Search Results

You searched for all publications:

with publication states 'Published (Approved)'
published in journal 'Scientific Reports'

Search Again...

These results only include publications that have been reviewed and processed by Diamond Light Source. To also view papers that have not yet been processed click here.

You can use the folder icon under Actions to collate papers as required. You can then click on View Folder in the left-hand navigation to review and/or download your folder.

Exact matches
Related results

269 items found (0 items not approved), displaying 1 to 10.[First/Prev] 1, 2, 3, 4, 5, 6, 7, 8 [Next/Last]

Instruments / Technical Area	Publication Details	Published
I13-1-Coherence	High-speed X-ray ptychographic tomography Darren Batey , Christoph Rau , Silvia Cipiccia Scientific Reports 12 DOI: 10.1038/s41598-022-11292-8 Diamond Proposal Number(s): [26240] Open Access Show Abstract ▼ Abstract: X-ray ptychography is a coherent scanning imaging technique widely used at synchrotron facilities for producing quantitative phase images beyond the resolution limit of conventional x-ray optics. The scanning nature of the technique introduces an inherent overhead to the collection at every scan position and limits the acquisition time of each 2D projection. The overhead associated with motion can be minimised with a continuous-scanning approach. Here we present an acquisition architecture based on continuous-scanning and up-triggering which allows to record ptychographic datasets at up to 9 kHz. We demonstrate the method by applying it to record 2D scans at up to 273 µm2/s and 3D scans of a (20 µm)3 volume in less than three hours. We discuss the current limitations and the outlook toward the development of sub-second 2D acquisition and minutes-long 3D ptychographic tomograms.	May 2022
I15-Extreme Conditions	Characterization of the high-pressure and high-temperature phase diagram and equation of state of chromium Simone Anzellini , Daniel Errandonea , Leonid Burakovsky , John E. Proctor , Robin Turnbull , Christine M. Beavers Scientific Reports 12 DOI: 10.1038/s41598-022-10523-2 Diamond Proposal Number(s): [26452, 28469] Open Access Show Abstract ▼ Abstract: The high-pressure and high-temperature phase diagram of chromium has been investigated both experimentally (in situ), using a laser-heated diamond-anvil cell technique coupled with synchrotron powder X-ray diffraction, and theoretically, using ab initio density-functional theory simulations. In the pressure–temperature range covered experimentally (up to 90 GPa and 4500 K, respectively) only the solid body-centred-cubic and liquid phases of chromium have been observed. Experiments and computer calculations give melting curves in agreement with each other that can both be described by the Simon–Glatzel equation 𝑇𝑚(𝑃)=2136𝐾(1+𝑃/25.9)0.41 T m ( P ) = 2136 K ( 1 + P / 25.9 ) 0.41 . In addition, a quasi-hydrostatic equation of state at ambient temperature has been experimentally characterized up to 131 GPa and compared with the present simulations. Both methods give very similar third-order Birch–Murnaghan equations of state with bulk moduli of 182–185 GPa and respective pressure derivatives of 4.74–5.15. According to the present calculations, the obtained melting curve and equation of state are valid up to at least 815 GPa, at which pressure the melting temperature is 9310 K. Finally, from the obtained results, it was possible to determine a thermal equation of state of chromium valid up to 65 GPa and 2100 K.	Apr 2022
I03-Macromolecular Crystallography I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans Rasheduzzaman Chowdhury , Martine I. Abboud , James Wiley , Anthony Tumber , Suzana Markolovic , Christopher J. Schofield Scientific Reports 12 DOI: 10.1038/s41598-022-10028-y Open Access Show Abstract ▼ Abstract: The JmjC family of 2-oxoglutarate dependent oxygenases catalyse a range of hydroxylation and demethylation reactions in humans and other animals. Jumonji domain-containing 7 (JMJD7) is a JmjC (3S)-lysyl-hydroxylase that catalyses the modification of Developmentally Regulated GTP Binding Proteins 1 and 2 (DRG1 and 2); JMJD7 has also been reported to have histone endopeptidase activity. Here we report biophysical and biochemical studies on JMJD7 from Drosophila melanogaster (dmJMJD7). Notably, crystallographic analyses reveal that the unusual dimerization mode of JMJD7, which involves interactions between both the N- and C-terminal regions of both dmJMJD7 monomers and disulfide formation, is conserved in human JMJD7 (hsJMJD7). The results further support the assignment of JMJD7 as a lysyl hydroxylase and will help enable the development of selective inhibitors for it and other JmjC oxygenases.	Apr 2022
I04-Macromolecular Crystallography	The distinctive roles played by the superoxide dismutases of the extremophile Acinetobacter sp. Ver3 Bruno Alejandro Steimbrüch , Mariana Gabriela Sartorio , Néstor Cortez , Daniela Albanesi , María-Natalia Lisa , Guillermo Daniel Repizo Scientific Reports 12 DOI: 10.1038/s41598-022-08052-z Open Access Show Abstract ▼ Abstract: Acinetobacter sp. Ver3 is a polyextremophilic strain characterized by a high tolerance to radiation and pro-oxidants. The Ver3 genome comprises the sodB and sodC genes encoding an iron (AV3SodB) and a copper/zinc superoxide dismutase (AV3SodC), respectively; however, the specific role(s) of these genes has remained elusive. We show that the expression of sodB remained unaltered in different oxidative stress conditions whereas sodC was up-regulated in the presence of blue light. Besides, we studied the changes in the in vitro activity of each SOD enzyme in response to diverse agents and solved the crystal structure of AV3SodB at 1.34 Å, one of the highest resolutions achieved for a SOD. Cell fractionation studies interestingly revealed that AV3SodB is located in the cytosol whereas AV3SodC is also found in the periplasm. Consistently, a bioinformatic analysis of the genomes of 53 Acinetobacter species pointed out the presence of at least one SOD type in each compartment, suggesting that these enzymes are separately required to cope with oxidative stress. Surprisingly, AV3SodC was found in an active state also in outer membrane vesicles, probably exerting a protective role. Overall, our multidisciplinary approach highlights the relevance of SOD enzymes when Acinetobacter spp. are confronted with oxidizing agents.	Mar 2022
NONE-No attached Diamond beamline	Advanced removal of Reactive Yellow 84 azo dye using functionalised amorphous calcium carbonates as adsorbent Loredana Brinza , Andreea Elena Maftei , Sorin Tascu , Florin Brinza , Mariana Neamtu Scientific Reports 12 DOI: 10.1038/s41598-022-07134-2 Open Access Show Abstract ▼ Abstract: Two environmentally friendly organics (ethylenediaminetetraacetic acid, EDTA and its easier biodegradabe isomer, ethylenediamine-N, N′-disuccinic acid, EDDS) were used to dope calcium carbonate (CC) nanoparticles intending to increase their adsorptive properties and evaluate adsorption performance (uptake capacity and removal efficiency) for the persistent Reactive Yellow 84 azo dye. Easily synthesized nanomaterials were fully characterized (morphology and size, mineralogy, organic content, surface area, pore size and hydrodynamic diameter). RY84 removal was performed using two consecutive processes: photodegradation after adsorption. The CC-EDTA particles were most efficient for dye removal as compared to the plain and CC-EDDS particles. Adsorption kinetics and isotherms were considered for the CC-EDTA system. 99% removal occurred via adsorption on 1 g/L of adsorbent at 5 mg/L dye concentration and pH of 8 and it decreased to 48% at 60 mg/L. Maximum uptake capacity as described by Langmuir is 39.53 mg/g. As post-adsorption, under UVA irradiation, in the presence of 40 mmol/L H2O2, at dye concentration of 10 mg/L the highest degradation was 49.11%. Substantial decrease of adsorption (ca. 4 times) and photodegradation (ca. 5 times) efficiencies were observed in wastewater effluent as compared to distilled water. The results have important implications to wastewater treatments and appropriate decisions making for the choice of treatment process, process optimization and scaling up to pilot and industrial levels.	Feb 2022
I13-2-Diamond Manchester Imaging	Temporal refinement of 3D CNN semantic segmentations on 4D time-series of undersampled tomograms using hidden Markov models Dimitrios Bellos , Mark Basham , Tony Pridmore , Andrew P. French Scientific Reports 11 DOI: 10.1038/s41598-021-02466-x Diamond Proposal Number(s): [9396] Open Access Show Abstract ▼ Abstract: Recently, several convolutional neural networks have been proposed not only for 2D images, but also for 3D and 4D volume segmentation. Nevertheless, due to the large data size of the latter, acquiring a sufficient amount of training annotations is much more strenuous than in 2D images. For 4D time-series tomograms, this is usually handled by segmenting the constituent tomograms independently through time with 3D convolutional neural networks. Inter-volume information is therefore not utilized, potentially leading to temporal incoherence. In this paper, we attempt to resolve this by proposing two hidden Markov model variants that refine 4D segmentation labels made by 3D convolutional neural networks working on each time point. Our models utilize not only inter-volume information, but also the prediction confidence generated by the 3D segmentation convolutional neural networks themselves. To the best of our knowledge, this is the first attempt to refine 4D segmentations made by 3D convolutional neural networks using hidden Markov models. During experiments we test our models, qualitatively, quantitatively and behaviourally, using prespecified segmentations. We demonstrate in the domain of time series tomograms which are typically undersampled to allow more frequent capture; a particularly challenging problem. Finally, our dataset and code is publicly available.	Dec 2021
I13-2-Diamond Manchester Imaging	Scaling the U-net: segmentation of biodegradable bone implants in high-resolution synchrotron radiation microtomograms Ivo M. Baltruschat , Hanna Cwieka , Diana Krüger , Berit Zeller-Plumhoff , Frank Schlünzen , Regine Willumeit-Römer , Julian Moosmann , Philipp Heuser Scientific Reports 11 DOI: 10.1038/s41598-021-03542-y Diamond Proposal Number(s): [22346] Open Access Show Abstract ▼ Abstract: Highly accurate segmentation of large 3D volumes is a demanding task. Challenging applications like the segmentation of synchrotron radiation microtomograms (SRμCT) at high-resolution, which suffer from low contrast, high spatial variability and measurement artifacts, readily exceed the capacities of conventional segmentation methods, including the manual segmentation by human experts. The quantitative characterization of the osseointegration and spatio-temporal biodegradation process of bone implants requires reliable, and very precise segmentation. We investigated the scaling of 2D U-net for high resolution grayscale volumes by three crucial model hyper-parameters (i.e., the model width, depth, and input size). To leverage the 3D information of high-resolution SRμCT, common three axes prediction fusing is extended, investigating the effect of adding more than three axes prediction. In a systematic evaluation we compare the performance of scaling the U-net by intersection over union (IoU) and quantitative measurements of osseointegration and degradation parameters. Overall, we observe that a compound scaling of the U-net and multi-axes prediction fusing with soft voting yields the highest IoU for the class “degradation layer”. Finally, the quantitative analysis showed that the parameters calculated with model segmentation deviated less from the high quality results than those obtained by a semi-automatic segmentation method.	Dec 2021
B16-Test Beamline I15-Extreme Conditions	First observation of radiolytic bubble formation in unstirred nano-powder sludges and a consistent model thereof Mel O'Leary , Aliaksandr Baidak , Martyn Barnes , Thomas Donoclift , Christopher Emerson , Catarina Figueira , Oliver Fox , Annette Kleppe , Aaron Mcculloch , Darryl Messer , Robin Orr , Fred Currell Scientific Reports 11 DOI: 10.1038/s41598-021-01868-1 Diamond Proposal Number(s): [21977, 20531, 20469, 19017, 17524, 17519, 16218] Open Access Show Abstract ▼ Abstract: Experiments involving the irradiation of water contained within magnesium hydroxide and alumina nanoparticle sludges were conducted and culminated in observations of an increased yield of molecular hydrogen when compared to the yield from the irradiation of bulk water. We show that there is a relationship linking this increased yield to the direct nanoscale ionization mechanism in the nanoparticles, indicating that electron emission from the nanoparticles drives new radiative pathways in the water. Because the chemical changes in these sludges are introduced by irradiation only, we have a genuinely unstirred system. This feature allows us to determine the diffusivity of the dissolved gas. Using the measured gas production rate, we have developed a method for modelling when hydrogen bubble formation will occur within the nanoparticle sludges. This model facilitates the determination of a consistent radiolytic consumption rate coinciding with the observations of bubble formation. Thus, we demonstrate a nanoscale radiation effect directly influencing the formation of molecular hydrogen.	Nov 2021
I13-2-Diamond Manchester Imaging	Evaporation kinetics in highly porous tetrapodal zinc oxide networks studied using in situ SRµCT Birte Hindenlang , Anna Gapeeva , Martina J. Baum , Sören Kaps , Lena M. Saure , Florian Rasch , Jorg Hammel , Julian Moosmann , Malte Storm , Rainer Adelung , Fabian Schütt , Berit Zeller-Plumhoff Scientific Reports 11 DOI: 10.1038/s41598-021-99624-y Diamond Proposal Number(s): [19205] Open Access Show Abstract ▼ Abstract: Tetrapodal zinc oxide (t-ZnO) is used to fabricate polymer composites for many different applications ranging from biomedicine to electronics. In recent times, macroscopic framework structures from t-ZnO have been used as a versatile sacrificial template for the synthesis of multi-scaled foam structures from different nanomaterials such as graphene, hexagonal boron nitride or gallium nitride. Many of these fabrication methods rely on wet-chemical coating processes using nanomaterial dispersions, leading to a strong interest in the actual coating mechanism and factors influencing it. Depending on the type of medium (e.g. solvent) used, different results regarding the homogeneity of the nanomaterial coating can be achieved. In order to understand how a medium influences the coating behavior, the evaporation process of water and ethanol is investigated in this work using in situ synchrotron radiation-based micro computed tomography (SRµCT). By employing propagation-based phase contrast imaging, both the t-ZnO network and the medium can be visualized. Thus, the evaporation process can be monitored non-destructively in three dimensions. This investigation showed that using a polar medium such as water leads to uniform evaporation and, by that, a homogeneous coating of the entire network.	Oct 2021
I03-Macromolecular Crystallography I04-Macromolecular Crystallography	Structure and stability of the designer protein WRAP-T and its permutants Bram Mylemans , Xiao Yin Lee , Ina Laier , Christine Helsen , Arnout R. D. Voet Scientific Reports 11 DOI: 10.1038/s41598-021-98391-0 Open Access Show Abstract ▼ Abstract: β-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats (‘blades’) each consisting of a 4-stranded anti-parallel β-sheet. So far, 4- to 12-bladed β-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric β-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each β-propeller sub-family.	Sep 2021

Publications Database

Search Results

You searched for all publications:

Search Again...

Subject Areas (check all that apply) select all

Instruments used to collect data (check all that apply) select all

Collaborations involved (check all that apply) select all

Diamond Offline Facilities used

Relevant Technical Areas (check all that apply) select all

Menu for Anonymous User