives and applications to surface scattering (2023)
    Hinderhofer, Alexander ; Greco, Alessandro ; Starostin, Vladimir ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-14
    Description: Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing‐incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.
    Description: The status, opportunities, challenges and limitations of machine learning are discussed as applied to X‐ray and neutron scattering techniques, with an emphasis on surface scattering.
    Keywords: ddc:548 ; surface scattering ; X‐ray diffraction ; neutron scattering ; machine learning ; data analysis
    Language: English
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  • 20
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    Hard X‐ray full‐field nanoimaging using a direct photon‐counting detector (2023)
    Flenner, Silja ; Hagemann, Johannes ; Wittwer, Felix ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-03-05
    Description: Full‐field X‐ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low‐absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X‐ray microscopy with Zernike phase contrast, near‐field holography and near‐field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal‐to‐noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single‐photon‐counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz‐Zentrum Hereon. Thanks to the long sample‐to‐detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single‐photon‐counting detector in combination with a long sample‐to‐detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal‐to‐noise level.
    Description: A direct photon‐counting detector was used for different nanoimaging phase contrast techniques, increasing the temporal resolution.
    Keywords: ddc:548 ; nanotomography ; full‐field X‐ray microscopy ; near‐field holography ; near‐field ptychography ; Zernike phase contrast ; single‐photon‐counting detector ; phase contrast
    Language: English
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    Symbiont transmission in marine sponges: reproduction, development, and metamorphosis (2022)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
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  • 22
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    Using diffraction losses of X‐rays in a single crystal for determination of its lattice parameters as well as for monochromator calibration (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-04
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A way has been developed to measure the unit‐cell parameters of a single crystal just from an energy scan with X‐rays, even when the exact energy of the X‐rays is not well defined due to an error in the pitch angle of the monochromator. The precision of this measurement reaches 〈italic〉da〈/italic〉/〈italic〉a〈/italic〉 ∼ 1 × 10〈sup〉−5〈/sup〉. The method is based on the analysis of diffraction losses of the beam, transmitted through a single crystal (the so‐called `glitch effect'). This method can be easily applied to any transmissive X‐ray optical element made of single crystals (for example, X‐ray lenses). The only requirements are the possibility to change the energy of the generated X‐ray beam and some intensity monitor to measure the transmitted intensity. The method is agnostic to the error in the monochromator tuning and it can even be used for determination of the absolute pitch (or 2gθ) angle of the monochromator. Applying the same method to a crystal with well known lattice parameters allows determination of the exact cell parameters of the monochromator at any energy.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Diffraction losses (glitches) at certain energies of the X‐ray beam, transmitted through a single crystal, can be used for lattice parameters determination as well as for calibrating the monochromator (absolute pitch angle and the unit‐cell parameter).〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2ay5590:jsy2ay5590-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray glitches ; diffraction losses ; unit‐cell parameter ; single‐crystal X‐ray optics ; monochromator calibration
    Language: English
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    Quantifying electron cascade size in various irradiated materials for free‐electron laser applications (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-12-12
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Studying electron‐ and X‐ray‐induced electron cascades in solids is essential for various research areas at free‐electron laser facilities, such as X‐ray imaging, crystallography, pulse diagnostics or X‐ray‐induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X‐ray lasers: Au, B〈sub〉4〈/sub〉C, diamond, Ni, polystyrene, Ru, Si, SiC, Si〈sub〉3〈/sub〉N〈sub〉4〈/sub〉 and W. Using classical Monte Carlo simulation in the atomic approximation, we study the dependence of the cascade size on the incident electron or photon energy and on the target parameters. The results show that an electron‐induced cascade is systematically larger than a photon‐induced cascade. Moreover, in contrast with the common assumption, the maximal cascade size does not necessarily coincide with the electron range. It was found that the cascade size can be controlled by careful selection of the photon energy for a particular material. Photon energy, just above an ionization potential, can essentially split the absorbed energy between two electrons (photo‐ and Auger), reducing their initial energy and thus shrinking the cascade size. This analysis suggests a way of tailoring the electron cascades for applications requiring either small cascades with a high density of excited electrons or large‐spread cascades with lower electron densities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Studying electron‐ and X‐ray‐induced electron cascades in solids is essential for various research areas at free‐electron laser facilities, such as X‐ray imaging, crystallography, pulse diagnostics or X‐ray‐induced damage. To better understand the fundamental factors that define the duration and spatial size of such cascades, this work investigates the electron propagation in ten solids relevant for the applications of X‐ray lasers. Using classical Monte Carlo simulation in the atomic approximation, the dependence of the cascade size on the incident electron or photon energy and on the target parameters is studied.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2gb5123:jsy2gb5123-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; electron cascades ; X‐ray free‐electron lasers ; Monte Carlo ; photon‐induced cascade ; electron transport
    Language: English
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    Digitization of imaging plates from Guinier powder X‐ray diffraction cameras (2022)
    Nasir, Jamal ; Steinbrück, Nils ; Xu, Ke ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-15
    Description: A Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X‐ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2gθ scale against a known reference material. It is shown using LaB6 that the exported X‐ray diffraction patterns provide a 2gθ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.
    Description: A program for the digitization of Guinier powder diffraction images is described, which works with images from both optical and laser scanners. Thus, processing of data from storage‐phosphor‐based imaging plates and Ag‐based photographic films is possible.
    Keywords: ddc:548 ; IPreader software ; Guinier cameras ; imaging plates (IPs) ; diffraction pattern conversion into data columns ; powder X‐ray diffraction ; data processing ; Guinier method
    Language: English
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  • 25
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    X‐ray diffraction with micrometre spatial resolution for highly absorbing samples (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-21
    Description: X‐ray diffraction with high spatial resolution is commonly used to characterize (poly)crystalline samples with, for example, respect to local strain, residual stress, grain boundaries and texture. However, the investigation of highly absorbing samples or the simultaneous assessment of high‐Z materials by X‐ray fluorescence have been limited due to the utilization of low photon energies. Here, a goniometer‐based setup implemented at the P06 beamline of PETRA III that allows for micrometre spatial resolution with a photon energy of 35 keV and above is reported. A highly focused beam was achieved by using compound refractive lenses, and high‐precision sample manipulation was enabled by a goniometer that allows up to 5D scans (three rotations and two translations). As experimental examples, the determination of local strain variations in martensitic steel samples with micrometre spatial resolution, as well as the simultaneous elemental distribution for high‐Z materials in a thin‐film solar cell, are demonstrated. The proposed approach allows users from the materials‐science community to determine micro‐structural properties even in highly absorbing samples.
    Description: A demonstration of high‐resolution micro X‐ray diffraction at high photon energies for highly absorbing samples.
    Keywords: ddc:548 ; X‐ray diffraction ; high spatial resolution ; high photon energy ; X‐ray fluorescence ; goniometers
    Language: English
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  • 26
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    Domain Auto Finder (DAFi) program: the analysis of single‐crystal X‐ray diffraction data from polycrystalline samples (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-21
    Description: This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single‐crystal X‐ray diffraction (SC‐XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single‐crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC‐XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X‐ray diffraction data sets obtained from real samples: a multi‐mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser‐heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC‐XRD data online during experiments at synchrotron facilities.
    Description: This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single‐crystal X‐ray diffraction (SC‐XRD) data from multiphase mixtures of microcrystalline solids and powders. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC‐XRD data and neither requires a priori crystallographic information nor is limited by the number of phases or individual domains.
    Keywords: ddc:548 ; single‐crystal domain auto finder ; DAFi ; single‐crystal X‐ray diffraction ; polycrystalline samples ; multiphase mixtures
    Language: English
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    High‐resolution XEOL spectroscopy setup at the X‐ray absorption spectroscopy beamline P65 of PETRA III (2022)
    Levcenko, S. ; Biller, R. ; Pfeiffelmann, T. ; [et al.]
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-01-25
    Description: A newly designed setup to perform steady‐state X‐ray excited optical luminescence (XEOL) spectroscopy and simultaneous XEOL and X‐ray absorption spectroscopy characterization at beamline P65 of PETRA III is described. The XEOL setup is equipped with a He‐flow cryostat and state‐of‐the‐art optical detection system, which covers a wide wavelength range of 300–1700 nm with a high spectral resolution of 0.4 nm. To demonstrate the setup functioning, low‐temperature XEOL studies on polycrystalline CuInSe2 thin film, single‐crystalline GaN thin film and single‐crystalline ZnO bulk semiconductor samples are performed.
    Description: X‐ray excited optical luminescence (XEOL) spectroscopy is increasingly important to understand the interplay between the optical properties, structure and chemical composition, providing insights into the mechanism of radiative recombination for a wide range of materials. This study demonstrates a newly implemented setup to perform steady‐state XEOL and simultaneous XEOL and XAFS characterizations at beamline P65 of PETRA III.
    Keywords: ddc:550.2 ; XEOL ; XAS ; CuInSe2 ; ZnO ; GaN
    Language: English
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    Small‐angle neutron scattering of long‐wavelength magnetic modulations in reduced sample dimensions (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-04
    Description: Magnetic small‐angle neutron scattering (SANS) is ideally suited to providing direct reciprocal‐space information on long‐wavelength magnetic modulations, such as helicoids, solitons, merons or skyrmions. SANS of such structures in thin films or micro‐structured bulk materials is strongly limited by the tiny scattering volume vis a vis the prohibitively high background scattering by the substrate and support structures. Considering near‐surface scattering just above the critical angle of reflection, where unwanted signal contributions due to substrate or support structures become very small, it is established that the scattering patterns of the helical, conical, skyrmion lattice and fluctuation‐disordered phases in a polished bulk sample of MnSi are equivalent for conventional transmission and near‐surface SANS geometries. This motivates the prediction of a complete repository of scattering patterns expected for thin films in the near‐surface SANS geometry for each orientation of the magnetic order with respect to the scattering plane.
    Description: Near‐surface SANS is discussed for its potential as a probe of long‐wavelength magnetic modulations in specimens with reduced sample dimensions.
    Keywords: ddc:548 ; small‐angle neutron scattering ; near‐surface SANS ; magnetism ; non‐collinear magnetism ; thin films ; skyrmions ; MnSi
    Language: English
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  • 29
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    Combining reverse Monte Carlo analysis of X‐ray scattering and extended X‐ray absorption fine structure spectra of very small nanoparticles (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2023-07-21
    Description: Finite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X‐ray scattering data and extended X‐ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long‐range order.
    Description: Computing scattering intensity using the Debye scattering equation after binning interatomic distances avoids finite size artefacts and is efficient enough for simultaneous refinement of scattering data and extended X‐ray absorption spectra by reverse Monte Carlo simulations.
    Keywords: ddc:548 ; extended X‐ray absorption fine structure ; EXAFS ; wide‐angle X‐ray scattering ; WAXS ; reverse Monte Carlo ; RMC ; nanocrystals ; LaFeO3
    Language: English
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  • 30
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    Extending MIEZE spectroscopy towards thermal wavelengths (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-05
    Description: A modulation of intensity with zero effort (MIEZE) setup is proposed for high‐resolution neutron spectroscopy at momentum transfers up to 3 Å〈sup〉−1〈/sup〉, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin‐depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin‐incoherent scattering. The second advantage is that multi‐analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin‐echo approximation towards shorter spin‐echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin‐echo spectroscopy and conventional high‐resolution neutron spectroscopy techniques such as triple‐axis, time‐of‐flight and back‐scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.
    Description: A modulation of intensity with zero effort (MIEZE) setup is proposed for high‐resolution neutron spectroscopy at momentum transfers up to 3 Å〈sup〉−1〈/sup〉, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons.
    Keywords: ddc:548 ; neutron resonant spin echo ; MIEZE ; quasielastic scattering ; thermal neutrons
    Language: English
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  • 31
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    Extreme conditions research using the large‐volume press at the P61B endstation, PETRA III (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-05
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Penetrating, high‐energy synchrotron X‐rays are in strong demand, particularly for high‐pressure research in physics, chemistry and geosciences, and for materials engineering research under less extreme conditions. A new high‐energy wiggler beamline P61 has been constructed to meet this need at PETRA III in Hamburg, Germany. The first part of the paper offers an overview of the beamline front‐end components and beam characteristics. The second part describes the performance of the instrumentation and the latest developments at the P61B endstation. Particular attention is given to the unprecedented high‐energy photon flux delivered by the ten wigglers of the PETRA III storage ring and the challenges faced in harnessing this amount of flux and heat load in the beam. Furthermore, the distinctiveness of the world's first six‐ram Hall‐type large‐volume press, Aster‐15, at a synchrotron facility is described for research with synchrotron X‐rays. Additionally, detection schemes, experimental strategies and preliminary data acquired using energy‐dispersive X‐ray diffraction and radiography techniques are presented.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The operation of the P61B endstation large‐volume press and optics of P61 are reviewed. The instrumentation at P61B, including the large‐volume press, detection systems and data acquisition for 〈italic〉in situ〈/italic〉 high‐pressure experiments are described.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2ju5040:jsy2ju5040-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; extreme conditions ; high‐pressure ; large‐volume press ; energy‐dispersive X‐ray diffraction ; radiography ; resistive heating ; ultrasonic interferometry ; acoustic emissions detection
    Language: English
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    The PERCIVAL detector: first user experiments (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-03-13
    Description: The PERCIVAL detector is a CMOS imager designed for the soft X‐ray regime at photon sources. Although still in its final development phase, it has recently seen its first user experiments: ptychography at a free‐electron laser, holographic imaging at a storage ring and preliminary tests on X‐ray photon correlation spectroscopy. The detector performed remarkably well in terms of spatial resolution achievable in the sample plane, owing to its small pixel size, large active area and very large dynamic range; but also in terms of its frame rate, which is significantly faster than traditional CCDs. In particular, it is the combination of these features which makes PERCIVAL an attractive option for soft X‐ray science.
    Keywords: ddc:548 ; X‐ray detectors ; soft X‐rays ; ptychography ; holographic imaging ; XPCS ; detectors
    Language: English
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    Automatic bad‐pixel mask maker for X‐ray pixel detectors with application to serial crystallography (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-14
    Description: X‐ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X‐ray sources and enabled by employing high‐frame‐rate X‐ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad‐pixel masks for large‐area X‐ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X‐ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.
    Description: Attention is focused on perhaps the biggest bottleneck in data analysis for serial crystallography at X‐ray free‐electron lasers, which has not received serious enough examination to date. An effective and reliable way is presented to identify anomalies in detectors, using machine learning and recently developed mathematical methods in the field referred to as `robust statistics'. image
    Keywords: ddc:548 ; bad‐pixel masks ; robust mask maker ; machine learning ; robust statistics ; serial crystallography
    Language: English
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    Updates in SASfit for fitting analytical expressions and numerical models to small‐angle scattering patterns (2022)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2024-02-22
    Description: Small‐angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve‐fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug‐in system for easier adoption by third‐party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal.13, 243–277], and regularization techniques such as the expectation‐maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am.62, 55; Lucy (1974). Astron. J.79, 745; Lucy (1994). Astron. Astrophys.289, 983–994], which is compared with fits of analytical size distributions via the non‐linear least‐squares method; and (d) new structure factors, especially for ordered nano‐ and meso‐scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small‐angle scattering intensity model used for fitting with SASfit.
    Description: Recent enhancements and additions to the SASfit program are discussed, including anisotropic scattering models, flexible distributions, regularization techniques such as the expectation‐maximization method, and new structure factors, especially for ordered nano‐ and meso‐scaled material. The Ornstein–Zernike solver for numerical structure factors is also introduced. image
    Keywords: ddc:548 ; small‐angle scattering ; SASfit ; numerical models ; structure factors ; form factors ; regularization techniques
    Language: English
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  • 35
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    Treatment of perioperative swelling by rest, ice, compression, and elevation (RICE) without and with additional application of negative pressure (RICE+) in patients with a unilateral ankle fracture: study protocol for a monocentric, evaluator-blinded randomized controlled pilot trial (2021)
    BioMed Central | Springer
    Details
    Publication Date: 2024-02-07
    Description: Background Edema is commonly seen after surgical fixation of ankle fractures. Rest, ice, compression, and elevation (RICE) is an established combination to prevent swelling but hardly able to stimulate lymphatic resorption. Recently, an epicutaneously applied negative pressure suction apparatus (LymphaTouch®) has been introduced to stimulate lymphatic flow. While postoperative recovery, soft tissue, and osseous healing as well as functional outcome are probably linked to the amount of postoperative swelling, estimates on this relative to prevention (RICE) or prevention + stimulated resorption (RICE + ) of fluid are scarce. Methods and analysis This is a single-center, evaluator-blinded randomized pilot trial to investigate postoperative swelling in adults requiring surgical fixation of a closed unilateral ankle fracture. A total of 50 patients will be recruited and randomly assigned to RICE or RICE + prior to surgery. All patients will undergo evaluator-blinded measurements of the ankle volume the day before surgery and subsequently from the evening of the 2nd postoperative day every 24 h until discharge. RICE will be initiated right after surgery and continued until discharge from the hospital in all patients. Additional application of negative pressure therapy (RICE + ) will be initiated on the morning of the 2nd postoperative day and repeated every 24 h until the time of discharge from the hospital. Outcome measures are (i) the relative amount and the time course of the postoperative swelling, (ii) the demand for analgesic therapy (type and amount) together with the perception of pain, (iii) the rate of complications, and (iv) mobility of the ankle joint and the recovery of walking abilities during a 12-weeks follow-up period. Serum and urine samples taken prior to sugery and during postoperative recovery will allow to evaluate the ratio of naturally occurring stable calcium isotopes (δ 44/42 Ca) as a marker of skeletal calcium accrual.
    Type: Article , PeerReviewed
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  • 36
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    Living and dead foraminiferal assemblage from the supratidal sand Japsand, North Frisian Wadden Sea: distributional patterns and controlling factors (2021)
    Springer | BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Supratidal sands are vitally important for coastal defence in the German Wadden Sea. They are less affected by human activities than other areas as they are located far off the mainland shore, touristical and commercial activities are generally prohibited. Therefore, supratidal sands are of high ecological interest. Nevertheless, the faunal inventory and distribution pattern of microorganisms on these sands were studied very little. The composition of living and dead foraminiferal assemblages was therefore investigated along a transect from the supratidal sand Japsand up to Hallig Hooge. Both assemblages were dominated by calcareous foraminifera of which Ammonia batava was the most abundant species. Elphidium selseyense and Elphidium williamsoni were also common in the living assemblage, but Elphidium williamsoni was comparably rare in the dead assemblage. The high proportions of Ammonia batava and Elphidium selseyense in the living assemblage arose from the reproduction season that differed between species. While Ammonia batava and Elphidium selseyense just finished their reproductive cycles, Elphidium williamsoni was just about to start. This was also confirmed by the size distribution patterns of the different species. The dead assemblage revealed 20 species that were not found in the living assemblage of which some were reworked from older sediments (e.g., Bucella frigida) and some were transported via tidal currents from other areas in the North Sea (e.g., Jadammina macrescens). The living foraminiferal faunas depicted close linkages between the open North Sea and the mainland. Key species revealing exchange between distant populations were Haynesina germanica, Ammonia batava and different Elphidium species. All these species share an opportunistic behaviour and are able to inhabit a variety of different environments; hence, they well may cope with changing environmental conditions. The benthic foraminiferal association from Japsand revealed that transport mechanisms via tides and currents play a major ecological role and strongly influence the faunal composition at this site.
    Type: Article , PeerReviewed
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    Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. Results: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. Conclusions: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. [MediaObject not available: see fulltext.].
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    Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis (2021)
    BioMed Central
    Details
    Publication Date: 2024-02-07
    Description: Background: Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. Results: Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. Conclusions: The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 39
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    Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-29
    Description: Background Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological "noise" in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (“persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate. Results We present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view. Conclusions ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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  • 40
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    Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.) (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. Results GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. Conclusions The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
    Electronic ISSN: 1471-2164
    Topics: Biology
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  • 42
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    Cost-effectiveness analysis of Vaborem in Carbapenem-resistant Enterobacterales (CRE) -Klebsiella pneumoniae infections in Italy (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Vaborem is a fixed dose combination of vaborbactam and meropenem with potent activity against target Carbapenem-resistant Enterobacterales (CRE) pathogens, optimally developed for Klebsiella pneumoniae carbapenemase (KPC). The study aims to evaluate the cost-effectiveness of Vaborem versus best available therapy (BAT) for the treatment of patients with CRE-KPC associated infections in the Italian setting. Methods A cost-effectiveness analysis was conducted based on a decision tree model that simulates the clinical pathway followed by physicians treating patients with a confirmed CRE-KPC infection in a 5-year time horizon. The Italian National Health System perspective was adopted with a 3% discount rate. The clinical inputs were mostly sourced from the phase 3, randomised, clinical trial (TANGO II). Unit costs were retrieved from the Italian official drug pricing list and legislation, while patient resource use was validated by a national expert. Model outcomes included life years (LYs) and quality adjusted life years (QALYs) gained, incremental costs, incremental cost-effectiveness ratio (ICER) and incremental cost-utility ratio (ICUR). Deterministic and probabilistic sensitivity analyses were also performed. Results Vaborem is expected to decrease the burden associated with treatment failure and reduce the need for chronic renal replacement therapy while costs related to drug acquisition and long-term care (due to higher survival) may increase. Treatment with Vaborem versus BAT leads to a gain of 0.475 LYs, 0.384 QALYs, and incremental costs of €3549, resulting in an ICER and ICUR of €7473/LY and €9246/QALY, respectively. Sensitivity analyses proved the robustness of the model and also revealed that the probability of Vaborem being cost-effective reaches 90% when willingness to pay is €15,850/QALY. Conclusions In the Italian setting, the introduction of Vaborem will lead to a substantial increase in the quality of life together with a minimal cost impact, therefore Vaborem is expected to be a cost-effective strategy compared to BAT.
    Electronic ISSN: 2191-1991
    Topics: Medicine , Economics
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    Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be “searching followed by evaluation”, which is infeasible for long gaps, or “searching by evaluation”, which heavily relies on heuristics and thus usually yields unreliable contig paths. Results We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. Conclusion Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing “searching by evaluation” strategy that relies on heuristics. Furthermore, unlike the “searching followed by evaluation” strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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  • 44
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    Decreased plasma lipid levels in a statin-free Danish primary health care cohort between 2001 and 2018 (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Lipid levels in blood have decreased considerably during the past decades in the general population partly due to use of statins. This study aims to investigate the trends in lipid levels between 2001 and 2018 in a statin-free population from primary health care, overall and by sex and age. Methods In a cohort of 634,119 patients from general practice with no diagnoses or medical treatments that affected lipid levels of total cholesterol (TC; n = 1,574,339) between 2001 and 2018 were identified. Similarly, measurements of low-density lipoprotein cholesterol (LDL-C; n = 1,302,440), high-density lipoprotein cholesterol (HDL-C; n = 1,417,857) and triglycerides (TG; n = 1,329,477) were identified. Results Mean TC decreased from 5.64 mmol/L (95% CI: 5.63–5.65) in 2001 to 5.17 mmol/L (95% CI: 5.16–5.17) in 2018 while LDL-C decreased from 3.67 mmol/L (95% CI: 3.66–3.68) to 3.04 mmol/L (95% CI: 3.03–3.04). Women aged 70–74 years experienced the largest decreases in TC levels corresponding to a decrease of 0.7 mmol/L. The decrease in LDL-C levels was most pronounced in men ≥85 years with a decrease of 0.9 mmol/L. For both genders, TC and LDL-C levels increased with advancing age until around age 50. After menopause the women had higher TC and LDL-C levels than the men. The median (geometric mean) TG level decreased by 0.4 mmol/L from 2001 to 2008, after which it increased slightly by 0.1 mmol/L until 2018. During life the TG levels of the men were markedly higher than the women’s until around age 65–70. HDL-C levels showed no trend during the study period. Conclusions The levels of TC and LDL-C decreased considerably in a statin-free population from primary health care from 2001 to 2018. These decreases were most pronounced in the elderly population and this trend is not decelerating. For TG, levels have started to increase, after an initial decrease.
    Electronic ISSN: 1476-511X
    Topics: Biology
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  • 45
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    Seed priming with proline improved photosystem II efficiency and growth of wheat (Triticum aestivum L.) (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Proline can promote growth of plants by increasing photosynthetic activity under both non-stress and abiotic stress conditions. However, its role in non-stressed conditions is least studied. An experiment was conducted to assess as to whether increase in growth of wheat due to seed priming with proline under non-stress condition was associated with proline-induced changes in photosystem II (PSII) activity. Seeds of four wheat varieties (S-24, Sehar-06, Galaxy-13, and Pasban-90) were primed with different concentrations of proline (0, 5, 15 and 25 mM) for 12 h and allowed to grow under normal conditions. Biomass accumulation and photosynthetic performance, being two most sensitive features/indicators of plant growth, were selected to monitor proline modulated changes. Results Seed priming with proline increased the fresh and dry weights of shoots and roots, and plant height of all four wheat varieties. Maximum increase in growth attributes was observed in all four wheat varieties at 15 mM proline. Maximum growth improvement due to proline was found in var. Galaxy-13, whereas the reverse was true for S-24. Moreover, proline treatment changed the Fo, Fm, Fv/Fo, PIABS, PITot in wheat varieties indicating changes in PSII activity. Proline induced changes in energy fluxes for absorption, trapping, electron transport and heat dissipation per reaction center indicated that var. Galaxy-13 had better ability to process absorbed light energy through photosynthetic machinery. Moreover, lesser PSII efficiency in var. S-24 was due to lower energy flux for electron transport and greater energy flux for heat dissipation. This was further supported by the fact that var. S-24 had disturbance at acceptor side of PSI as reflected by reduction in ΔVIP, probability and energy flux for electron transport at the PSI end electron acceptors. Conclusion Seed priming with proline improved the growth of wheat varieties, which depends on type of variety and concentration of proline applied. Seed priming with proline significantly changed the PSII activity in wheat varieties, however, its translation in growth improvement depends on potential of processing of absorbed light energy by electron acceptors of electron transport chain, particularly those present at PSI end.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Clinical characteristics of cardiovascular patients with extremely low levels of high-density lipoprotein cholesterol (2021)
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    Publication Date: 2021-10-30
    Description: Background Extremely low levels of high-density lipoprotein cholesterol (HDL-C) are related to high cardiovascular mortality. The underlying mechanism is not well known. This research aims to study the clinical characteristics of cardiovascular patients with extremely low levels of HDL-C. Methods All cardiovascular patients in a single Chinese cardiology center that were admitted from January to December 2019 were reviewed. The clinical characteristics of those with HDL-C
    Electronic ISSN: 1476-511X
    Topics: Biology
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    Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    A drug repositioning algorithm based on a deep autoencoder and adaptive fusion (2021)
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    Publication Date: 2021-10-30
    Description: Background Drug repositioning has caught the attention of scholars at home and abroad due to its effective reduction of the development cost and time of new drugs. However, existing drug repositioning methods that are based on computational analysis are limited by sparse data and classic fusion methods; thus, we use autoencoders and adaptive fusion methods to calculate drug repositioning. Results In this study, a drug repositioning algorithm based on a deep autoencoder and adaptive fusion was proposed to mitigate the problems of decreased precision and low-efficiency multisource data fusion caused by data sparseness. Specifically, a drug is repositioned by fusing drug-disease associations, drug target proteins, drug chemical structures and drug side effects. First, drug feature data integrated by drug target proteins and chemical structures were processed with dimension reduction via a deep autoencoder to characterize feature representations more densely and abstractly. Then, disease similarity was computed using drug-disease association data, while drug similarity was calculated with drug feature and drug-side effect data. Predictions of drug-disease associations were also calculated using a top-k neighbor method that is commonly used in predictive drug repositioning studies. Finally, a predicted matrix for drug-disease associations was acquired after fusing a wide variety of data via adaptive fusion. Based on experimental results, the proposed algorithm achieves a higher precision and recall rate than the DRCFFS, SLAMS and BADR algorithms with the same dataset. Conclusion The proposed algorithm contributes to investigating the novel uses of drugs, as shown in a case study of Alzheimer's disease. Therefore, the proposed algorithm can provide an auxiliary effect for clinical trials of drug repositioning.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    LongStitch: high-quality genome assembly correction and scaffolding using long reads (2021)
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    Publication Date: 2021-10-30
    Description: Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    Mesenchymal stem cells-derived exosomes for drug delivery (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Exosomes are extracellular vesicles secreted by various cells, mainly composed of lipid bilayers without organelles. In recent years, an increasing number of researchers have focused on the use of exosomes for drug delivery. Targeted drug delivery in the body is a promising method for treating many refractory diseases such as tumors and Alzheimer's disease (AD). Finding a suitable drug delivery carrier in the body has become a popular research today. In various drug delivery studies, the exosomes secreted by mesenchymal stem cells (MSC-EXOs) have been broadly researched due to their immune properties, tumor-homing properties, and elastic properties. While MSC-EXOs have apparent advantages, some unresolved problems also exist. This article reviews the studies on MSC-EXOs for drug delivery, summarizes the characteristics of MSC-EXOs, and introduces the primary production and purification methods and drug loading methods to provide solutions for existing problems and suggestions for future studies.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Effects of dyslipidemia on E antigen seroconversion of patients with chronic hepatitis B treated by nucleoside (acid) analogs (2021)
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    Publication Date: 2021-10-30
    Description: Background The prevalence of dyslipidemia in China is increasing annually. Current studies suggest that dyslipidemia affects the antiviral efficacy of hepatitis C virus (HCV) therapies, while recent studies suggest that serum lipids influence the response rates of chronic hepatitis B (CHB) patients receiving PEGylated interferon-alpha (Peg IFN-α) treatment. However, the role of dyslipidemia in the efficacy of nucleoside (acid) analogues (NAs) in CHB patients remains unclear. Methods From January 2010 to December 2013, data from 179 treatment-naive patients with CHB who were hepatitis B e antigen (HBeAg)-positive and had visited the first affiliated hospital of Wenzhou Medical University were assessed. Of these patients, 68 were assigned to the dyslipidemia group (diagnosed with CHB complicated with dyslipidemia) and 111 to the normolipidemic group. The following 3 treatment strategies were performed for all CHB patients over a 5-year period: lamivudine (LAM) plus adefovir dipivoxil (ADV) combination therapy, telbivudine (LdT) monotherapy, and entecavir (ETV) monotherapy. Serum assessments, blood biochemistry, HBV serological markers, HBV DNA before treatment and HBeAg serological conversion and virological responses at different timepoints after treatment were compared between the two groups. Measurement data were compared by τ tests and enumeration data by χ2 tests. Correlation analysis was performed using binary logistic regression analysis. Results The rates of HBeAg seroconversion in the dyslipidemia group at years 1, 2, 3, and 4 were 10.3, 13.2, 17.6, and 22.1%, respectively, which were not significantly lower than those of the normolipidemic group (11.7, 16.2, 18.0 and 33.3%; χ2 = 0.085, 0.293, 0.004, and 2.601, respectively; Ρ 〉 0.05). However, the rates of HBeAg seroconversion in the dyslipidemia group were significantly lower than those in the normolipidemic group at year 5 (27.9% vs. 43.2%, χ2 = 4.216, Ρ 
    Electronic ISSN: 1476-511X
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    Population variation alters aggression-associated oxytocin and vasopressin expressions in brains of Brandt’s voles in field conditions (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Density-dependent change in aggressive behavior contributes to the population regulation of many small rodents, but the underlying neurological mechanisms have not been examined in field conditions. We hypothesized that crowding stress and aggression-associated oxytocin (OT) and arginine vasopressin (AVP) in specific regions of the brain may be closely related to aggressive behaviors and population changes of small rodents. We analyzed the association of OT and AVP expression, aggressive behavior, and population density of Brandt’s voles in 24 large semi-natural enclosures (0.48 ha each) in Inner Mongolia grassland. We tested the effects of population density on the OT/AVP system and aggressive behavior by experimentally manipulating populations of Brandt’s voles in the grassland enclosures. High density was positively and significantly associated with more aggressive behavior, and increased expression of mRNA and protein of AVP and its receptor, but decreased expression of mRNA and protein of OT and its receptor in specific brain regions of the voles. Our study suggests that changes in OT/AVP expression are likely a result of the increased psychosocial stress that these voles experience during overcrowding, and thus the OT/AVP system can be used as indicators of density-dependent stressors in Brandt’s voles.
    Electronic ISSN: 1742-9994
    Topics: Biology
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    Assessing the suitability of general practice electronic health records for clinical prediction model development: a data quality assessment (2021)
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    Publication Date: 2021-10-30
    Description: Background The use of general practice electronic health records (EHRs) for research purposes is in its infancy in Australia. Given these data were collected for clinical purposes, questions remain around data quality and whether these data are suitable for use in prediction model development. In this study we assess the quality of data recorded in 201,462 patient EHRs from 483 Australian general practices to determine its usefulness in the development of a clinical prediction model for total knee replacement (TKR) surgery in patients with osteoarthritis (OA). Methods Variables to be used in model development were assessed for completeness and plausibility. Accuracy for the outcome and competing risk were assessed through record level linkage with two gold standard national registries, Australian Orthopaedic Association National Joint Replacement Registry (AOANJRR) and National Death Index (NDI). The validity of the EHR data was tested using participant characteristics from the 2014–15 Australian National Health Survey (NHS). Results There were substantial missing data for body mass index and weight gain between early adulthood and middle age. TKR and death were recorded with good accuracy, however, year of TKR, year of death and side of TKR were poorly recorded. Patient characteristics recorded in the EHR were comparable to participant characteristics from the NHS, except for OA medication and metastatic solid tumour. Conclusions In this study, data relating to the outcome, competing risk and two predictors were unfit for prediction model development. This study highlights the need for more accurate and complete recording of patient data within EHRs if these data are to be used to develop clinical prediction models. Data linkage with other gold standard data sets/registries may in the meantime help overcome some of the current data quality challenges in general practice EHRs when developing prediction models.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
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    Risk factors for development of nephropathy in patients with a diabetic Charcot foot (2021)
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    Publication Date: 2021-10-30
    Description: Objective Charcot foot is a rare complication to neuropathy and can cause severe foot deformities and ulcerations, which often require prolonged antibiotical treatment. The objective of this retrospective study was to investigate whether this treatment is associated to impaired renal function. Results In total, 163 patients were included, of whom 105 (64%) had received β-lactam antibiotics for a mean total duration of 13.0 months. There was a significant increase in the urine albumin/creatinine ratio in the group that received antibiotics (p = 0.017), and the use of antibiotics was associated to a subsequent diagnosis of nephropathy (p = 0.01). Patients treated with antibiotics had a 21.9% risk of developing subsequent nephropathy versus 5.2% for patients not treated with antibiotics. We suggest increased awareness on signs of nephropathy in patients with severe Charcot foot.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
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    Alien balsams, strawberries and their pollinators in a warmer world (2021)
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    Publication Date: 2021-10-30
    Description: Background Strawberries are a common crop whose yield success depends on the availability of pollinators. Invasive alien plants, such as Impatiens glandulifera and I. parviflora, are also attractive for bees and hoverflies, respectively, and occur in close proximity to strawberry cultivation areas. The aim of the study was to test whether alien plants may decrease pollination of strawberry cultivation. However, even if the pollinators are abundant, efficiency of their pollination may decrease as a result of revisits of flowers that were already probed. It is addressed by pollinators by scent marking. Moreover, such revisits can be determined by nectar replenishment, which may occur rapidly in nectar-rich flowers. We studied revisits to I. glandulifera by bumblebees and defined the factors that influence the probability of revisits (air temperature; pollinator species; family caste and size; flower area; sun radiation; and time of day). Results We found that the two alien species decreased the number of pollinators visiting strawberries. Apoidea, Bombini and Syrphidae significantly decreased on Fragaria × ananassa when alien Impatiens were present. We also revealed the influence of increasing air temperature on bumblebee foraging, which was particularly significant for female workers. At very high temperatures (〉 37°C), bumblebee males revisited probed flowers less often than female workers. Conclusions Our results demonstrate that in experimental conditions attractive alien species decrease pollination of strawberries, which may negatively affect production of this crop. Although the results have not been verified in real-life strawberry fields yet, we recommend that alien plant species that share the same pollinators and occur in close proximity of strawberries are controlled. Moreover, we found that revisits of probed flowers may weaken feeding efficiency of bumblebees. If revisits are not induced by nectar replenishment, then global warming may pose a serious threat to the survival of colonies, which may have consequences also for the plants that attract them, e.g., for strawberries.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Gender representation in food and beverage print advertisements found in corner stores around schools in Peru and Guatemala (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Objective The objective of this study is to assess gender representation in food and beverage print advertisements. Results The study follows a quantitative descriptive approach. Using a content analysis technique, we assessed the gender representation in 200 food and beverage print advertisements found in corner stores located in four areas around schools in Lima, Peru, and Guatemala City, Guatemala (100 advertisements per country). A total of 36% of the print advertisements exhibited a male main character for the case of Guatemala, while in Peru 14% of the print advertisements presented a male main character. Furthermore, in Guatemala, 22% of the main characters were male animated characters. Moreover, 27% of the print advertisements in Guatemala and 17%, in Peru were visually male-oriented. Overall, male characters appeared alongside sports references and in varied settings, whereas female characters were usually holding or consuming the product. In conclusion, although the majority of variables used to assess the representation of gender in food and beverage print advertisements were gender-neutral, those showing gender representation were mostly male-oriented. Despite its limited findings, the study provides evidence for the formulation of public policies and educational content aimed to protect children’s and adolescents’ health from the effects of food marketing.
    Electronic ISSN: 1756-0500
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    Mitochondrial dysfunction, UPRmt signaling, and targeted therapy in metastasis tumor (2021)
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    Publication Date: 2021-10-30
    Description: In modern research, mitochondria are considered a more crucial energy plant in cells. Mitochondrial dysfunction, including mitochondrial DNA (mtDNA) mutation and denatured protein accumulation, is a common feature of tumors. The dysfunctional mitochondria reprogram molecular metabolism and allow tumor cells to proliferate in the hostile microenvironment. One of the crucial signaling pathways of the mitochondrial dysfunction activation in the tumor cells is the retrograde signaling of mitochondria-nucleus interaction, mitochondrial unfolded protein response (UPRmt), which is initiated by accumulation of denatured protein and excess ROS production. In the process of UPRmt, various components are activitated to enhance the mitochondria-nucleus retrograde signaling to promote carcinoma progression, including hypoxia-inducible factor (HIF), activating transcription factor ATF-4, ATF-5, CHOP, AKT, AMPK. The retrograde signaling molecules of overexpression ATF-5, SIRT3, CREB, SOD1, SOD2, early growth response protein 1 (EGR1), ATF2, CCAAT/enhancer-binding protein-d, and CHOP also involved in the process. Targeted blockage of the UPRmt pathway could obviously inhibit tumor proliferation and metastasis. This review indicates the UPRmt pathways and its crucial role in targeted therapy of metastasis tumors.
    Electronic ISSN: 2045-3701
    Topics: Biology
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    Synergistic stimulation of osteoblast differentiation of rat mesenchymal stem cells by leptin and 25(OH)D3 is mediated by inhibition of chaperone-mediated autophagy (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Vitamin D is important for the mineralization of bones by stimulating osteoblast differentiation of bone marrow mesenchymal stem cells (BMMSCs). BMMSCs are a target of vitamin D action, and the metabolism of 25(OH)D3 to biologically active 1α,25(OH)2D3 in BMMSCs promotes osteoblastogenesis in an autocrine/paracrine manner. Our previous study with human BMMSCs showed that megalin is required for the 25(OH)D3-DBP complex to enter cells and for 25(OH)D3 to stimulate osteoblast differentiation in BMMSCs. Furthermore, we reported that leptin up-regulates megalin in those cells. Leptin is a known inhibitor of PI3K/AKT-dependent chaperone-mediated autophagy (CMA). In this study, we tested the hypothesis that leptin acts synergistically with 25(OH)D3 to promote osteoblastogenesis in rat BMMSCs by a mechanism that entails inhibition of PI3K/AKT-dependent CMA. Methods BMMSCs were isolated from rat bone marrow (4-week-old male SD rats); qRT-PCR and western immunoblots or immunofluorescence were used to evaluate the expression of megalin, ALP, COL1A1, RUNX2, OSX, OSP, and CMA in rBMMSCs. The osteoblast differentiation was evaluated by ALP activity, ALP staining, and calcium deposition. The viability of rBMMSCs was assessed with the CCK-8 kit. Biosynthesis of 1α,25(OH)2D3 was measured by a Rat 1α,25(OH)2D3 ELISA Kit. Results The combination of leptin and 25(OH)D3 treatment significantly enhanced osteoblast differentiation as shown by ALP activity, ALP staining, and calcium deposition, the expression of osteogenic genes ALP, COL1A1, RUNX2, OSX, and OSP by qRT-PCR and western immunoblots in rBMMSCs. Leptin enhanced the expression of megalin and synthesis of 1α,25(OH)2D3 in rBMMSCs. Our data showed that leptin inhibited CMA activity of rBMMSCs by activating PI3K/AKT signal pathway; the ability of leptin to enhance 25(OH)D3 promoted osteoblast differentiation of rBMMSCs was weakened by the PI3K/AKT signal pathway inhibitor. Conclusions Our data reveal the mechanism by which leptin and 25(OH)D3 promote osteoblast differentiation in rBMMSCs. Leptin promoted the expression of megalin by inhibiting CMA, increased the utilization of 25(OH)D3 by rBMMSCs, and enhanced the ability of 25(OH)D3 to induce osteoblast differentiation of rBMMSCs. PI3K/AKT is at least partially involved in the regulation of CMA. These data indicate the importance of megalin in BMMSCs for vitamin D’s role in skeletal health.
    Electronic ISSN: 1757-6512
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    Wharton’s jelly mesenchymal stem cells embedded in PF-127 hydrogel plus sodium ascorbyl phosphate combination promote diabetic wound healing in type 2 diabetic rat (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Diabetic cutaneous ulcers (DCU) are a complication of diabetes with diabetic foot ulcers being the most common, and the wounds are difficult to heal, increasing the risk of bacterial infection. Cell-based therapy utilizing mesenchymal stem cells (MSCs) is currently being investigated as a therapeutic avenue for both chronic diabetic ulcers and severe burns. Wharton’s jelly mesenchymal stem cell (WJMSC) with PF-127 hydrogel and sodium ascorbyl phosphate (SAP) improved skin wound healing in mice. Whether this combination strategy is helpful to diabetic ulcers wound healing remains to be explored. Methods Firstly, the WJMSCs embedded in PF-127 and SAP combination were transplanted onto excisional cutaneous wound bed in type 2 diabetic Sprague Dawley (SD) rats. Two weeks after transplantation, the skin tissue was collected for histological and immunohistochemical analysis. Further, overexpressing-EGFP WJMSCs were performed to investigate cell engraftment in the diabetic cutaneous ulcer. The apoptosis of WJMSCs which encapsulated with combination of PF-127 and SAP was detected by TUNEL fluorescence assay and RT-PCR in vitro. And the mitochondrial damage induced by oxidative stress assessed by MitoTracker and CMH2DCFDA fluorescence assay. Results In diabetic cutaneous wound rat model, PF-127 plus SAP-encapsulated WJMSCs transplantation promoted diabetic wound healing, indicating improving dermis regeneration and collagen deposition. In diabetic wound healing, less pro-inflammatory M1 macrophages, more anti-inflammatory M2 tissue-healing macrophages, and neovascularization were observed in PF-127 + SAP + WJMSCs group compared with other groups. SAP supplementation alleviated the apoptosis ratio of WJMSCs embedded in the PF-127 in vitro and promoted cell survival in vivo. Conclusion PF-127 plus SAP combination facilitates WJMSCs-mediated diabetic wound healing in rat through promoting cell survival, the macrophage transformation, and angiogenesis. Our findings may potentially provide a helpful therapeutic strategy for patients with diabetic cutaneous ulcer.
    Electronic ISSN: 1757-6512
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    Ex vivo expansion and characterization of human corneal endothelium for transplantation: a review (2021)
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    Publication Date: 2021-10-30
    Description: The corneal endothelium plays a key role in maintaining corneal transparency. Its dysfunction is currently treated with penetrating or lamellar keratoplasty. Advanced cell therapy methods seek to address the persistent global deficiency of donor corneas by enabling the renewal of the endothelial monolayer with tissue-engineered grafts. This review provides an overview of recently published literature on the preparation of endothelial grafts for transplantation derived from cadaveric corneas that have developed over the last decade (2010–2021). Factors such as the most suitable donor parameters, culture substrates and media, endothelial graft storage conditions, and transplantation methods are discussed. Despite efforts to utilize alternative cellular sources, such as induced pluripotent cells, cadaveric corneas appear to be the best source of cells for graft preparation to date. However, native endothelial cells have a limited natural proliferative capacity, and they often undergo rapid phenotype changes in ex vivo culture. This is the main reason why no culture protocol for a clinical-grade endothelial graft prepared from cadaveric corneas has been standardized so far. Currently, the most established ex vivo culture protocol involves the peel-and-digest method of cell isolation and cell culture by the dual media method, including the repeated alternation of high and low mitogenic conditions. Culture media are enriched by additional substances, such as signaling pathway (Rho-associated protein kinase, TGF-β, etc.) inhibitors, to stimulate proliferation and inhibit unwanted morphological changes, particularly the endothelial-to-mesenchymal transition. To date, this promising approach has led to the development of endothelial grafts for the first in-human clinical trial in Japan. In addition to the lack of a standard culture protocol, endothelial-specific markers are still missing to confirm the endothelial phenotype in a graft ready for clinical use. Because the corneal endothelium appears to comprise phenotypically heterogeneous populations of cells, the genomic and proteomic expression of recently proposed endothelial-specific markers, such as Cadherin-2, CD166, or SLC4A11, must be confirmed by additional studies. The preparation of endothelial grafts is still challenging today, but advances in tissue engineering and surgery over the past decade hold promise for the successful treatment of endothelial dysfunctions in more patients worldwide.
    Electronic ISSN: 1757-6512
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    Activation of adult mammalian retinal stem cells in vivo via antagonism of BMP and sFRP2 (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The adult mammalian retina does not have the capacity to regenerate cells lost due to damage or disease. Therefore, retinal injuries and blinding diseases result in irreversible vision loss. However, retinal stem cells (RSCs), which participate in retinogenesis during development, persist in a quiescent state in the ciliary epithelium (CE) of the adult mammalian eye. Moreover, RSCs retain the ability to generate all retinal cell types when cultured in vitro, including photoreceptors. Therefore, it may be possible to activate endogenous RSCs to induce retinal neurogenesis in vivo and restore vision in the adult mammalian eye. Methods To investigate if endogenous RSCs can be activated, we performed combinatorial intravitreal injections of antagonists to BMP and sFRP2 proteins (two proposed mediators of RSC quiescence in vivo), with or without growth factors FGF and Insulin. We also investigated the effects of chemically-induced N-methyl-N-Nitrosourea (MNU) retinal degeneration on RSC activation, both alone and in combination withthe injected factors. Further, we employed inducible Msx1-CreERT2 genetic lineage labeling of the CE followed by stimulation paradigms to determine if activated endogenous RSCs could migrate into the retina and differentiate into retinal neurons. Results We found that in vivo antagonism of BMP and sFRP2 proteins induced CE cells in the RSC niche to proliferate and expanded the RSC population. BMP and sFRP2 antagonism also enhanced CE cell proliferation in response to exogenous growth factor stimulation and MNU-induced retinal degeneration. Furthermore, Msx1-CreERT2 genetic lineage tracing revealed that CE cells migrated into the retina following stimulation and/or injury, where they expressed markers of mature photoreceptors and retinal ganglion cells. Conclusions Together, these results indicate that endogenous adult mammalian RSCs may have latent regenerative potential that can be activated by modulating the RSC niche and hold promise as a means for endogenous retinal cell therapy to repair the retina and improve vision.
    Electronic ISSN: 1757-6512
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    Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω 〉 1) had a higher correlation coefficient than that of experienced purifying selection (ω 
    Electronic ISSN: 1471-2164
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    A practical biphasic contrast media injection protocol strongly enhances the aorta and pulmonary artery simultaneously using a single CT angiography scan (2021)
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    Publication Date: 2021-10-30
    Description: Background Enhancement profiles of the pulmonary artery (PA) and aorta differ when using computed tomography (CT) angiography. Our aim was to determine the optimal CT protocol for a one-time CT scan that assesses both blood vessels. Methods We prospectively enrolled 101 cases of CT angiography in patients with suspected pulmonary embolism or aortic dissection from our center between 2018 and 2020. We also retrospectively collected the data of 40 patients who underwent traditional two-time CT scans between 2015 and 2018. Patients were divided into four groups: test bolus (TB) I, TB II, bolus-tracking (BT) I, and BT II. The enhancement of the PA and aorta, and the radiation doses used in the four groups were collected. Those who underwent two-time scans were classified into the traditional PA or aorta scan groups. Data were compared between the BT and traditional groups. Results The aortic enhancement was highest in BT II (294.78 ± 64.48 HU) followed BT I (285.18 ± 64.99 HU), TB II (186.58 ± 57.53 HU), and TB I (173.62 ± 69.70 HU). The radiation dose used was lowest in BT I (11.85 ± 5.55 mSv) and BT II (9.07 ± 3.44 mSv) compared with that used in the traditional groups (20.07 ± 7.78 mSv) and accounted for half of the traditional group (45.17–59.02%). The aortic enhancement was also highest in BT II (294.78 ± 64.48 HU) followed by BT I (285.18 ± 64.99 HU) when compared with that in the traditional aorta scan group (234.95 ± 94.18 HU). Conclusion Our CT protocol with a BT technique allows for a lower radiation dose and better image quality of the PA and aorta than those obtained using traditional CT scans. Trial registration: NCT04832633, retrospectively registered in April 2021 to the clinical trial registry.
    Electronic ISSN: 1471-2342
    Topics: Biology
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    Distinct patterns of whole blood transcriptional responses are induced in mice following immunisation with adenoviral and poxviral vector vaccines encoding the same antigen (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Viral vectors, including adenovirus (Ad) and modified vaccinia Ankara (MVA), have gained increasing attention as vaccine platforms in recent years due to their capacity to express antigens from a wide array of pathogens, their rapid induction of humoral and cellular protective immune responses, and their relatively low production costs. In particular, the chimpanzee Ad vector, ChAdOx1, has taken centre stage as a leading COVID-19 vaccine candidate. However, despite mounting data, both clinical and pre-clinical, demonstrating effective induction of adaptive immune responses, the innate immune signals that precede the protective responses that make these vectors attractive vaccine platforms remain poorly understood. Results In this study, a mouse immunisation model was used to evaluate whole blood gene expression changes 24 h after either a single dose or heterologous prime-boost regimen of an Ad and/or MVA vaccine. We demonstrate through comparative analysis of Ad vectors encoding different antigens that a transgene product-specific gene signature can be discerned from the vector-induced transcriptional response. Expression of genes involved in TLR2 stimulation and γδ T cell and natural killer cell activation were induced after a single dose of Ad, while MVA led to greater expression of type I interferon genes. The order of prime-boost combinations was found to influence the magnitude of the gene expression changes, with MVA/Ad eliciting greater transcriptional perturbation than Ad/MVA. Contrasting the two regimens revealed significant enrichment of epigenetic regulation pathways and augmented expression of MHC class I and II molecules associated with MVA/Ad. Conclusion These data demonstrate that the order in which vaccines from heterologous prime-boost regimens are administered leads to distinct transcriptional responses and may shape the immune response induced by such combinations. The characterisation of early vaccine-induce responses strengthens our understanding of viral vector vaccine mechanisms of action ahead of their characterisation in human clinical trials and are a valuable resource to inform the pre-clinical design of appropriate vaccine constructs for emerging infectious diseases.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The evaluation of alternative splicing, including differential isoform expression and differential exon usage, can provide some insights on the transcriptional changes that occur in response to environmental perturbations. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to assess potential changes in splicing events in the longissimus dorsi muscle of beef calves gestated under control or methionine-rich diets. RNA sequencing and whole-genome bisulfite sequencing were used to evaluate muscle transcriptome and methylome, respectively. Results Alternative splicing patterns were significantly altered by maternal methionine supplementation. Most of the altered genes were directly implicated in muscle development, muscle physiology, ATP activities, RNA splicing and DNA methylation, among other functions. Interestingly, there was a significant association between DNA methylation and differential exon usage. Indeed, among the set of genes that showed differential exon usage, significant differences in methylation level were detected between significant and non-significant exons, and between contiguous and non-contiguous introns to significant exons. Conclusions Overall, our findings provide evidence that a prenatal diet rich in methyl donors can significantly alter the offspring transcriptome, including changes in isoform expression and exon usage, and some of these changes are mediated by changes in DNA methylation.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Abatacept is useful in auto-immune cytopenia with immunopathologic manifestations caused by CTLA-4 defects (2021)
    American Society of Hematology
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    Publication Date: 2021-10-29
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
    Published by American Society of Hematology
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    GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Background Phylogenetic profiling is widely used to predict novel members of large protein complexes and biological pathways. Although methods combined with phylogenetic trees have significantly improved prediction accuracy, computational efficiency is still an issue that limits its genome-wise application. Results Here we introduce a new tree-based phylogenetic profiling algorithm named GFICLEE, which infers common single and continuous loss (SCL) events in the evolutionary patterns. We validated our algorithm with human pathways from three databases and compared the computational efficiency with current tree-based with 10 different scales genome dataset. Our algorithm has a better predictive performance with high computational efficiency. Conclusions The GFICLEE is a new method to infers genome-wide gene function. The accuracy and computational efficiency of GFICLEE make it possible to explore gene functions at the genome-wide level on a personal computer.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    In the Asia-Pacific region, the COI DNA test revealed the divergence of the bivalve mollusc Mactra chinensis into three species; can these species be distinguished using shell coloration and sperm structure? (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: According to COI DNA barcoding testing, the marine bivalve mollusc Mactra chinensis, which is native to the Asia-Pacific region, diverged into three species. These species were preliminary characterized as M. chinensis COI clade I, M. chinensis COI clade II and M. chinensis COI clade III. To find out whether it is possible to morphologically distinguish samples representing genetic clades, we examined the color of the shells and the structure of the spermatozoa. It was found that the number of detected coloration types exceeds the number of detected species. In addition, it was shown that individuals belonging to the same genetic clade can have shells of different colors. Consequently, it is impossible to choose one type of shell coloration as a species-specific trait. For sperm, the sperm morphological patterns found in each of the three species are consistent with the M. chinensis sperm model described in previous reports. However, the single sperm variant is also not applicable to discriminate between species derived from M. chinensis, since heterogeneous variants of spermatozoa differing in the length of the acrosomal rod were found. We hypothesized that genetic divergence of species could cause a shift towards predominance of one of the sperm variants, and that species-specific sperm morphs could be quantitatively dominant in molluscs belonging to different clades. However, the dominant sperm morphs were the same in COI clade I and COI clade III. Thus, dominant sperm morphs are useless as species-specific traits. However, shell color and sperm parameters are specific to different geographic regions, and it seems that unique environmental factors can determine shell color and sperm morphology. As a result, both shells and spermatozoa can be used to distinguish the geographical forms of M. chinensis, regardless of the belonging of the forms to a particular genetic clade. Here we propose the introduction of geographic identifiers, in which the shell color and parameters of sperm sets are used as morphological criteria to determine the geographical origin of mollusc specimens belonging to the M. chinensis species complex.
    Print ISSN: 1438-387X
    Electronic ISSN: 1438-3888
    Topics: Biology
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    Route of Zika virus infection in Aedes aegypti by transmission electron microscopy (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Zika fever has been a global health security threat, especially in the tropical and subtropical regions where most of the cases occur. The disease is caused by Zika virus (ZIKV), which belongs to the family Flaviviridae, genus Flavivirus. The virus is transmitted by Aedes mosquitoes, mostly by Aedes aegypti, during its blood meal. In this study we present a descriptive analysis, by transmission electron microscopy (TEM), of ZIKV infection in A. aegypti elected tissues at the 3rd day of infection. ZIKV vertical transmission experiments by oral infection were conducted to explore an offspring of natural infection. Results Gut and ovary tissues harbored a higher number of viral particles. The ZIKV genome was also detected, by RT-qPCR technique, in the organism of orally infected female mosquitoes and in their eggs laid. Conclusions The data obtained suggest that the ovary is an organ susceptible to be infected with ZIKV and that virus can be transmitted from mother to a fraction of the progeny.
    Electronic ISSN: 1471-2180
    Topics: Biology
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    Characterization of the gut microbiome in a porcine model of thoracic spinal cord injury (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The gut microbiome is a diverse network of bacteria which inhabit our digestive tract and is crucial for efficient cellular metabolism, nutrient absorption, and immune system development. Spinal cord injury (SCI) disrupts autonomic function below the level of injury and can alter the composition of the gut microbiome. Studies in rodent models have shown that SCI-induced bacterial imbalances in the gut can exacerbate the spinal cord damage and impair recovery. In this study we, for the first time, characterized the composition of the gut microbiome in a Yucatan minipig SCI model. We compared the relative abundance of the most dominant bacterial phyla in control samples to those collected from animals who underwent a contusion-compression SCI at the 2nd or 10th Thoracic level. Results We identify specific bacterial fluctuations that are unique to SCI animals, which were not found in uninjured animals given the same dietary regimen or antibiotic administration. Further, we identified a specific time-frame, “SCI-acute stage”, during which many of these bacterial fluctuations occur before returning to “baseline” levels. Conclusion This work presents a dynamic view of the microbiome changes that accompany SCI, establishes a resource for future studies and to understand the changes that occur to gut microbiota after spinal cord injury and may point to a potential therapeutic target for future treatment.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Fusobacterium nucleatum predicts a high risk of metastasis for esophageal squamous cell carcinoma (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Esophageal squamous cell carcinoma (ESCC) is the major type of esophageal cancer in China. The role of the bacteria present in ESCC tissue in neoplastic progression has not been fully elucidated. This study aimed to uncover different bacterial communities in ESCC tissues and examine the correlation between the abundance of the esophageal flora and clinicopathologic characteristics of ESCC. Results Microorganisms in tumors and normal tissues showed obvious clustering characteristics. The abundance of Fusobacterium (P = 0.0052) was increased in tumor tissues. The high level of Fusobacterium nucleatum was significantly associated with pT stage (P = 0.039) and clinical stage (P = 0.0039). The WES data showed that COL22A1, TRBV10–1, CSMD3, SCN7A and PSG11 were present in only the F. nucleatum-positive ESCC samples. GO and protein domain enrichment results suggested that epidermal growth factor might be involved in the regulation of cell apoptosis in F. nucleatum-positive ESCC. Both a higher mutational burden and F. nucleatum-positive was observed in tumors with metastasis than in tumors without metastasis. Conclusion F. nucleatum is closely related to the pT stage and clinical stage of ESCC. The abundance of F. nucleatum and tumor mutation burden may be used in combination as a potential method to predict metastasis in ESCC.
    Electronic ISSN: 1471-2180
    Topics: Biology
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    Pulmonary lesions: correlative study of dynamic triple-phase enhanced CT perfusion imaging with tumor angiogenesis and vascular endothelial growth factor expression (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background To investigate value of the quantitative perfusion parameters of dynamic triple-phase enhanced CT in differential diagnosis of pulmonary lesions, and explore the correlation between perfusion parameters of lung cancer with microvessel density (MVD) and vascular endothelial growth factor (VEGF). Methods 73 consecutive patients with lung lesions who successfully underwent pre-operative CT perfusion examination with dynamic triple-phase enhanced CT and received a final diagnosis by postoperative pathology or a clinical follow-up. The cases were divided into malignant and benign groups according to the pathological results. CT perfusion parameters, such as Median, Mean, Standard deviation (Std), Q10, Q25, Q50, Q75, Q90 of pulmonary artery perfusion (PAP), bronchial artery perfusion (BAP), perfusion index (PI) and arterial enhancement fraction (AEF) were obtained by performing computed tomography perfusion imaging (CTPI). Computed tomography perfusion (CTP) parameters were compared between malignant and benign lesions. The receiver operating characteristic (ROC) curve was used to assess the diagnostic efficiency of CTP parameters in diagnosing malignant lesions. The correlations between CTP parameters with MVD and VEGF were analysed in 36 lung cancer patients who had extra sections be used for immunohistochemistry staining of CD34 and VEGF. Results BAP (Mean, Std, Q90) and PI Std of benign lesions were higher than malignant lesions (p 
    Electronic ISSN: 1471-2342
    Topics: Biology
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    Adult stem cell transplantation combined with conventional therapy for the treatment of end-stage liver disease: a systematic review and meta-analysis (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: End-stage liver disease (ESLD) is characterized by the deterioration of liver function and a subsequent high mortality rate. Studies have investigated the use of adult stem cells to treat ESLD. Here, a systematic review and meta-analysis was conducted to determine the efficacy of a combination therapy with adult stem cell transplantation and traditional medicine for treating ESLD. Four databases—including PubMed, Web of Science, Embase, and Cochrane Library—were investigated for studies published before January 31, 2021. The main outcome indicators were liver function index, model for end-stage liver disease (MELD) scores, and Child‒Turcotte‒Pugh (CTP) scores. Altogether, 1604 articles were retrieved, of which eight met the eligibility criteria; these studies included data for 579 patients with ESLD. Combination of adult stem cell transplantation with conventional medicine significantly improved its efficacy with respect to liver function index, CTP and MELD scores, but this effect gradually decreased over time. Moreover, a single injection of stem cells was more effective than two injections with respect to MELD and CTP scores and total bilirubin (TBIL) and albumin (ALB) levels, with no significant difference in aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels. With respect to the TBIL levels, patients receiving mononuclear cells (MNCs) experienced a significantly greater therapeutic effect—starting from twenty-four weeks after the treatment—whereas with respect to ALB levels, CD34+ autologous peripheral blood stem cells (CD34+ APBSCs) and MNCs had similar therapeutic effects. Severe complications associated with adult stem cell treatment were not observed. Although the benefits of combination therapy with respect to improving liver function were slightly better than those of the traditional treatment alone, they gradually decreased over time.Systematic review registration: PROSPERO registration number: CRD42021238576.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Treatment of knee osteoarthritis with intra-articular injection of allogeneic adipose-derived stem cells (ADSCs) ELIXCYTE®: a phase I/II, randomized, active-control, single-blind, multiple-center clinical trial (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Objective To evaluate the safety and efficacy of intra-articular (IA) injection of allogeneic adipose-derived stem cells (ADSCs) ELIXCYTE® for knee osteoarthritis. Methods This was a patient-blind, randomized, active-control trial consisted of 4 arms including hyaluronic acid (HA) control and 3 ELIXCYTE® doses. A total of 64 subjects were screened, and 57 subjects were randomized. The primary endpoints included the changes from baseline to post-treatment visit of Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) pain score at Week 24 and the incidence of adverse events (AEs) and serious adverse events (SAEs). Results No ELIXCYTE®-related serious adverse events were reported during 96 weeks of follow-up and no suspected unexpected serious adverse reaction (SUSAR) or death was reported. The changes of the primary endpoint, WOMAC pain score at Week 24, showed significant differences in all ELIXCYTE® groups, as well as in HA groups between post-treatment visit and baseline. The ELIXCYTE® groups revealed significant decreases at Week 4 compared to HA group in WOMAC total scores, stiffness scores, functional limitation scores suggested the potential of ELIXCYTE® in earlier onset compared to those from HA. The significant differences of visual analog scale (VAS) pain score and Knee Society Clinical Rating System (KSCRS) functional activities score at Week 48 after ELIXCYTE® administration suggested the potential of ELIXCYTE® in the longer duration of the effectiveness compared to HA group. Conclusions ELIXCYTE® for knee osteoarthritis treatment was effective, safe, and well-tolerated. The efficacy results were showed that ELIXCYTE® conferred the earlier onset of reductions in pain scores and improvements in functional scores than HA group. Trial registration: ClinicalTrials.gov Identifier: NCT02784964. Registered 16 May, 2016—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02784964
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Analysis of vascularization in thyroid gland nodes with superb microvascular imaging (SMI) and CD34 expression histology: a pilot study (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The Doppler sonography technique known as "superb microvascular imaging" (SMI) is advancing sonographic micro vascularization imaging in various disciplines. In this study, we aimed to determine whether SMI could reliably reproduce the blood flow in thyroid nodes and whether malignancy could be diagnosed, based on vascularization properties. Immunhistochemical staining by CD34 and SMI where used to determine the vascularization of nodes in terms of quantified vascularization parameters gained by computational evaluation. Methods We used image analysis programs to investigate whether the quantitative value for vascularization strength in the thyroid node, measured with SMI, was correlated with the actual degree of vascularization, determined microscopically. We included 16 patients that underwent thyroid resections. We prepared thyroid gland tissue slices for immunohistochemistry and labelled endothelial cells with CD34 to visualize blood vessels microscopically. We used image analysis programs, ImageJ, to quantify SMI Doppler sonographic measurements and CellProfiler to quantify CD34 expression in histological sections. We evaluated the numeric values for diagnostic value in node differentiation. Furthermore, we compared these values to check for correlations. Results Among the 16 nodes studied, three harboured malignant tumours (18.75%): two papillary and one follicular carcinoma. Among the 13 benign lesions (81.25%), four harboured follicular adenomas. Malignant and benign nodes were not significantly different in sonographic (0.88 ± 0.89 vs. 1.13 ± 0.19; p = 0.2790) or immunohistochemical measurements of vascularization strength (0.05 ± 0.05 vs. 0.08 ± 0.06; p = 0.2260). Conclusion We found a positive, significant correlation (r = 0.55588; p = 0.0254) between SMI (quantitative values for vascularization strength) and immunohistochemistry (CD34 staining) evaluations of thyroid nodes.
    Electronic ISSN: 1471-2342
    Topics: Biology
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    Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco. Results One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth. Conclusion We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background The molecular complexity of neural retina development remains poorly studied. Knowledge of retinal neurogenesis regulation sheds light on retinal degeneration therapy exploration. Therefore, we integrated the time-series circRNA, lncRNA, miRNA, and mRNA expression profiles of the developing retina through whole-transcriptome sequencing. The key functional ncRNAs and the ceRNA network regulating retinal neurogenesis were identified. Results Transcriptomic analysis identified circRNA as the most variable ncRNA subtype. We screened a series of neurogenesis-related circRNAs, lncRNAs, and miRNAs using different strategies based on their diversified molecular functions. The expression of circCDYL, circATXN1, circDYM, circPRGRIP, lncRNA Meg3, and lncRNA Vax2os was validated by quantitative real-time PCR. These circRNAs and lncRNAs participate in neurotransmitter transport and multicellular organism growth through the intricate circRNA/lncRNA-miRNA-mRNA network. Conclusion Whole-transcriptome sequencing and bioinformatics analysis systematically screened key ncRNAs in retinal neurogenesis. The validated ncRNAs and their circRNA/lncRNA-miRNA-mRNA network involve neurotransmitter transport and multicellular organism growth during retinal development.
    Electronic ISSN: 1471-2164
    Topics: Biology
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    Stem cell-based therapy for ameliorating intrauterine adhesion and endometrium injury (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Intrauterine adhesion refers to endometrial repair disorders which are usually caused by uterine injury and may lead to a series of complications such as abnormal menstrual bleeding, recurrent abortion and secondary infertility. At present, therapeutic approaches to intrauterine adhesion are limited due to the lack of effective methods to promote regeneration following severe endometrial injury. Therefore, to develop new methods to prevent endometrial injury and intrauterine adhesion has become an urgent need. For severely damaged endometrium, the loss of stem cells in the endometrium may affect its regeneration. This article aimed to discuss the characteristics of various stem cells and their applications for uterine tissue regeneration.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Single cell Raman spectroscopy to identify different stages of proliferating human hepatocytes for cell therapy (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background Cell therapy provides hope for treatment of advanced liver failure. Proliferating human hepatocytes (ProliHHs) were derived from primary human hepatocytes (PHH) and as potential alternative for cell therapy in liver diseases. Due to the continuous decline of mature hepatic genes and increase of progenitor like genes during ProliHHs expanding, it is challenge to monitor the critical changes of the whole process. Raman microspectroscopy is a noninvasive, label free analytical technique with high sensitivity capacity. In this study, we evaluated the potential and feasibility to identify ProliHHs from PHH with Raman spectroscopy. Methods Raman spectra were collected at least 600 single spectrum for PHH and ProliHHs at different stages (Passage 1 to Passage 4). Linear discriminant analysis and a two-layer machine learning model were used to analyze the Raman spectroscopy data. Significant differences in Raman bands were validated by the associated conventional kits. Results Linear discriminant analysis successfully classified ProliHHs at different stages and PHH. A two-layer machine learning model was established and the overall accuracy was at 84.6%. Significant differences in Raman bands have been found within different ProliHHs cell groups, especially changes at 1003 cm−1, 1206 cm−1 and 1440 cm−1. These changes were linked with reactive oxygen species, hydroxyproline and triglyceride levels in ProliHHs, and the hypothesis were consistent with the corresponding assay results. Conclusions In brief, Raman spectroscopy was successfully employed to identify different stages of ProliHHs during dedifferentiation process. The approach can simultaneously trace multiple changes of cellular components from somatic cells to progenitor cells.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
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    Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Background In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance. Results 15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A1, A2, B1, B2, B3), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B3 → B2 → B1 → A). Conclusions Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    Predictive markers of transmission in areas with different malaria endemicity in north-eastern Tanzania based on seroprevalence of antibodies against Plasmodium falciparum (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: Objective A community-based cross-sectional study was done to assess Plasmodium falciparum exposure in areas with different malaria endemicity in north-eastern Tanzania using serological markers; PfAMA-1 and PfMSP-119. Results Bondo had a higher seroprevalence 36.6% (188) for PfAMA-1 as compared to Hai 13.8% (33), χ2 = 34.66, p 
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
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    Right and left ventricular function and flow quantification in pediatric patients with repaired tetralogy of Fallot using four-dimensional flow magnetic resonance imaging (2021)
    BioMed Central
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    Publication Date: 2021-10-31
    Description: Background To assess the accuracy and reproducibility of right ventricular (RV) and left ventricular (LV) function and flow measurements in children with repaired tetralogy of Fallot (rTOF) using four-dimensional (4D) flow, compared with conventional two-dimensional (2D) magnetic resonance imaging (MRI) sequences. Methods Thirty pediatric patients with rTOF were retrospectively enrolled to undergo 2D balanced steady-state free precession cine (2D b-SSFP cine), 2D phase contrast (PC), and 4D flow cardiac MRI. LV and RV volumes and flow in the ascending aorta (AAO) and main pulmonary artery (MPA) were quantified. Pearson’s or Spearman’s correlation tests, paired t-tests, the Wilcoxon signed-rank test, Bland–Altman analysis, and intraclass correlation coefficients (ICC) were performed. Results The 4D flow scan time was shorter compared with 2D sequences (P  0.05), and showed strong correlations (r 〉 0.90, P  0.60, P  0.85). Conclusions RV and LV function and flow quantification in pediatric patients with rTOF using 4D flow MRI can be measured accurately and reproducibly compared to those with conventional 2D sequences.
    Electronic ISSN: 1471-2342
    Topics: Biology
    Published by BioMed Central
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    “The PLCP gene family of grapevine (Vitis vinifera L.): characterization and differential expression in response to Plasmopara Viticola” (2021)
    BioMed Central
    Details
    Publication Date: 2021-10-30
    Description: Background Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases, are structurally related to papain. The members belonging to PLCPs family contribute to plant immunity, senescence, and defense responses in plants. The PLCP gene family has been identified in Arabidopsis, rice, soybean, and cotton. However, no systematic analysis of PLCP genes has been undertaken in grapevine. Since Plasmopara viticola as a destructive pathogen could affect immunity of grapes in the field, we considered that the members belonged to PLCPs family could play a crucial role in defensive mechanisms or programmed cell death. We aimed to evaluate the role of PLCPs in 2 different varieties of grapevines and compared the changes of their expressions with the transcriptional data in response to P. viticola. Results In this study, 23 grapevine PLCP (VvPLCP) genes were identified by comprehensive bioinformatics analysis. Subsequently, the chromosomal localizations, gene structure, conserved domains, phylogenetic relationship, gene duplication, and cis-acting elements were analyzed. Numerous cis-acting elements related to plant development, hormone, and stress responses were identified in the promoter of the VvPLCP genes. Phylogenetic analysis grouped the VvPLCP genes into nine subgroups. The transcription of VvPLCP in different inoculation time points and varieties indicated that VvPLCP may have vital functions in grapevine defense against Plasmopara viticola. According to transcriptome data and qPCR analysis, we observed the increasing expression levels of VvRD21–1 at 72 h after inoculation in resistant variety, inferring that it was related to grape downy mildew resistance. Meanwhile, 3 genes including VvXBCP1, VvSAG12–1, and VvALP1 showed higher expression at 24 h after pathogen inoculation in the susceptible variety and might be related to the downy mildew phenotype. We nominated these four genes to function during hypersensitive response (HR) process, inferring that these genes could be associated with downy mildew resistance in grapes. Conclusions Our results provide the reference for functional studies of PLCP gene family, and highlight its functions in grapevine defense against P. viticola. The results help us to better understand the complexity of the PLCP gene family in plant immunity and provide valuable information for future functional characterization of specific genes in grapevine.
    Electronic ISSN: 1471-2229
    Topics: Biology
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    The solid and liquid states of chromatin (2021)
    BioMed Central
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    Publication Date: 2021-10-30
    Description: The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid–solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid–liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
    Electronic ISSN: 1756-8935
    Topics: Biology , Medicine
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    Cell surface sphingomyelin: key role in cancer initiation, progression, and immune evasion (2021)
    BioMed Central
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    Publication Date: 2021-10-31
    Description: Cell surface biochemical changes, notably excessive increase in outer leaflet sphingomyelin (SM) content, are important in cancer initiation, growth, and immune evasion. Innumerable reports describe methods to initiate, promote, or enhance immunotherapy of clinically detected cancer, notwithstanding the challenges, if not impossibility, of identification of tumor-specific, or associated antigens, the lack of tumor cell surface membrane expression of major histocompatibility complex (MHC) class I alpha and β2 microglobulin chains, and lack of expression or accessibility of Fas and other natural killer cell immune checkpoint molecules. Conversely, SM synthesis and hydrolysis are increasingly implicated in initiation of carcinogenesis and promotion of metastasis. Surface membrane SM readily forms inter- and intra- molecular hydrogen bond network, which excessive tightness would impair cell-cell contact inhibition, inter- and intra-cellular signals, metabolic pathways, and susceptibility to host immune cells and mediators. The present review aims at clarifying the tumor immune escape mechanisms, which face common immunotherapeutic approaches, and attracting attention to an entirely different, neglected, key aspect of tumorigenesis associated with biochemical changes in the cell surface that lead to failure of contact inhibition, an instrumental tumorigenesis mechanism. Additionally, the review aims to provide evidence for surface membrane SM levels and roles in cells resistance to death, failure to respond to growth suppressor signals, and immune escape, and to suggest possible novel approaches to cancer control and cure.
    Electronic ISSN: 1476-511X
    Topics: Biology
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    isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Background Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches. Results We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets. Conclusions isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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    PRCC reduces the sensitivity of cancer cells to DNA damage by inhibiting JNK and ATM/ATR pathways and results in a poor prognosis in hepatocellular carcinoma (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Background and aim The proline rich mitotic checkpoint control factor (PRCC) is involved in the splicing process of pre-mRNA. This study aims to elucidate PRCC molecular function, regulatory mechanism and diagnostic value in hepatocellular carcinoma (HCC). Methods The tissue microarray and serum samples from HCC patients were used to investigate the clinical value of PRCC. The biological function and molecular mechanism of PRCC were demonstrated by cell biology, biochemical and animal experiments. The relationship between PRCC and intratumoral heterogeneity (ITH) was analyzed by bioinformatics. Results PRCC was highly expressed in HCC tissues and related to the poor prognosis of HCC patients, its contents were elevated in the preoperative sera of HCC patients. PRCC exhibited high application potential as a substitute or adjuvant of alpha-fetoprotein (AFP) for clinical diagnosis of HCC. It had no significant effect on the proliferation of cancer cells, but could inhibit spheroid formation and metastasis of HCC cells in vitro and in vivo. The high ectopic expression of PRCC made cancer cells insensitive to DNA damage, and enhanced the heterogeneity of HCC cells by inhibiting the JNK/ATM/ATR/ATF2 axis. The HCC patients with high PRCC expression had high ITH, which corresponded to a short overall survival in patients. Conclusions PRCC has high application potential as a substitute or adjuvant of AFP for clinical diagnosis of HCC. The high ectopic expression of PRCC not only caused HCC cells to resist to cell death induced by DNA damage, but also endowed cancer cells with numerous DNA mutations to become increasingly heterogeneous, finally leading to a poor prognosis in HCC patients. These data suggested PRCC could be a promising therapeutic target in HCC patients.
    Electronic ISSN: 2045-3701
    Topics: Biology
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    Comparative transcriptome analysis uncovers cell wall reorganization and repressed cell division during cotton fiber initiation (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Background Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. Results Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. Totally, 5516 DEGs including 1840 upregulated and 3676 downregulated were identified. GO enrichment analysis revealed that the downregulated DEGs were mainly associated with biological processes such as transcription related biosynthesis and metabolism, organic cyclic compound biosynthesis and metabolism, photosynthesis, and plant cell wall organization, with molecular functions involving transcription related binding, organic cyclic compound binding, and dioxygenase activity, while the upregulated DEGs were associated with DNA replication and phospholipid biosynthetic related processes. Among the 490 DEGs annotated as transcription factor genes, 86.5% were downregulated in the mutant including the Malvaceae-specific MMLs, expression patterns of which were confirmed during the central period of lint fiber initiation. Investigation of the 16 genes enriched in the cell wall organization revealed that 15 were EXPA coding genes. Conclusions Overall, our data indicate that lint fiber initiation is a complicated process involving cooperation of multiple transcription factor families, which might ultimately lead to the reorganization of the cell wall and terminated cell division of the differentiating fiber initials.
    Electronic ISSN: 1471-213X
    Topics: Biology , Medicine
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  • 89
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    Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq) technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has cataloged software tools for analyzing scRNA-seq data. With the number of tools in the database passing 1000, we provide an update on the state of the project and the field. This data shows the evolution of the field and a change of focus from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find that open science practices reward developers with increased recognition and help accelerate the field.
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
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  • 90
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    Synthesis, crystal structure and magnetic properties of a one-dimensional Mn2+ complex constructed from (+)-dibenzoyltartaric acid and 2,2′-bipyridine (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: The self-assembly reaction of (+)-dibenzoyltartaric acid (D-H2DBTA) with 2,2′-bipyridine (bpy) and Mn(CH3CO2)2·4H2O yielded a new coordination polymer, namely, catena-poly[[[diaqua(2,2′-bipyridine-κ2 N,N′)manganese(II)]-μ-2,3-bis(benzoyloxy)butanedioato-κ2 O 2:O 3] dihydrate], {[Mn(C18H12O8)(C10H8N2)(H2O)2]·2H2O} n or {[Mn(DBTA)(bpy)(H2O)2]·2H2O} n , (I). Complex (I) has been characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis (TGA) and single-crystal and powder X-ray diffraction. It crystallizes in the orthorhombic space group P212121. In the complex, the Mn2+ cation displays a distorted octahedral {MnO4N2} geometry, formed from two carboxylate O atoms of two DBTA2− ligands, two cis-oriented N atoms from one chelating 2,2′-bipyridine ligand and two trans-oriented O atoms from coordinated water molecules. The polymer displays a 1D chain with an Mn...Mn distance of 9.428 (1) Å. Due to the presence of flexible polycarboxylate and rigid bipyridyl ligands in the molecular structure, a high thermal stability of the complex is attained. The magnetic properties of (I) were analyzed based on the mononuclear Mn2+ model due to the long intramolecular Mn...Mn distance. The zero field splitting (ZFS) contribution in the high-spin Mn2+ cation is almost negligible and there are weak antiferromagnetic couplings between 1D chains [zJ′ = −0.062 (5) cm−1], corresponding to an intermolecular Mn...Mn distance of 7.860 (2) Å.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by International Union of Crystallography
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  • 91
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    Crystal structure studies of 4-ethylpiperazin-1-ium 3,5-dinitrobenzoate, 4-methylpiperazin-1-ium 3,5-dinitrobenzoate and 4-methylpiperazin-1-ium 4-iodobenzoate (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-21
    Description: As part of our ongoing investigation on the chemical and biological properties of piperazinium salts, we synthesized three novel compounds: 1-ethylpiperazinium 3,5-dinitrobenzoate (I), 1-methylpiperazinium 3,5-dinitrobenzoate (II) and 1-methylpiperazinium 4-iodobenzoate (III). The crystal structures of these compounds are built up of organic layers formed by the strong connection between the molecules by hydrogen bonds of type N—H...O. These layers are linked through N—H...O hydrogen bonds and C—H...O interactions or C—I...N halogen bonding, leading to the formation of a three-dimensional network.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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  • 92
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    Synthesis and crystal structure of a solvated CoIII complex with 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone ligands (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-21
    Description: The title CoIII complex, bis[bis(2-hydroxy-3-methoxybenzaldehyde thiosemicarbazonato)cobalt(III)] dithionate–dimethylformamide–methanol (1/4/3), [Co(C9H10N3O2S)2]2(S2O6)·4C3H7NO·3CH3OH, with monodeprotonated 2-hydroxy-3-methoxybenzaldehyde thiosemicarbazone as ligands crystallizes in the space group Poverline{1}. The asymmetric unit consists of two mononuclear [CoL 2]+ cations, one dithionate anion (S2O6)2− as counter-anion and seven solvate molecules (four dimethylmethanamide and three methanol). Each CoIII ion has a moderately distorted octahedral S2N2O2 geometry. In the crystal, the components are linked by numerous N—H...O and O—H...O contacts.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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    Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-20
    Description: The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine–aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment (2021)
    BioMed Central
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    Publication Date: 2021-10-29
    Description: Background Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens. Results The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola. Conclusions Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria.
    Electronic ISSN: 1471-2180
    Topics: Biology
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    The structure of natively iodinated bovine thyroglobulin (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-29
    Description: Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T4; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T3; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor–donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II–transducer complex (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-20
    Description: Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII–NpHtrII) was performed. The influence of the polydispersity of NpSRII–NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.
    Electronic ISSN: 2059-7983
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    A two-dimensional calcium (II) coordination polymer constructed from 2,2′-[terephthaloylbis(azanediyl)]diacetate: synthesis, structure and properties (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-18
    Description: A new two-dimensional (2D) coordination polymer, namely, poly[[diaqua-[μ4-2,2′-[terephthaloylbis(azanediyl)]diacetato]calcium(II)] monohydrate], {[Ca(C12H10N2O6)(H2O)2]·H2O} n , (I), has been synthesized by the reaction of CaCl2 with 2,2′-[terephthaloylbis(azanediyl)]diacetic acid (H2 L). The title compound was structurally characterized by single-crystal X-ray diffraction analysis, elemental analysis and IR spectroscopy. In the crystal structure of (I), each CaII cation binds to six carboxylate groups from four symmetry-related L 2− dianions. The hexadentate L 2− ligand links four symmetry-related calcium cations into a 2D layer-like structure, which can be simplified as a uninodal SP 2-periodic (3,6)III net with the point symbol (43·63). In the lattice, all layers pack in parallel arrays through weak interlayer hydrogen bonding and π–π interactions. The thermal stability and photoluminescence properties of (I) have been investigated. Thermogravimetric analysis reveals the different thermal stabilities of the two coordinated water molecules due to their different hydrogen-bonding interactions. The title coordination polymer exhibits an excitation-wavelength-dependent fluorescence in the solid state.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    New solvates and a salt of the anti-HIV compound etravirine (2021)
    International Union of Crystallography
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    Publication Date: 2021-10-19
    Description: Four new solvates of the anti-HIV compound etravirine [systematic name: 4-({6-amino-5-bromo-2-[(4-cyanophenyl)amino]pyrimidin-4-yl}oxy)-3,5-dimethylbenzonitrile, C20H15BrN6O] with dimethyl sulfoxide (C2H6OS, two distinct monosolvates), 1,4-dioxane (C4H8O2, the 0.75-solvate) and N,N-dimethylacetamide (C4H9NO, the monosolvate), which exhibit conversion to the same anhydrous etravirine phase upon desolvation, and a stable etravirinium oxalate salt {6-amino-5-bromo-4-(4-cyano-2,6-dimethylphenoxy)-2-[(4-cyanophenyl)amino]pyrimidin-1-ium hemioxalate, C20H16BrN6O+·0.5C2O4 2−} were obtained. The crystal structures were solved by single-crystal X-ray diffraction and analyzed by powder X-ray diffraction, and the intermolecular interactions were explored by Hirshfeld surface analysis. Lattice energies were evaluated using the atom–atom force field Coulomb–London–Pauli (AA CLP) approximation, which distributes the total energy as four separate contributions: Coulombic, polarization, dispersion and repulsion. The formation of the solvates and the oxalate salt was further characterized by thermal analysis and IR spectroscopy.
    Electronic ISSN: 2053-2296
    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    Synthesis and crystal structure of a new chiral α-aminooxime nickel(II) complex (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: A dinuclear nickel complex with (S)-limonene based aminooxime ligand has been isolated and its crystal structure determined. The resolved structure of dichloridobis{(2S,5R)-2-methyl-5-(prop-1-en-2-yl)-2-[(pyridin-2-yl)methylamino]cyclohexan-1-one oxime}dinickel(II), [Ni2Cl2(C16H23ClN3O)2], at 100 K has monoclinic (P21) symmetry. The two NiII ions in the dinuclear complex are each coordinated in a distorted octahedral environment by three nitrogen atoms, a terminal chloride and two μ bridging chlorides. Each oxime ligand is coordinated to nickel(II) by the three nitrogen atoms, leading to two five-membered chelate rings, each displaying an envelope conformation. In the crystal, numerous intermolecular and intramolecular hydrogen bonds lead to the formation of a three-dimensional network structure.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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    Crystal structure and Hirshfeld surface analysis of bis[(ethoxymethanethioyl)sulfanido](N,N,N′,N′-tetramethylethane-1,2-diamine)mercury(II) (2021)
    International Union of Crystallography
    Details
    Publication Date: 2021-10-19
    Description: The title four-coordinate mononuclear complex, [Hg(C3H5OS2)2(C6H16N2)] or [Hg(C3H5OS2)2(tmeda)] (tmeda: N,N,N′,N′-tetramethylethane-1,2-diamine), has a distorted tetrahedral geometry. The HgII ion is coordinated to two N atoms of the N,N,N′,N′-tetramethylethylenediamine ligand and two S atoms from two ethylxanthate xanthate ligands. In the crystal, molecules are linked by weak C—H...S hydrogen bonds, forming a two-dimensional supramolecular architecture in the ab plane. The most important contributions for the crystal packing are from H...H (59.3%), S...H (27.4%) and O...H (7.5%) interactions.
    Electronic ISSN: 2056-9890
    Topics: Chemistry and Pharmacology , Geosciences
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