301 results on '"Lee PD"'
Search Results
2. Pulmonary and systemic pathology in COVID-19—holistic pathological analyses
- Author
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Jonigk, D, Werlein, C, Lee, PD, Kauczor, H-U, Länger, F, and Ackermann, M
- Subjects
Post-Acute COVID-19 Syndrome ,SARS-CoV-2 ,COVID-19 ,Humans ,1103 Clinical Sciences ,Thrombosis ,Review Article ,General Medicine ,Lung ,Pandemics ,1117 Public Health and Health Services - Abstract
Hintergrund: Die COVID-19-Pandemie stellt den dritten weltweiten Coronavirus-assoziierten Erkrankungsausbruch der letzten 20 Jahre dar. Klinisch dominiert die pulmonale Beteiligung mit einem akuten Lungenversagen (ARDS) bei schweren Verläufen, jedoch können auch andere Organsysteme wie das Herz-Kreislauf-System, Zentralnervensystem und der Gastrointestinaltrakt betroffen sein. Der Pathomechanismus der Organschädigung sowohl für die Lunge wie auch für die nichtpulmonalen Organsysteme war zu Beginn der Pandemie weitestgehend unklar. Methode: Selektive Literaturübersicht bezüglich der morphologischen Veränderungen und zugrunde liegenden Pathomechanismen bei COVID-19 mit Fokussierung auf bildgebende Verfahren. Ergebnisse: Immunhistochemische, elektronenmikroskopische und molekularpathologische Analysen an Autopsiegewebe führten zu einem besseren Verständnis der Pathophysiologie von COVID-19 einschließlich der molekularen Regulationsmechanismen. Hierbei konnte gezeigt werden, dass die sogenannte intussuszeptive Angiogenese (IA) in den betroffenen Organen von COVID-19-Patienten ein zentrales Schadensmuster darstellt. Bei der IA verändert sich ein bestehendes Gefäß durch Einstülpung des Endothels und Ausbildung eines intraluminalen Septums, wodurch schließlich zwei neue Lumina entstehen. Hierdurch verändert sich die Hämodynamik, unter anderem durch Verlust der laminaren Strömung mit Ausbildung turbulenter inhomogener Flussgeschwindigkeiten. Die Induktion der IA ist einerseits auf eine thrombotisch bedingte Ischämie zurückzuführen, doch geht sie andererseits selbst mit einem erhöhten Risiko für weitere Mikrothromben einher, die bei COVID-19-Patientinnen und Patienten in Lunge, Herz, Leber, Nieren, Gehirn und Plazenta nachgewiesen wurden. Schlussfolgerung: In Autopsiematerial von Patientinnen und Patienten mit COVID-19 konnten ultrastrukturell in verschiedenen Geweben eine veränderte Mikrovaskularität, eine IA sowie multifokale Thromben nachgewiesen werden. Diese Veränderungen sind als mögliche Faktoren für postakute interstitiell-fibrotische Organveränderungen wie auch das klinische Bild des Long COVID zu betrachten.
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- 2022
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3. Detection and Tracking Volumes of Interest in 3D Printed Tissue Engineering Scaffolds using 4D Imaging Modalities
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Kondarage, AI, Gayani, B, Poologasundarampillai, G, Nommeots-Nomm, A, Lee, PD, Lalitharatne, TD, Nanayakkara, ND, Jones, JR, Karunaratne, A, and National Institute for Health Research
- Subjects
Tissue Engineering ,Tissue Scaffolds ,Printing, Three-Dimensional ,Humans ,X-Ray Microtomography - Abstract
Additive manufacturing (AM) platforms allow the production of patient tissue engineering scaffolds with desirable architectures. Although AM platforms offer exceptional control on architecture, post-processing methods such as sintering and freeze-drying often deform the printed scaffold structure. In-situ 4D imaging can be used to analyze changes that occur during post-processing. Visualization and analysis of changes in selected volumes of interests (VOIs) over time are essential to understand the underlining mechanisms of scaffold deformations. Yet, automated detection and tracking of VOIs in the 3D printed scaffold over time using 4D image data is currently an unsolved image processing task. This paper proposes a new image processing technique to segment, detect and track volumes of interest in 3D printed tissue engineering scaffolds. The method is validated using a 4D synchrotron sourced microCT image data captured during the sintering of bioactive glass scaffolds in-situ. The proposed method will contribute to the development of scaffolds with controllable designs and optimum properties for the development of patient-specific scaffolds.
- Published
- 2021
- Full Text
- View/download PDF
4. Enabling three-dimensional densitometric measurements using laboratory source X-ray micro-computed tomography
- Author
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Pankhurst, MJ, Fowler, R, Courtois, L, Nonni, S, Zuddas, F, Atwood, RC, Davis, GR, and Lee, PD
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lcsh:Computer software ,Technology ,Beam characterisation ,Science & Technology ,Three-dimensional densitometry ,Laboratory X-ray micro-computed tomography ,QUANTIFICATION ,Computer Science, Software Engineering ,lcsh:QA76.75-76.765 ,Computer Science ,GROWTH ,Beam hardening ,PERMEABILITY ,Python - Abstract
We present new software allowing significantly improved quantitative mapping of the three-dimensional density distribution of objects using laboratory source polychromatic X-rays via a beam characterisation approach (c.f. filtering or comparison to phantoms). One key advantage is that a precise representation of the specimen material is not required. The method exploits well-established, widely available, non-destructive and increasingly accessible laboratory-source X-ray tomography. Beam characterisation is performed in two stages: (1) projection data are collected through a range of known materials utilising a novel hardware design integrated into the rotation stage; and (2) a Python code optimises a spectral response model of the system. We provide hardware designs for use with a rotation stage able to be tilted, yet the concept is easily adaptable to virtually any laboratory system and sample, and implicitly corrects the image artefact known as beam hardening. Keywords: Laboratory X-ray micro-computed tomography, Beam characterisation, Python, Beam hardening, Three-dimensional densitometry
- Published
- 2018
5. Multiscale analyses reveal native-like lamellar bone repair and near perfect bone-contact with porous strontium-loaded bioactive glass
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Autefage, H, Allen, F, Tang, HM, Kallepitis, C, Gentleman, E, Reznikov, N, Nitiputri, K, Nommeots-Nomm, A, Young, G, Lee, PD, Pierce, BF, Wagermaier, W, Fratzl, P, Goodship, A, Jones, JR, Blunn, G, Stevens, M, and Wellcome Trust
- Subjects
Raman spectroscopy ,MD Multidisciplinary ,Biomedical Engineering ,SAXS ,Strontium-releasing materials ,FIB-SEM ,3D porous bioactive glass ,Critical-sized bone repair - Abstract
The efficient healing of critical-sized bone defects using synthetic biomaterial-based strategies is promising but remains challenging as it requires the development of biomaterials that combine a 3D porous architecture and a robust biological activity. Bioactive glasses (BGs) are attractive candidates as they stimulate a biological response that favors osteogenesis and vascularization, but amorphous 3D porous BGs are difficult to produce because conventional compositions crystallize during processing. Here, we rationally designed a porous, strontium-releasing, bioactive glass-based scaffold (pSrBG) whose composition was tailored to deliver strontium and whose properties were optimized to retain an amorphous phase, induce tissue infiltration and encourage bone formation. The hypothesis was that it would allow the repair of a critical-sized defect in an ovine model with newly-formed bone exhibiting physiological matrix composition and structural architecture. Histological and histomorphometric analyses combined with indentation testing showed pSrBG encouraged near perfect bone-to-material contact and the formation of well-organized lamellar bone. Analysis of bone quality by a combination of Raman spectral imaging, small-angle X-ray scattering, X-ray fluorescence and focused ion beam-scanning electron microscopy demonstrated that the repaired tissue was akin to that of normal, healthy bone, and incorporated small amounts of strontium in the newly formed bone mineral. These data show the potential of pSrBG to induce an efficient repair of critical-sized bone defects and establish the importance of thorough multi-scale characterization in assessing biomaterial outcomes in large animal models.
- Published
- 2019
6. 4D synchrotron X-ray tomographic quantification of the transition from cellular to dendrite growth during directional solidification
- Author
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Cai, B, Wang, J, Kao, A, Pericleous, K, Phillion, AB, Atwood, RC, and Lee, PD
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Technology ,VIDEO MICROSCOPY ,Interface instability ,Polymers and Plastics ,Materials Science ,INITIAL INSTABILITY ,Materials Science, Multidisciplinary ,FLUID-FLOW ,RADIOGRAPHY ,Dendrite ,Solidification ,0912 Materials Engineering ,Al alloy ,Materials ,Science & Technology ,REAL-TIME ,Metals and Alloys ,EVOLUTION ,Electronic, Optical and Magnetic Materials ,Ceramics and Composites ,Metallurgy & Metallurgical Engineering ,IN-SITU OBSERVATION ,AL-CU ALLOY ,FRAGMENTATION ,X-ray tomography ,PATTERN-FORMATION ,0913 Mechanical Engineering - Abstract
Solidification morphology directly impacts the mechanical properties of materials; hence many models of the morphological evolution of dendritic structures have been formulated. However, there is a paucity of validation data for directional solidification models, especially the direct observations of metallic alloys, both for cellular and dendritic structures. In this study, we performed 4D synchrotron X-ray tomographic imaging (three spatial directions plus time), to study the transition from cellular to a columnar dendritic morphology and the subsequent growth of columnar dendrite in a temperature gradient stage. The cellular morphology was found to be highly complex, with frequent lateral bridging. Protrusions growing out of the cellular front with the onset of morphological instabilities were captured, together with the subsequent development of these protrusions into established dendrites. Other mechanisms affecting the solidification microstructure, including dendrite fragmentation/pinch-off were also captured and the quantitative results were compared to proposed mechanisms. The results demonstrate that 4D imaging can provide new data to both inform and validate solidification models.
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- 2016
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7. A Review of Techniques for Visualising Soft Tissue Microstructure Deformation and Quantifying Strain Ex Vivo
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Disney, CM, Lee, PD, Hoyland, JA, Sherratt, MJ, and Bay, BK
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Microscopy ,in situ imaging ,tendon ,digital volume correlation (DVC) ,intervertebral disc (IVD) ,0204 Condensed Matter Physics ,0601 Biochemistry And Cell Biology ,micro-CT ,MicroCT ,0912 Materials Engineering ,Artery - Abstract
Many biological tissues have a complex hierarchical structure allowing them to function under demanding physiological loading conditions. Structural changes caused by ageing or disease can lead to loss of mechanical function. Therefore, it is necessary to characterise tissue structure to understand normal tissue function and the progression of disease. Ideally intact native tissues should be imaged in 3D and under physiological loading conditions. The current published in situ imaging methodologies demonstrate a compromise between imaging limitations and maintaining the samples native mechanical function. This review gives an overview of in situ imaging techniques used to visualise microstructural deformation of soft tissue, including three case studies of different tissues (tendon, intervertebral disc and artery). Some of the imaging techniques restricted analysis to observational mechanics or discrete strain measurement from invasive markers. Full-field local surface strain measurement has been achieved using digital image correlation. Volumetric strain fields have successfully been quantified from in situ X-ray microtomography (micro-CT) studies of bone using digital volume correlation but not in soft tissue due to low X-ray transmission contrast. With the latest developments in micro-CT showing in-line phase contrast capability to resolve native soft tissue microstructure, there is potential for future soft tissue mechanics research where 3D local strain can be quantified. These methods will provide information on the local 3D micromechanical environment experienced by cells in healthy, aged and diseased tissues. It is hoped that future applications of in situ imaging techniques will impact positively on the design and testing of potential tissue replacements or regenerative therapies.
- Published
- 2018
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8. The influence of nanoparticles on dendritic grain growth in Mg alloys
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Guo, E, Shuai, S, Kazantsev, D, Karagadde, S, Phillion, AB, Jing, T, Li, W, and Lee, PD
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Technology ,Iterative image reconstruction ,Science & Technology ,IN-SITU ,Materials Science ,AL ALLOYS ,Dendritic solidification ,ZN ALLOYS ,Materials Science, Multidisciplinary ,MECHANICAL-PROPERTIES ,METAL-MATRIX COMPOSITES ,RAY TOMOGRAPHIC QUANTIFICATION ,MAGNESIUM ALLOYS ,HETEROGENEOUS NUCLEATION ,Nanoparticles ,Metallurgy & Metallurgical Engineering ,0912 Materials Engineering ,Materials ,Tomography ,ORIENTATION SELECTION ,ALPHA-MG ,0913 Mechanical Engineering ,Metal matrix nanocomposites - Abstract
Melt processing offers a cost effective method for producing metal matrix nanocomposite (MMNC) components; however, the influence of nanoparticles on the evolving microstructure during solidification is still not well understood. In this study, the effect of SiC nanoparticles on alpha-Mg dendrite evolution in a Mg-25Zn-7Al (wt.%) alloy was investigated through 4D (three dimensions plus time) synchrotron tomographic quantification of solidification experiments conducted at different cooling rates with and without nanoparticles. Key features of the solidifying primary alpha-Mg dendritic grains were quantified, including grain morphology, size distribution, and dendrite tip velocity. To obtain the high-contrast tomography dataset necessary for structure quantification, a new image reconstruction and processing methodology was implemented. The results reveal that the addition of nanoparticles increases grain nucleation whilst restricting dendritic growth and altering the dendritic grain growth morphology. Using LGK model calculations, it is shown that these changes in solidification microstructure occur as a result of nanoparticle-induced restriction in Zn's effective diffusivity ahead of the dendrite tips, reducing tip velocity. The results both suggest the key phenomena required to be simulated when numerically modelling solidifying Mg-based MMNC and provide the data required to validate those models. (C) 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
- Published
- 2018
9. Effects of strain rate on hot tear formation in Al-Si-Cu alloys
- Author
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Bhagavath, S, primary, Cai, B, additional, Atwood, R, additional, Lee, PD, additional, and Karagadde, S, additional
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- 2019
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10. Atomic Layer Deposition of a Silver Nanolayer on Advanced Titanium Orthopedic Implants Inhibits Bacterial Colonization and Supports Vascularized de Novo Bone Ingrowth
- Author
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Devlin-Mullin, A, Todd, NM, Golrokhi, Z, Geng, H, Konerding, MA, Ternan, NG, Hunt, JA, Potter, RJ, Sutcliffe, C, Jones, E, Lee, PD, and Mitchell, CA
- Subjects
angiogenesis ,atomic layer deposition ,Staphylococcus epidermidis ,silver ,titanium ,methicillin-resistant Staphylococcus aureus ,bone - Abstract
Joint replacement surgery is associated with significant morbidity and mortality following infection with either methicillin-resistant Staphylococcus aureus (MRSA) or Staphylococcus epidermidis. These organisms have strong biofilm-forming capability in deep wounds and on prosthetic surfaces, with 10(3) -10(4) microbes resulting in clinically significant infections. To inhibit biofilm formation, we developed 3D titanium structures using selective laser melting and then coated them with a silver nanolayer using atomic layer deposition. On bare titanium scaffolds, S. epidermidis growth was slow but on silver-coated implants there were significant further reductions in both bacterial recovery (p < 0.0001) and biofilm formation (p < 0.001). MRSA growth was similarly slow on bare titanium scaffolds and not further affected by silver coating. Ultrastructural examination and viability assays using either human bone or endothelial cells, demonstrated strong adherence and growth on titanium-only or silver-coated implants. Histological, X-ray computed microtomographic, and ultrastructural analyses revealed that silver-coated titanium scaffolds implanted into 2.5 mm defects in rat tibia promoted robust vascularization and conspicuous bone ingrowth. We conclude that nanolayer silver of titanium implants significantly reduces pathogenic biofilm formation in vitro, facilitates vascularization and osseointegration in vivo making this a promising technique for clinical orthopedic applications.
- Published
- 2017
11. Synchrotron tomographic quantification of strain and fracture during simulated thermal maturation of an organic-rich shale, UK Kimmeridge Clay
- Author
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Pilz, FF, Dowey, PJ, Fauchille, A-L, Courtois, L, Bay, B, Ma, L, Taylor, KG, Mecklenburgh, J, and Lee, PD
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Geochemistry & Geophysics ,X-RAY TOMOGRAPHY ,Science & Technology ,maturation ,PYROLYSIS ,DORSET ,POROSITY ,MICROSCOPY ,DIGITAL VOLUME CORRELATION ,PARAMETERS ,shale ,strain ,NORTH-SEA ,fracture ,DEFORMATION ,Physical Sciences ,PRESERVATION ,synchrotron tomography - Abstract
Analyzing the development of fracture networks in shale is important to understand both hydrocarbon migration pathways within and from source rocks and the effectiveness of hydraulic stimulation upon shale reservoirs. Here we use time‐resolved synchrotron X‐ray tomography to quantify in four dimensions (3‐D plus time) the development of fractures during the accelerated maturation of an organic‐rich mudstone (the UK Kimmeridge Clay), with the aim of determining the nature and timing of crack initiation. Electron microscopy (EM, both scanning backscattered and energy dispersive) was used to correlatively characterize the microstructure of the sample preheating and postheating. The tomographic data were analyzed by using digital volume correlation (DVC) to measure the three‐dimensional displacements between subsequent time/heating steps allowing the strain fields surrounding each crack to be calculated, enabling crack opening modes to be determined. Quantification of the strain eigenvectors just before crack propagation suggests that the main mode driving crack initiation is the opening displacement perpendicular to the bedding, mode I. Further, detailed investigation of the DVC measured strain evolution revealed the complex interaction of the laminar clay matrix and the maximum principal strain on incipient crack nucleation. Full field DVC also allowed accurate calculation of the coefficients of thermal expansion (8 × 10−5/°C perpendicular and 6.2 × 10−5/°C parallel to the bedding plane). These results demonstrate how correlative imaging (using synchrotron tomography, DVC, and EM) can be used to elucidate the influence of shale microstructure on its anisotropic mechanical behavior.
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- 2017
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12. Visualising the 3D microstructure of stained and native intervertebral discs using X-ray microtomography
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Disney, CM, Madi, K, Bodey, AJ, Lee, PD, Hoyland, JA, and Sherratt, MJ
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Science & Technology ,ResearchInstitutes_Networks_Beacons/MICRA ,lcsh:R ,lcsh:Medicine ,DEGENERATION ,ANULUS FIBROSUS ,COLLAGEN ,PREVALENCE ,Multidisciplinary Sciences ,ANNULUS FIBROSUS ,Manchester Institute for Collaborative Research on Ageing ,MICROCT ,Science & Technology - Other Topics ,ELECTRON TOMOGRAMS ,lcsh:Q ,CONTRAST AGENTS ,lcsh:Science ,HIGH-RESOLUTION ,LOW-BACK-PAIN - Abstract
Intervertebral disc degeneration (IVDD) is linked to low back pain. Microstructural changes during degeneration have previously been imaged using 2D sectioning techniques and 3D methods which are limited to small specimens and prone to inducing artefacts from sample preparation. This study explores micro computed X-ray tomography (microCT) methods with the aim of resolving IVD 3D microstructure whilst minimising sample preparation artefacts. Low X-ray absorption contrast in non-mineralised tissue can be enhanced using staining and phase contrast techniques. A step-wise approach, including comparing three stains, was used to develop microCT for bovine tail IVD using microfocus tube (‘laboratory’) and synchrotron sources. Staining successfully contrasted collagenous structures; however not all regions were stained and the procedure induced macroscopic structural changes. Phase contrast microCT of chemically fixed yet unstained samples resolved the nucleus pulposus, annulus fibrosus and constituent lamellae, and finer structures including collagen bundles and cross-bridges. Using the same imaging methods native tissue scans were of slightly lower contrast but free from sample processing artefacts. In the future these methods may be used to characterise structural remodelling in soft (non-calcified) tissues and to conduct in situ studies of native loaded tissues and constructs to characterise their 3D mechanical properties.
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- 2017
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13. The dynamic nature of crystal growth in pores
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Godinho, JR, Gerke, KM, Stack, AG, and Lee, PD
- Abstract
The kinetics of crystal growth in porous media controls a variety of natural processes such as ore genesis and crystallization induced fracturing that can trigger earthquakes and weathering, as well as, sequestration of CO2 and toxic metals into geological formations. Progress on understanding those processes has been limited by experimental difficulties of dynamically studying the reactive surface area and permeability during pore occlusion. Here, we show that these variables cause a time-dependency of barite growth rates in microporous silica. The rate is approximately constant and similar to that observed on free surfaces if fast flow velocities predominate and if the time-dependent reactive surface area is accounted for. As the narrower flow paths clog, local flow velocities decrease, which causes the progressive slowing of growth rates. We conclude that mineral growth in a microporous media can be estimated based on free surface studies when a) the growth rate is normalized to the time-dependent surface area of the growing crystals, and b) the local flow velocities are above the limit at which growth is transport-limited. Accounting for the dynamic relation between microstructure, flow velocity and growth rate is shown to be crucial towards understanding and predicting precipitation in porous rocks.
- Published
- 2016
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14. Synchrotron X-ray Tomographic Quantification of Deformation Induced Strain Localisation in Semi-solid Al-15wt.% Cu
- Author
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Cai, B, Karagadde, S, Marrow, TJ, Connolley, T, Lee, PD, and IOP
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Materials science ,Alloy ,X-ray ,engineering.material ,Synchrotron ,law.invention ,Crystallography ,Shear (geology) ,Beamline ,law ,Indentation ,engineering ,Tomography ,Composite material ,Semi solid - Abstract
Uniaxial compression and indentation of a semi-solid Al-15wt.%Cu alloy was investigated by high speed synchrotron X-ray microtomography, quantifying the microstructural response of a solidifying alloy to applied strain. Tomograms were continuously acquired whilst performing deformation using a precision thermal-mechanical rig on a synchrotron beamline. The results illustrate how defects and shear bands can form in response to different loading conditions. Using digital volume correlation, the global and localised strains were measured, providing quantitative datasets for granular flow models of semi-solid deformation.
- Published
- 2016
15. Investigating the effect of thermal gradients on stress in solid oxide fuel cell anodes using combined synchrotron radiation and thermal imaging
- Author
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Robinson, JB, Brown, LD, Jervis, R, Taiwo, OO, Heenan, TMM, Millichamp, J, Mason, TJ, Neville, TP, Clague, R, Eastwood, DS, Reinhard, C, Lee, PD, Brett, DJL, and Shearing, PR
- Subjects
Technology ,STEADY-STATE ,Thermal imaging ,Energy & Fuels ,Stress analysis ,Materials Science ,Infrared imaging ,Energy Engineering and Power Technology ,Materials Science, Multidisciplinary ,RED-OX CYCLE ,09 Engineering ,Solid oxide fuel cell ,SOFC ANODE ,Electrochemistry ,FAILURE ,Physical and Theoretical Chemistry ,Electrical and Electronic Engineering ,TEMPERATURE ,Science & Technology ,Energy ,Synchrotron radiation ,Chemistry, Physical ,Renewable Energy, Sustainability and the Environment ,RESIDUAL-STRESSES ,MECHANICAL-PROPERTIES ,X-ray diffraction ,Chemistry ,PROBABILITY ,Physical Sciences ,03 Chemical Sciences ,FINITE-ELEMENT ,BEHAVIOR - Abstract
Thermal gradients can arise within solid oxide fuel cells (SOFCs) due to start-up and shut-down, non-uniform gas distribution, fast cycling and operation under internal reforming conditions. Here, the effects of operationally relevant thermal gradients on Ni/YSZ SOFC anode half cells are investigated using combined synchrotron X-ray diffraction and thermal imaging. The combination of these techniques has identified significant deviation from linear thermal expansion behaviour in a sample exposed to a one dimensional thermal gradient. Stress gradients are identified along isothermal regions due to the presence of a proximate thermal gradient, with tensile stress deviations of up to 75 MPa being observed across the sample at a constant temperature. Significant strain is also observed due to the presence of thermal gradients when compared to work carried out at isothermal conditions.
- Published
- 2015
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16. 4D-CT reconstruction with unified spatial-temporal patch-based regularization
- Author
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Kazantsev, D, Thompson, WM, Lionheart, WRB, Van Eyndhoven, G, Kaestner, AP, Dobson, KJ, Withers, PJ, and Lee, PD
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Science & Technology ,Physics ,ALGORITHMS ,Mathematics, Applied ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Time lapse tomography ,GPU acceleration ,spatial-temporal penalties ,NOISE ,Physics, Mathematical ,ITERATIVE RECONSTRUCTION ,PET ,neutron tomography ,SPECT ,Physical Sciences ,non local means ,TA170 ,COMPUTED-TOMOGRAPHY ,NONLOCAL REGULARIZATION ,INVERSE PROBLEMS ,Mathematics ,CT - Abstract
In this paper, we consider a limited data reconstruction problem for temporarily evolving computed tomography (CT), where some regions are static during the whole scan and some are dynamic (intensely or slowly changing). When motion occurs during a tomographic experiment one would like to minimize the number of projections used and reconstruct the image iteratively. To ensure stability of the iterative method spatial and temporal constraints are highly desirable. Here, we present a novel spatial-temporal regularization approach where all time frames are reconstructed collectively as a unified function of space and time. Our method has two main differences from the state-of-the-art spatial-temporal regularization methods. Firstly, all available temporal information is used to improve the spatial resolution of each time frame. Secondly, our method does not treat spatial and temporal penalty terms separately but rather unifies them in one regularization term. Additionally we optimize the temporal smoothing part of the method by considering the non-local patches which are most likely to belong to one intensity class. This modification significantly improves the signal-to-noise ratio of the reconstructed images and reduces computational time. The proposed approach is used in combination with golden ratio sampling of the projection data which allows one to find a better trade-off between temporal and spatial resolution scenarios.
- Published
- 2015
17. The dynamic nature of crystal growth in pores
- Author
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Godinho, JRA, Gerke, KM, Stack, AG, Lee, PD, Godinho, JRA, Gerke, KM, Stack, AG, and Lee, PD
- Abstract
The kinetics of crystal growth in porous media controls a variety of natural processes such as ore genesis and crystallization induced fracturing that can trigger earthquakes and weathering, as well as, sequestration of CO2 and toxic metals into geological formations. Progress on understanding those processes has been limited by experimental difficulties of dynamically studying the reactive surface area and permeability during pore occlusion. Here, we show that these variables cause a time-dependency of barite growth rates in microporous silica. The rate is approximately constant and similar to that observed on free surfaces if fast flow velocities predominate and if the time-dependent reactive surface area is accounted for. As the narrower flow paths clog, local flow velocities decrease, which causes the progressive slowing of growth rates. We conclude that mineral growth in a microporous media can be estimated based on free surface studies when a) the growth rate is normalized to the time-dependent surface area of the growing crystals, and b) the local flow velocities are above the limit at which growth is transport-limited. Accounting for the dynamic relation between microstructure, flow velocity and growth rate is shown to be crucial towards understanding and predicting precipitation in porous rocks.
- Published
- 2016
18. Revealing the micromechanisms behind semi-solid metal deformation with time-resolved X-ray tomography
- Author
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Kareh, KM, Lee, PD, Atwood, RC, Connolley, T, Gourlay, CM, and Engineering & Physical Science Research Council (EPSRC)
- Subjects
GRANULAR MODEL ,Science & Technology ,MUSHY ZONE ,ALLOYS ,IN-SITU ,SUSPENSIONS ,MECHANICAL-BEHAVIOR ,RHEOLOGICAL BEHAVIOR ,DILATANCY ,Article ,Multidisciplinary Sciences ,SOLIDIFICATION ,COALESCENCE ,Science & Technology - Other Topics - Abstract
The behaviour of granular solid–liquid mixtures is key when deforming a wide range of materials from cornstarch slurries to soils, rock and magma flows. Here we demonstrate that treating semi-solid alloys as a granular fluid is critical to understanding flow behaviour and defect formation during casting. Using synchrotron X-ray tomography, we directly measure the discrete grain response during uniaxial compression. We show that the stress–strain response at 64–93% solid is due to the shear-induced dilation of discrete rearranging grains. This leads to the counter-intuitive result that, in unfed samples, compression can open internal pores and draw the free surface into the liquid, resulting in cracking. A soil mechanics approach shows that, irrespective of initial solid fraction, the solid packing density moves towards a constant value during deformation, consistent with the existence of a critical state in mushy alloys analogous to soils., Soil-like granular flow has previously been shown when deforming semi-solid metals. Here, the authors measure bulk and grain-level deformation in semi-solid alloys in three dimensions using X-ray tomography, exploring shear-induced dilation between 64–93% solid and finding hints of a critical state.
- Published
- 2014
19. Technical note monitoring the magmas fuelling volcanic eruptions in near-real-time using x-ray micro-computed tomography
- Author
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Pankhurst, MJ, Morgan, DJ, Dobson, KJ, Lee, PD, Courtois, L, Loughlin, SC, and Thordarson, TH
- Abstract
A novel application of X-ray micro-computed tomography is described, which can be used to rapidly characterize chemical populations of natural olivine crystals in erupted basalts.This technique can be deployed during volcanic crises to directly track changes in magma components of an erupting system in near-real-time. Such changes are fundamental in controlling eruption style, duration and intensity.We demonstrate a method that can generate data from hundreds of crystalswithin hours, which allows time-series petrological data to be recorded and interpreted alongside various complementarymonitoring techniques (e.g.seismicity, ground deformation). Our direct-detection will allow greater understanding of the dynamics of sub-volcanic magma plumbing systems, and can provide important insights into how an eruption may evolve.The same technique can also be used to generate rich baseline datasets from eruption sequences in the geological record in amore efficient manner than conventional methods allow.
- Published
- 2014
20. Failure modes in high strength and stiffness to weight scaffolds produced by Selective Laser Melting
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Sercombe, TB, Xu, X, Challis, VJ, Green, R, Yue, S, Zhang, Z, Lee, PD, Sercombe, TB, Xu, X, Challis, VJ, Green, R, Yue, S, Zhang, Z, and Lee, PD
- Abstract
The production of porous scaffold structures using additive manufacturing is becoming widespread, however a detailed understanding of the scaffold failure mechanisms is lacking. In this research, Selective Laser Melting (SLM) is used to produce Ti-6Al-4V scaffold structures consisting of a regular array of unit cells previously designed using topology optimisation. Interrupted compression testing and subsequent X-Ray Micro Tomography (XMT) characterisation is used to study the deformation and failure of the scaffolds for a range of solid fractions. Further, the XMT data of the unloaded scaffolds is used to generate meshes for finite element analysis which allowed direct comparison of desired and as built behaviour. Likely failure sites predicted from the finite element analysis compare favourably with the experimentally observed ones. Failure is initiated in areas that exhibit the greatest tensile stress, while the onset of the commonly observed layered failure occurs afterwards. The XMT of the unloaded scaffolds also highlights the inaccuracies in the SLM build process, which contributes to stress concentrations in the horizontal arms within the scaffolds. The results indicate that although the strength of the topology optimised structures is very high, further refinement in both the unit cell design and build quality would further increase the strength.
- Published
- 2015
21. Heterogeneous nucleation of solid Al from the melt by TiB2 and Al3Ti: An ab initio molecular dynamics study
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Wang, J, Horsfield, A, Schwingenschloegl, U, and Lee, PD
- Published
- 2010
22. Simulation of the Columnar-to-Equiaxed Transition in Alloy Solidification - The Effect of Nucleation Undercooling, Density of Nuclei in Bulk Liquid and Alloy Solidification Range on the Transition
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Dai, Hj, Hongbiao Dong, Atkinson, Hv, and Lee, Pd
- Published
- 2008
- Full Text
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23. Insulin-like growth factor-binding protein-3 is partially responsible for high-serum-induced apoptosis in PC-3 prostate cancer cells
- Author
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Rajah, R, primary, Khare, A, additional, Lee, PD, additional, and Cohen, P, additional
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- 1999
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24. Effect of the somatostatin analog, octreotide, and of other hormones on the release of the acid-labile subunit of the 150 kDa complex by rat hepatocyte in primary culture
- Author
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Barreca, AM, primary, Voci, A, additional, Lee, PD, additional, Arvigo, M, additional, Ghigliotti, V, additional, Fugassa, E, additional, Giordano, G, additional, and Minuto, F, additional
- Published
- 1997
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25. Quantitative analysis of multidrug resistance gene expression in human osteosarcomas
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Lee, PD, primary, Noble-Topham, SE, additional, Bell, RS, additional, and Andrulis, IL, additional
- Published
- 1996
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26. Bioactive glass scaffolds for bone regeneration and their hierarchical characterisation.
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Jones JR, Lin S, Yue S, Lee PD, Hanna JV, Smith ME, Newport RJ, Jones, J R, Lin, S, Yue, S, Lee, P D, Hanna, J V, Smith, M E, and Newport, R J
- Abstract
Scaffolds are needed that can act as temporary templates for bone regeneration and actively stimulate vascularized bone growth so that bone grafting is no longer necessary. To achieve this, the scaffold must have a suitable interconnected pore network and be made of an osteogenic material. Bioactive glass is an ideal material because it rapidly bonds to bone and degrades over time, releasing soluble silica and calcium ions that are thought to stimulate osteoprogenitor cells. Melt-derived bioactive glasses, such as the original Bioglass composition, are available commercially, but porous scaffolds have been difficult to produce because Bioglass and similar compositions crystallize on sintering. Sol-gel foam scaffolds have been developed that avoid this problem. They have a hierarchical pore structure comprising interconnected macropores, with interconnect diameters in excess of the 100 microm that is thought to be needed for vascularized bone ingrowth, and an inherent nanoporosity of interconnected mesopores (2-50 nm) which is beneficial for the attachment of osteoprogenitor cells. They also have a compressive strength in the range of cancellous bone. This paper describes the optimized sol-gel foaming process and illustrates the importance of optimizing the hierarchical structure from the atomic through nano, to the macro scale with respect to biological response. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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27. Metformin extended release treatment of adolescent obesity: a 48-week randomized, double-blind, placebo-controlled trial with 48-week follow-up.
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Wilson DM, Abrams SH, Aye T, Lee PD, Lenders C, Lustig RH, Osganian SV, Feldman HA, and Glaser Pediatric Research Network Obesity Study Group
- Published
- 2010
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28. The chondro-osseous continuum: is it possible to unlock the potential assigned within?
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Javaheri, B, Razi, H, Piles, M, De Souza, R, Chang, Y M, Maric-Mur, I, Hopkinson, M, Lee, PD, and Pitsillides, A A
29. X-ray Tomographic Imaging of Tensile Deformation Modes of Electrospun Biodegradable Polyester Fibers
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Maksimcuka, J, Obata, A, Sampson, WW, Blanc, R, Gao, C, Withers, PJ, Tsigkou, O, Kasuga, T, Lee, PD, and Poologasundarampillai, G
- Subjects
RELEASE ,Technology ,SOLVENT ,Science & Technology ,synchrotron X-ray ,Materials Science ,DIAMETER ,in situ ,fiber necking ,Materials Science, Multidisciplinary ,tissue regeneration ,MECHANICAL-PROPERTIES ,MATS ,scaffolds ,DRUG-DELIVERY ,ORIENTATION ,BEHAVIOR ,SYSTEM ,NANOFIBERS - Abstract
Electrospinning allows the production of fibrous networks for tissue engineering, drug delivery, and wound healing in health care. It enables the production of constructs with large surface area and a fibrous morphology that closely resembles the extracellular matrix of many tissues. A fibrous structure not only promotes cell attachment and tissue formation but could also lead to very interesting mechanical properties. Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)) is a biodegradable polyester that exhibits a large (>400%) elongation before failure. In this study, synchrotron X-ray phase contrast imaging was performed during tensile deformation to failure on a non-woven fiber mat of P(3HB-co-4HB) fibers. Significant reorientation of the fibers in the straining direction was observed, followed by localized necking and eventual failure. From an original average fiber diameter of 4.3 µm, a bimodal distribution of fiber diameter (modal diameters of 1.9 and 3.7 µm) formed after tensile deformation. Extensive localized necking (thinning) of fibers between (thicker) fiber–fiber contacts was found to be the cause for non-uniform thinning of the fibers, a phenomenon that is expected but has not been observed in 3D previously. The data presented here have implications not only in tissue regeneration but for fibrous materials in general.
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30. Joint image reconstruction method with correlative multi-channel prior for x-ray spectral computed tomography
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Kazantsev, D, Jorgensen, JS, Andersen, MS, Lionheart, WRB, Lee, PD, and Withers, PJ
- Subjects
multi-spectral ,materials science ,Mathematics, Applied ,VARIATION MINIMIZATION ,TV ,0101 Pure Mathematics ,Theoretical Computer Science ,structural regularization ,0102 Applied Mathematics ,GENERAL FRAMEWORK ,ALGORITHM ,OPTIMIZATION ,CT DATA ,Mathematical Physics ,Science & Technology ,0105 Mathematical Physics ,inverse problems ,Physics ,Applied Mathematics ,x-ray imaging ,image reconstruction ,Computer Science Applications ,Physics, Mathematical ,total variation ,Physical Sciences ,Signal Processing ,TOTAL NUCLEAR VARIATION ,Mathematics - Abstract
Rapid developments in photon-counting and energy-discriminating detectors have the potential to provide an additional spectral dimension to conventional x-ray grayscale imaging. Reconstructed spectroscopic tomographic data can be used to distinguish individual materials by characteristic absorption peaks. The acquired energy-binned data, however, suffer from low signal-to-noise ratio, acquisition artifacts, and frequently angular undersampled conditions. New regularized iterative reconstruction methods have the potential to produce higher quality images and since energy channels are mutually correlated it can be advantageous to exploit this additional knowledge. In this paper, we propose a novel method which jointly reconstructs all energy channels while imposing a strong structural correlation. The core of the proposed algorithm is to employ a variational framework of parallel level sets to encourage joint smoothing directions. In particular, the method selects reference channels from which to propagate structure in an adaptive and stochastic way while preferring channels with a high data signal-to-noise ratio. The method is compared with current state-of-the-art multi-channel reconstruction techniques including channel-wise total variation and correlative total nuclear variation regularization. Realistic simulation experiments demonstrate the performance improvements achievable by using correlative regularization methods.
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31. Imaging Three-Dimensional Airway Morphology in Congenital Pulmonary Airway Malformation Using Hierarchical Phase-Contrast Tomography.
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Verleden SE, Urban T, Brunet J, Wen W, Peeters DJE, Lapperre TS, Walsh C, Tafforeau P, Dejea H, Jonigk D, Ackermann M, Van Hoorenbeeck K, Lee PD, Jacob J, and Hendriks JMH
- Published
- 2024
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32. Calcium sources can increase mechanical properties of 3D printed bioactive hybrid bone scaffolds.
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Heyraud A, Tallia F, Chen S, Liu J, Chen J, Turner J, Jell G, Lee PD, and Jones JR
- Abstract
Inorganic/organic hybrid biomaterials have been developed to obtain synergy of the inorganic and organic co-networks for implant and 3D printed scaffold applications, providing combinations of bioactivity, toughness and controlled biodegradation. SiO
2 -CaOCME /PTHF/PCL-diCOOH sol-gel hybrids previously showed potential for osteogenesis due to the addition of calcium to the silicate network of the hybrid, using calcium methoxyethoxide (CME) as the calcium source. Here, we investigate other calcium sources to improve mechanical properties and printability of the hybrid inks. The aim was to produce porous scaffolds with mechanical properties similar to trabecular bone. The original Ca-free hybrid composition SiO2 /PTHF/PCL-diCOOH was highly elastic and the addition of Ca increased strength while introducing bioactivity, with hydroxyapatite formation in simulated body fluid (SBF), and no negative effects on the metabolic activity of human bone marrow stromal cells (hBMSCs). However, when the hybrid was 3D printed by Direct Ink Writing, the mechanical properties were insufficient for a load sharing bone scaffold. Alternative calcium sources were investigated here, using concentrated CME (cCME), calcium hydroxide (CH), calcium ethoxide (CE), and calcium ethoxyethoxide (CEE). CEE improved the overall printability and final structure of the hybrid scaffold obtained and apatite formed on its surface in SBF. This hybrid reached the highest stress at failure (0.55 ± 0.08 MPa) and toughness modulus (0.13 ± 0.03 MPa), with a corresponding strain of >50%. With this calcium source and the optimal 70 : 30 TEOS : CEE molar ratio, scaffold properties were optimised by increasing the strut size whilst maintaining the interconnected channel size >400 μm and increasing the inorganic : organic ratio. Using a TEOS : PCL-diCOOH ratio of 85 : 15 wt%, giving a final inorganic content of 35.7 wt%, showed the optimal mechanical properties with a stress at failure of 3.1 ± 0.54 MPa for strain of 26%, and a toughness modulus of 0.58 ± 0.06 MPa, whilst keeping an open porosity >38%. Compressive strength was within the lower range of trabecular bone (2-12 MPa), and there was no observed cytotoxic effect on hBMSCs, indicating potential for use of this hybrid for bone regeneration., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)- Published
- 2024
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33. Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney.
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Yagis E, Aslani S, Jain Y, Zhou Y, Rahmani S, Brunet J, Bellier A, Werlein C, Ackermann M, Jonigk D, Tafforeau P, Lee PD, and Walsh CL
- Subjects
- Humans, Image Processing, Computer-Assisted methods, Blood Vessels diagnostic imaging, Deep Learning, Kidney diagnostic imaging, Kidney blood supply, Imaging, Three-Dimensional methods, Tomography, X-Ray Computed methods
- Abstract
Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation using a new imaging modality, Hierarchical Phase-Contrast Tomography (HiP-CT). We begin with an extensive review of current machine-learning approaches for vascular segmentation across various organs. Our work introduces a meticulously curated training dataset, verified by double annotators, consisting of vascular data from three kidneys imaged using HiP-CT as part of the Human Organ Atlas Project. HiP-CT pioneered at the European Synchrotron Radiation Facility in 2020, revolutionizes 3D organ imaging by offering a resolution of around 20 μm/voxel and enabling highly detailed localised zooms up to 1-2 μm/voxel without physical sectioning. We leverage the nnU-Net framework to evaluate model performance on this high-resolution dataset, using both known and novel samples, and implementing metrics tailored for vascular structures. Our comprehensive review and empirical analysis on HiP-CT data sets a new standard for evaluating machine learning models in high-resolution organ imaging. Our three experiments yielded Dice similarity coefficient (DSC) scores of 0.9523, 0.9410, and 0.8585, respectively. Nevertheless, DSC primarily assesses voxel-to-voxel concordance, overlooking several crucial characteristics of the vessels and should not be the sole metric for deciding the performance of vascular segmentation. Our results show that while segmentations yielded reasonably high scores-such as centerline DSC ranging from 0.82 to 0.88, certain errors persisted. Specifically, large vessels that collapsed due to the lack of hydrostatic pressure (HiP-CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors, particularly in significant vessels, obstruct the understanding of the structures by interrupting vascular tree connectivity. Our study establishes the benchmark across various evaluation metrics, for vascular segmentation of HiP-CT imaging data, an imaging technology that has the potential to substantively shift our understanding of human vascular networks., (© 2024. The Author(s).)
- Published
- 2024
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34. Micro to macro scale anatomical analysis of the human hippocampal arteries with synchrotron hierarchical phase-contrast tomography.
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Bellier A, Tafforeau P, Bouziane A, Angelloz-Nicoud T, Lee PD, and Walsh C
- Subjects
- Humans, Male, Aged, Middle Aged, Female, Tomography, X-Ray Computed, Cerebral Arteries diagnostic imaging, Cerebral Arteries anatomy & histology, Hippocampus blood supply, Hippocampus diagnostic imaging, Hippocampus anatomy & histology, Synchrotrons
- Abstract
Purpose: To date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature., Methods: Two preserved human brains from, a 69-year-old female and a 63-year-old male body donors were imaged using hierarchical phase-contrast tomography (HiP-CT) with synchrotron radiation at multiple voxel resolutions from 25.08 μm down to 2.45 μm. Subsequent manual and semi-automatic artery segmentation were performed followed by morphometric analyses. These data were compared to published data from alternative methodologies., Results: HiP-CT made it possible to segment in context the arterial architecture of the human hippocampus. Our analysis identified anterior, medial and posterior hippocampal arteries arising from the P2 segment of the posterior cerebral artery on the image slices. We mapped arterial branches with external diameters greater than 50 μm in the hippocampal region. We visualised vascular asymmetry and quantified arterial structures with diameters as small as 7 μm., Conclusions: Through the application of HiP-CT, we have provided the first imaging visualisation and quantification of the arterial system of the human hippocampus at high resolution in the context of whole brain imaging. Our results bridge the gap between anatomical and histological scales., (© 2024. The Author(s).)
- Published
- 2024
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- View/download PDF
35. Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys.
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Jain Y, Walsh CL, Yagis E, Aslani S, Nandanwar S, Zhou Y, Ha J, Gustilo KS, Brunet J, Rahmani S, Tafforeau P, Bellier A, Weber GM, Lee PD, and Börner K
- Abstract
Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global machine learning competition, engaging 1,401 participants, to help develop new deep learning methods for 3D blood vessel segmentation. This paper presents a detailed analysis of the top-performing solutions using manually curated 3D Hierarchical Phase-Contrast Tomography datasets of the human kidney, focusing on the segmentation accuracy and morphological analysis, thereby establishing a benchmark for future studies in blood vessel segmentation within phase-contrast tomography imaging., Competing Interests: Competing Interests GMW is a paid consultant for the NIH-funded Human BioMolecular Atlas Program (HuBMAP). Other authors declare no competing interests.
- Published
- 2024
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- View/download PDF
36. Direct observation of degassing during decompression of basaltic magma.
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Bonechi B, Polacci M, Arzilli F, La Spina G, Hazemann JL, Brooker RA, Atwood R, Marussi S, Lee PD, Wogelius RA, Fellowes J, and Burton MR
- Abstract
Transitions in eruptive style during volcanic eruptions strongly depend on how easily gas and magma decouple during ascent. Stronger gas-melt coupling favors highly explosive eruptions, whereas weaker coupling promotes lava fountaining and lava flows. The mechanisms producing these transitions are still poorly understood because of a lack of direct observations of bubble dynamics under natural magmatic conditions. Here, we combine x-ray radiography with a novel high-pressure/high-temperature apparatus to observe and quantify in real-time bubble growth and coalescence in basaltic magmas from 100 megapascals to surface. For low-viscosity magmas, bubbles coalesce and recover a spherical shape within 3 seconds, implying that, for lava fountaining activity, gas and melt remain coupled during the ascent up to the last hundred meters of the conduit. For higher-viscosity magmas, recovery times become longer, promoting connected bubble pathways. This apparatus opens frontiers in unraveling magmatic/volcanic processes, leading to improved hazard assessment and risk mitigation.
- Published
- 2024
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- View/download PDF
37. Deep Learning for 3D Vascular Segmentation in Phase Contrast Tomography.
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Yagis E, Aslani S, Jain Y, Zhou Y, Rahmani S, Brunet J, Bellier A, Werlein C, Ackermann M, Jonigk D, Tafforeau P, Lee PD, and Walsh C
- Abstract
Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation using a new imaging modality, Hierarchical Phase-Contrast Tomography (HiP-CT). We begin with an extensive review of current machine learning approaches for vascular segmentation across various organs. Our work introduces a meticulously curated training dataset, verified by double annotators, consisting of vascular data from three kidneys imaged using Hierarchical Phase-Contrast Tomography (HiP-CT) as part of the Human Organ Atlas Project. HiP-CT, pioneered at the European Synchrotron Radiation Facility in 2020, revolutionizes 3D organ imaging by offering resolution around 20 μm /voxel, and enabling highly detailed localized zooms up to 1 μm /voxel without physical sectioning. We leverage the nnU-Net framework to evaluate model performance on this high-resolution dataset, using both known and novel samples, and implementing metrics tailored for vascular structures. Our comprehensive review and empirical analysis on HiP-CT data sets a new standard for evaluating machine learning models in high-resolution organ imaging. Our three experiments yielded Dice scores of 0.9523 and 0.9410, and 0.8585, respectively. Nevertheless, DSC primarily assesses voxel-to-voxel concordance, overlooking several crucial characteristics of the vessels and should not be the sole metric for deciding the performance of vascular segmentation. Our results show that while segmentations yielded reasonably high scores-such as centerline Dice values ranging from 0.82 to 0.88, certain errors persisted. Specifically, large vessels that collapsed due to the lack of hydro-static pressure (HiP-CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors, particularly in significant vessels, obstruct the understanding of the structures by interrupting vascular tree connectivity. Through our review and outputs, we aim to set a benchmark for subsequent model evaluations using various modalities, especially with the HiP-CT imaging database., Competing Interests: Competing interests The authors declare no competing interests.
- Published
- 2024
- Full Text
- View/download PDF
38. Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography.
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Rahmani S, Jafree DJ, Lee PD, Tafforeau P, Brunet J, Nandanwar S, Jacob J, Bellier A, Ackermann M, Jonigk DD, Shipley RJ, Long DA, and Walsh CL
- Abstract
The architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.
- Published
- 2024
- Full Text
- View/download PDF
39. Multidimensional Analysis of the Adult Human Heart in Health and Disease Using Hierarchical Phase-Contrast Tomography.
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Brunet J, Cook AC, Walsh CL, Cranley J, Tafforeau P, Engel K, Arthurs O, Berruyer C, Burke O'Leary E, Bellier A, Torii R, Werlein C, Jonigk DD, Ackermann M, Dollman K, and Lee PD
- Subjects
- Humans, Middle Aged, Male, Female, Aged, 80 and over, Heart Diseases diagnostic imaging, Synchrotrons, Tomography, X-Ray Computed methods, Heart diagnostic imaging
- Abstract
Background Current clinical imaging modalities such as CT and MRI provide resolution adequate to diagnose cardiovascular diseases but cannot depict detailed structural features in the heart across length scales. Hierarchical phase-contrast tomography (HiP-CT) uses fourth-generation synchrotron sources with improved x-ray brilliance and high energies to provide micron-resolution imaging of intact adult organs with unprecedented detail. Purpose To evaluate the capability of HiP-CT to depict the macro- to microanatomy of structurally normal and abnormal adult human hearts ex vivo. Materials and Methods Between February 2021 and September 2023, two adult human donor hearts were obtained, fixed in formalin, and prepared using a mixture of crushed agar in a 70% ethanol solution. One heart was from a 63-year-old White male without known cardiac disease, and the other was from an 87-year-old White female with a history of multiple known cardiovascular pathologies including ischemic heart disease, hypertension, and atrial fibrillation. Nondestructive ex vivo imaging of these hearts without exogenous contrast agent was performed using HiP-CT at the European Synchrotron Radiation Facility. Results HiP-CT demonstrated the capacity for high-spatial-resolution, multiscale cardiac imaging ex vivo, revealing histologic-level detail of the myocardium, valves, coronary arteries, and cardiac conduction system across length scales. Virtual sectioning of the cardiac conduction system provided information on fatty infiltration, vascular supply, and pathways between the cardiac nodes and adjacent structures. HiP-CT achieved resolutions ranging from gross (isotropic voxels of approximately 20 µm) to microscopic (approximately 6.4-µm voxel size) to cellular (approximately 2.3-µm voxel size) in scale. The potential for quantitative assessment of features in health and disease was demonstrated. Conclusion HiP-CT provided high-spatial-resolution, three-dimensional images of structurally normal and diseased ex vivo adult human hearts. Whole-heart image volumes were obtained with isotropic voxels of approximately 20 µm, and local regions of interest were obtained with resolution down to 2.3-6.4 µm without the need for sectioning, destructive techniques, or exogenous contrast agents. Published under a CC BY 4.0 license Supplemental material is available for this article. See also the editorial by Bluemke and Pourmorteza in this issue.
- Published
- 2024
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40. A closer look at high-energy X-ray-induced bubble formation during soft tissue imaging.
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Xian RP, Brunet J, Huang Y, Wagner WL, Lee PD, Tafforeau P, and Walsh CL
- Subjects
- X-Rays, Animals, Gases chemistry, Chromatography, Gas methods, Ethanol chemistry, Synchrotrons
- Abstract
Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image quality and integrity of the samples. By combining in-line phase-contrast imaging with gas chromatography in real time, we were able to track the onset and evolution of high-energy X-ray-induced gas bubbles in ethanol-embedded soft tissue samples for tens of minutes (two to three times the typical scan times). We demonstrate quantitatively that vacuum degassing of the sample during preparation can significantly delay bubble formation, offering up to a twofold improvement in dose tolerance, depending on the tissue type. However, once nucleated, bubble growth is faster in degassed than undegassed samples, indicating their distinct metastable states at bubble onset. Gas chromatography analysis shows increased solvent vaporization concurrent with bubble formation, yet the quantities of dissolved gasses remain unchanged. By coupling features extracted from the radiographs with computational analysis of bubble characteristics, we uncover dose-controlled kinetics and nucleation site-specific growth. These hallmark signatures provide quantitative constraints on the driving mechanisms of bubble formation and growth. Overall, the observations highlight bubble formation as a critical yet often overlooked hurdle in upscaling X-ray imaging for biological tissues and soft materials and we offer an empirical foundation for their understanding and imaging protocol optimization. More importantly, our approaches establish a top-down scheme to decipher the complex, multiscale radiation-matter interactions in these applications., (open access.)
- Published
- 2024
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41. Pore evolution mechanisms during directed energy deposition additive manufacturing.
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Zhang K, Chen Y, Marussi S, Fan X, Fitzpatrick M, Bhagavath S, Majkut M, Lukic B, Jakata K, Rack A, Jones MA, Shinjo J, Panwisawas C, Leung CLA, and Lee PD
- Abstract
Porosity in directed energy deposition (DED) deteriorates mechanical performances of components, limiting safety-critical applications. However, how pores arise and evolve in DED remains unclear. Here, we reveal pore evolution mechanisms during DED using in situ X-ray imaging and multi-physics modelling. We quantify five mechanisms contributing to pore formation, migration, pushing, growth, removal and entrapment: (i) bubbles from gas atomised powder enter the melt pool, and then migrate circularly or laterally; (ii) small bubbles can escape from the pool surface, or coalesce into larger bubbles, or be entrapped by solidification fronts; (iii) larger coalesced bubbles can remain in the pool for long periods, pushed by the solid/liquid interface; (iv) Marangoni surface shear flow overcomes buoyancy, keeping larger bubbles from popping out; and (v) once large bubbles reach critical sizes they escape from the pool surface or are trapped in DED tracks. These mechanisms can guide the development of pore minimisation strategies., (© 2024. The Author(s).)
- Published
- 2024
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- View/download PDF
42. Multidimensional Analysis of the Adult Human Heart in Health and Disease using Hierarchical Phase-Contrast Tomography (HiP-CT).
- Author
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Brunet J, Cook AC, Walsh CL, Cranley J, Tafforeau P, Engel K, Berruyer C, O'Leary EB, Bellier A, Torii R, Werlein C, Jonigk DD, Ackermann M, Dollman K, and Lee PD
- Abstract
Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP-CT), using new (4
th ) generation synchrotron sources, potentially overcomes this limitation, allowing micron resolution imaging of intact adult organs with unprecedented detail. In this proof of principle study (n=2), we show the utility of HiP-CT to image whole adult human hearts ex-vivo: one 'control' without known cardiac disease and one with multiple known cardiopulmonary pathologies. The resulting multiscale imaging was able to demonstrate exemplars of anatomy in each cardiac segment along with novel findings in the cardiac conduction system, from gross (20 um/voxel) to cellular scale (2.2 um/voxel), non-destructively, thereby bridging the gap between macroscopic and microscopic investigations. We propose that the technique represents a significant step in virtual autopsy methods for studying structural heart disease, facilitating research into abnormalities across scales and age-groups. It opens up possibilities for understanding and treating disease; and provides a cardiac 'blueprint' with potential for in-silico simulation, device design, virtual surgical training, and bioengineered heart in the future., Competing Interests: Competing interests The authors declare no competing interests.- Published
- 2023
- Full Text
- View/download PDF
43. 3D printed hybrid scaffolds for bone regeneration using calcium methoxyethoxide as a calcium source.
- Author
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Heyraud A, Tallia F, Sory D, Ting HK, Tchorzewska A, Liu J, Pilsworth HL, Lee PD, Hanna JV, Rankin SM, and Jones JR
- Abstract
Introduction: Hybrids consist of inorganic and organic co-networks that are indistinguishable above the nanoscale, which can lead to unprecedented combinations of properties, such as high toughness and controlled degradation. Methods: We present 3D printed bioactive hybrid scaffolds for bone regeneration, produced by incorporating calcium into our "Bouncy Bioglass", using calcium methoxyethoxide (CME) as the calcium precursor. SiO
2 -CaOCME /PTHF/PCL-diCOOH hybrid "inks" for additive manufacturing (Direct Ink Writing) were optimised for synergy of mechanical properties and open interconnected pore channels. Results and Discussion: Adding calcium improved printability. Changing calcium content (5, 10, 20, 30, and 40 mol.%) of the SiO2 -CaOCME /PTHF/PCL-diCOOH hybrids affected printability and mechanical properties of the lattice-like scaffolds. Hybrids containing 30 mol.% calcium in the inorganic network (70S30CCME -CL) printed with 500 µm channels and 100 µm strut size achieved the highest strength (0.90 ± 0.23 MPa) and modulus of toughness (0.22 ± 0.04 MPa). These values were higher than Ca-free SiO2 /PTHF/PCL-diCOOH hybrids (0.36 ± 0.14 MPa strength and 0.06 ± 0.01 MPa toughness modulus). Over a period of 90 days of immersion in simulated body fluid (SBF), the 70S30CCME -CL hybrids also kept a stable strain to failure (~30 %) and formed hydroxycarbonate apatite within three days. The extracts released by the 70S30CCME -CL hybrids in growth medium did not cause cytotoxic effects on human bone marrow stromal cells over 24 h of culture., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Heyraud, Tallia, Sory, Ting, Tchorzewska, Liu, Pilsworth, Lee, Hanna, Rankin and Jones.)- Published
- 2023
- Full Text
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44. Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility.
- Author
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Brunet J, Walsh CL, Wagner WL, Bellier A, Werlein C, Marussi S, Jonigk DD, Verleden SE, Ackermann M, Lee PD, and Tafforeau P
- Subjects
- Humans, Animals, X-Ray Microtomography methods, Imaging, Three-Dimensional methods, Multimodal Imaging, Synchrotrons, Brain diagnostic imaging
- Abstract
Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolution imaging, however, is challenging due to limitations such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe the preparation, stabilization, dehydration and mounting of large soft-tissue samples for X-ray microtomography. We detail the protocol applied to whole human organs and hierarchical phase-contrast tomography at the European Synchrotron Radiation Facility, yet it is applicable to a range of biological samples, including complete organisms. The protocol enhances the contrast when using X-ray imaging, while preventing sample motion during the scan, even with different sample orientations. Bubbles trapped during mounting and those formed during scanning (in the case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging, computed tomography and histological observation. The sample preparation and mounting require 24-36 d for a large organ such as a whole human brain or heart. The preparation time varies depending on the composition, size and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local voxel size of 1 μm. The protocol requires users with expertise in handling human or animal organs, laboratory operation and X-ray imaging., (© 2023. Springer Nature Limited.)
- Published
- 2023
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45. Novel Insight into Pulmonary Fibrosis and Long COVID.
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Kamp JC, Werlein C, Plucinski EKJ, Neubert L, Welte T, Lee PD, Tafforeau P, Walsh C, Kuehnel MP, Schuppan D, Hoeper MM, Jonigk DD, and Ackermann M
- Subjects
- Humans, Post-Acute COVID-19 Syndrome, Pulmonary Fibrosis etiology, COVID-19
- Published
- 2023
- Full Text
- View/download PDF
46. Comment on: Intrapulmonary shunt and alveolar dead space in a cohort of patients with acute COVID-19 pneumonitis and early recovery.
- Author
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Ackermann M, Tafforeau P, Brunet J, Kamp JC, Werlein C, Kühnel MP, Jacob J, Walsh CL, Lee PD, Welte T, and Jonigk DD
- Subjects
- Humans, Lung, Respiratory Dead Space, Respiratory Physiological Phenomena, COVID-19, Pneumonia
- Abstract
Competing Interests: Conflict of interest: P. Tafforeau, C.L. Walsh and P.D. Lee report grants from Chan Zuckerberg Initiative; outside the submitted work. J. Jacob reports consulting fees from Boehringer Ingelheim, Roche, GlaxoSmithKline and NHSX; lecture honoraria from Boehringer Ingelheim, Roche, GlaxoSmithKline and Takeda; travel support from Boehringer Ingelheim; UK patent application number 2113765.8; advisory board participation with Boehringer Ingelheim and Roche; outside the submitted work. T. Welte reports grants from Bundesminissterium für Bildung und Forschung (Ministry for Research and Education); outside the submitted work. All other authors have nothing to disclose.
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- 2023
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47. Image quality and scan time optimisation for in situ phase contrast x-ray tomography of the intervertebral disc.
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Disney CM, Vo NT, Bodey AJ, Bay BK, and Lee PD
- Subjects
- Tomography, X-Ray Computed, Synchrotrons, Time Factors, Intervertebral Disc diagnostic imaging
- Abstract
In-line phase contrast synchrotron tomography combined with in situ mechanical loading enables the characterisation of soft tissue micromechanics via digital volume correlation (DVC) within whole organs. Optimising scan time is important for reducing radiation dose from multiple scans and to limit sample movement during acquisition. Also, although contrasted edges provided by in-line phase contrast tomography of soft tissues are useful for DVC, the effect of phase contrast imaging on its accuracy has yet to be investigated. Due to limited time at synchrotron facilities, scan parameters are often decided during imaging and their effect on DVC accuracy is not fully understood. Here, we used previously published data of intervertebral disc phase contrast tomography to evaluate the influence of i) fibrous image texture, ii) number of projections, iii) tomographic reconstruction method, and iv) phase contrast propagation distance on DVC results. A greater understanding of how image texture influences optimal DVC tracking was obtained by visualising objective function mapping, enabling tracking inaccuracies to be identified. When reducing the number of projections, DVC was minimally affected by image high frequency noise but with a compromise in accuracy. Iterative reconstruction methods improved image signal-to-noise and consequently significantly lowered DVC displacement uncertainty. Propagation distance was shown to affect DVC accuracy. Consistent DVC results were achieved within a propagation distance range which provided contrast to the smallest scale features, where; too short a distance provided insufficient features to track, whereas too long led to edge effect inconsistencies, particularly at greater deformations. Although limited to a single sample type and image setup, this study provides general guidelines for future investigations when optimising image quality and scan times for in situ phase contrast x-ray tomography of fibrous connective tissues., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2023
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48. Quantification of Interdependent Dynamics during Laser Additive Manufacturing Using X-Ray Imaging Informed Multi-Physics and Multiphase Simulation.
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Leung CLA, Luczyniec D, Guo E, Marussi S, Atwood RC, Meisnar M, Saunders B, and Lee PD
- Abstract
Laser powder bed fusion (LPBF) can produce high-value metallic components for many industries; however, its adoption for safety-critical applications is hampered by the presence of imperfections. The interdependency between imperfections and processing parameters remains unclear. Here, the evolution of porosity and humps during LPBF using X-ray and electron imaging, and a high-fidelity multiphase process simulation, is quantified. The pore and keyhole formation mechanisms are driven by the mixing of high temperatures and high metal vapor concentrations in the keyhole is revealed. The irregular pores are formed via keyhole collapse, pore coalescence, and then pore entrapment by the solidification front. The mixing of the fast-moving vapor plume and molten pool induces a Kelvin-Helmholtz instability at the melt track surface, forming humps. X-ray imaging and a high-fidelity model are used to quantify the pore evolution kinetics, pore size distribution, waviness, surface roughness, and melt volume under single layer conditions. This work provides insights on key criteria that govern the formation of imperfections in LPBF and suggest ways to improve process reliability., (© 2022 The Authors. Advanced Science published by Wiley-VCH GmbH.)
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- 2022
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49. Instantaneous 4D micro-particle image velocimetry (µPIV) via multifocal microscopy (MUM).
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Guastamacchia MGR, Xue R, Madi K, Pitkeathly WTE, Lee PD, Webb SED, Cartmell SH, and Dalgarno PA
- Subjects
- Stress, Mechanical, Microscopy, Confocal, Rheology methods
- Abstract
Multifocal microscopy (MUM), a technique to capture multiple fields of view (FOVs) from distinct axial planes simultaneously and on one camera, was used to perform micro-particle image velocimetry (µPIV) to reconstruct velocity and shear stress fields imposed by a liquid flowing around a cell. A diffraction based multifocal relay was used to capture images from three different planes with 630 nm axial spacing from which the axial positions of the flow-tracing particles were calculated using the image sharpness metric. It was shown that MUM can achieve an accuracy on the calculated velocity of around (0.52 ± 0.19) µm/s. Using fixed cells, MUM imaged the flow perturbations at sub-cellular level, which showed characteristics similar to those observed in the literature. Using live cells as an exemplar, MUM observed the effect of changing cell morphology on the local flow during perfusion. Compared to standard confocal laser scanning microscope, MUM offers a clear advantage in acquisition speed for µPIV (over 300 times faster). This is an important characteristic for rapidly evolving biological systems where there is the necessity to monitor in real time entire volumes to correlate the sample responses to the external forces., (© 2022. The Author(s).)
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- 2022
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50. The fatal trajectory of pulmonary COVID-19 is driven by lobular ischemia and fibrotic remodelling.
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Ackermann M, Kamp JC, Werlein C, Walsh CL, Stark H, Prade V, Surabattula R, Wagner WL, Disney C, Bodey AJ, Illig T, Leeming DJ, Karsdal MA, Tzankov A, Boor P, Kühnel MP, Länger FP, Verleden SE, Kvasnicka HM, Kreipe HH, Haverich A, Black SM, Walch A, Tafforeau P, Lee PD, Hoeper MM, Welte T, Seeliger B, David S, Schuppan D, Mentzer SJ, and Jonigk DD
- Subjects
- Humans, Lung diagnostic imaging, Lung pathology, Fibrosis, Biomarkers analysis, Ischemia pathology, Post-Acute COVID-19 Syndrome, COVID-19, Lung Diseases, Interstitial pathology
- Abstract
Background: COVID-19 is characterized by a heterogeneous clinical presentation, ranging from mild symptoms to severe courses of disease. 9-20% of hospitalized patients with severe lung disease die from COVID-19 and a substantial number of survivors develop long-COVID. Our objective was to provide comprehensive insights into the pathophysiology of severe COVID-19 and to identify liquid biomarkers for disease severity and therapy response., Methods: We studied a total of 85 lungs (n = 31 COVID autopsy samples; n = 7 influenza A autopsy samples; n = 18 interstitial lung disease explants; n = 24 healthy controls) using the highest resolution Synchrotron radiation-based hierarchical phase-contrast tomography, scanning electron microscopy of microvascular corrosion casts, immunohistochemistry, matrix-assisted laser desorption ionization mass spectrometry imaging, and analysis of mRNA expression and biological pathways. Plasma samples from all disease groups were used for liquid biomarker determination using ELISA. The anatomic/molecular data were analyzed as a function of patients' hospitalization time., Findings: The observed patchy/mosaic appearance of COVID-19 in conventional lung imaging resulted from microvascular occlusion and secondary lobular ischemia. The length of hospitalization was associated with increased intussusceptive angiogenesis. This was associated with enhanced angiogenic, and fibrotic gene expression demonstrated by molecular profiling and metabolomic analysis. Increased plasma fibrosis markers correlated with their pulmonary tissue transcript levels and predicted disease severity. Plasma analysis confirmed distinct fibrosis biomarkers (TSP2, GDF15, IGFBP7, Pro-C3) that predicted the fatal trajectory in COVID-19., Interpretation: Pulmonary severe COVID-19 is a consequence of secondary lobular microischemia and fibrotic remodelling, resulting in a distinctive form of fibrotic interstitial lung disease that contributes to long-COVID., Funding: This project was made possible by a number of funders. The full list can be found within the Declaration of interests / Acknowledgements section at the end of the manuscript., Competing Interests: Declaration of interests HHK received fees for lectures and consultations from Roche Pharma AG, Novartis, AstraZeneca, Genomic Health, Pfizer, and Amgen, all outside the present study. MMH received fees for lectures and consultations from Acceleron, Actelion, Bayer, GSK, Janssen, MSD, and Pfizer, all outside the present study. TW declares funding by the German Ministry of Research and Education. MAK and DJL declare the possession of “Nordic Bioscience” stock options. BS received fees for lectures from Boehringer Ingelheim. The other authors have no potential conflicts of interest to report., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)
- Published
- 2022
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