LitCovid-sentences  

PMC:7473770 / 31942-43850 JSONTXT 11 Projects

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Id Subject Object Predicate Lexical cue
T241 0-21 Sentence denotes Materials and methods
T242 23-74 Sentence denotes Autopsy, clinical background and tissue preparation
T243 75-173 Sentence denotes In total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020).
T244 174-296 Sentence denotes A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a.
T245 297-438 Sentence denotes Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2.
T246 439-563 Sentence denotes All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs.
T247 564-776 Sentence denotes Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure).
T248 777-892 Sentence denotes Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.
T249 893-901 Sentence denotes Table 2.
T250 903-934 Sentence denotes Sample and medical information.
T251 935-1153 Sentence denotes Age and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.
T252 1154-1164 Sentence denotes Sample no.
T253 1166-1258 Sentence denotes Age group, gender Hospitalization, clinical, radiological, and histological characteristics
T254 1259-1287 Sentence denotes I 60–70, F 5-10d, GGO, DAD
T255 1288-1318 Sentence denotes II 80–90, M 5-10d, C, I, DAD
T256 1319-1352 Sentence denotes III 90–100, M 1-4d, GGO, C, DAD
T257 1353-1392 Sentence denotes IV 70–80, M 1-4d, NIV, S, GGO, C, DAD
T258 1393-1432 Sentence denotes V 60–70, M 5-10d, NIV, S, GGO, C, DAD
T259 1433-1467 Sentence denotes VI 70–80, M 1-4d, S, GGO, C, DAD
T260 1468-1596 Sentence denotes CTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed.
T261 1597-1725 Sentence denotes To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained.
T262 1726-1841 Sentence denotes Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block.
T263 1842-2018 Sentence denotes The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration.
T264 2019-2136 Sentence denotes From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size.
T265 2137-2377 Sentence denotes The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings.
T266 2378-2435 Sentence denotes A sketch of the sample preparation is shown in Figure 1b.
T267 2436-2677 Sentence denotes The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution.
T268 2679-2704 Sentence denotes Phase contrast tomography
T269 2705-2825 Sentence denotes For Covid-19 lung tissue, the scans were recorded at the GINIX endstation of the PETRA III storage ring (DESY, Hamburg).
T270 2826-3028 Sentence denotes The projections were acquired at two different photon energies Eph, 8⁢keV and 13.8⁢keV, using the first and third harmonic of the 5 m P10 undulator and a Si(111) channel-cut monochromator, respectively.
T271 3029-3123 Sentence denotes Data are shown here only for 8⁢keV, which gave highest contrast for the unstained lung tissue.
T272 3124-3209 Sentence denotes Two tomography configurations were combined to cover a larger range of length scales:
T273 3211-3228 Sentence denotes (1–parallel beam)
T274 3229-3409 Sentence denotes Recordings with the unfocused quasi-parallel beam illumination and a high resolution microscope detection system, resulting in in a FOV of 1.6 mm sampled at a pixel size of 650 nm.
T275 3411-3424 Sentence denotes (2–cone beam)
T276 3425-3711 Sentence denotes Holographic recordings with the divergent and coherence filtered beam emanating from a compound focusing system composed of a Kirkpatrick-Baez (KB) mirrors system and an x-ray waveguide, resulting in a FOV of 0.4 mm sampled at a pixel size of about 167 nm (depending on exact geometry).
T277 3712-3859 Sentence denotes Both configurations were implemented side-by-side, using the same fully-motorized tomography stage and mounting, as detailed in Frohn et al., 2020.
T278 3860-3914 Sentence denotes A sketch of both configurations is shown in Figure 1 .
T279 3915-4014 Sentence denotes First, parallel-beam overview scans were acquired of the entire tissue volume embedded in paraffin.
T280 4015-4243 Sentence denotes To this end a 3.5 mm biopsy punch was taken from the multi-sample tissue block, and then scanned in a stitching-mode yielding a large overview reconstruction, composed of up to 20 individual tomograms (depending on tissue size).
T281 4244-4504 Sentence denotes To increase image quality and avoid artifacts related to region-of-interest (ROI) or local tomography, a selected 1 mm punch was then taken from the already scanned larger tissue cylinder, and re-scanned, first in the parallel- and then the cone-beam geometry.
T282 4505-4591 Sentence denotes Experimental and acquisition parameters used for the data shown are listed in Table 3.
T283 4592-4600 Sentence denotes Table 3.
T284 4602-4679 Sentence denotes Data acquisition parameters for x-ray phase-contrast tomography measurements.
T285 4680-4712 Sentence denotes Cone geometry Parallel geometry
T286 4713-4751 Sentence denotes FOV 0.4 mm × 0.35 mm 1.6 mm × 1.4 mm
T287 4752-4778 Sentence denotes Pixel size 167 nm 650 nm
T288 4779-4794 Sentence denotes z 01 125 mm -
T289 4795-4824 Sentence denotes z 12 4975 mm 10 mm − 100 mm
T290 4825-4861 Sentence denotes Regime holographic direct contrast
T291 4862-4894 Sentence denotes Rotation start-stop continuous
T292 4895-4920 Sentence denotes Exposure 2 s 0.035 ⁢ s
T293 4921-4957 Sentence denotes Total exposure ≃ 63 m i n ≃ 75 s
T294 4958-5099 Sentence denotes Volumetric flowrate 1.16 × 10 4 μ m / 3 s 3.75 × 10 7 μ m / 3 s The configuration for (1–parallel beam) is depicted in Figure 1c.
T295 5100-5370 Sentence denotes The high-resolution microscope detection system (Optique Peter, France) was based on a 50⁢μ⁢m thick LuAG:Ce scintillator imaged with a 10× magnifying microscope objective onto a sCMOS sensor (pco.edge 5.5, PCO, Germany), resulting in an effective pixel size of 0.65⁢μ⁢m.
T296 5371-5531 Sentence denotes The high photon flux density allowed for image acquisition with continuous motor movement, short acquisition time of 35 ms per frame, and a framerate of 20 fps.
T297 5532-5661 Sentence denotes Single-distance tomogram recordings with about 1500 projections, and flat images before and after the scan, took less than 2 min.
T298 5662-5859 Sentence denotes For these scans, the focusing optics (KB-mirrors and waveguide) as well as the fastshutter (Cedrat technologies) were moved out of the beam, and beam size was adjusted by the upstream slit systems.
T299 5860-5950 Sentence denotes To avoid detector saturation, the beam was attenuated by 4× single crystal silicon wafers.
T300 5951-6012 Sentence denotes The configuration for (2–cone beam) is depicted in Figure 1d:
T301 6013-6068 Sentence denotes The beam was focused by the KB-mirrors to about 300 nm.
T302 6069-6524 Sentence denotes To further reduce the secondary source size, to increase coherence, and to achieve a smooth wavefront for holographic illumination, an x-ray waveguide formed by 1 mm long lithographic channels in silicon with a cross-section of about 100 nm was positioned in the focal plane of the KB-mirrors, resulting in an exit flux of 1–4⋅109 photon/s (depending on alignment and storage ring), as measured with the single photon counting detector (Pilatus, Dectris).
T303 6525-6661 Sentence denotes The sample was positioned at variable (defocus) distances behind the focus (waveguide exit), typically z01=125mm for the first distance.
T304 6662-6863 Sentence denotes The geometrically magnified holograms were recorded by a fibre-coupled sCMOS sensor (Zyla HF 5.5 detector, Andor Technologies) with a customized 15⁢μ⁢m thick Gadox scintillator, and 6.5⁢μ⁢m pixel size.
T305 6864-7043 Sentence denotes The detector position at about z02=5100mm behind the focus resulted in a magnification of about M=41 (for the first defocus distance), and hence an effective pixel size of 167 nm.
T306 7044-7127 Sentence denotes 1442 projections were recorded, with a typical exposure time of 2 s per projection.
T307 7129-7184 Sentence denotes Phase retrieval, image reconstruction, and segmentation
T308 7186-7220 Sentence denotes Phase retrieval and reconstruction
T309 7221-7569 Sentence denotes Phase retrieval was performed from dark and empty beam corrected holograms, using both linearised single step CTF-approach (Cloetens et al., 1999; Turner et al., 2004), and non-linear generalizations of the CTF-method based on Tikhonov regularization (NL-CTF), using our code package HoloTomoToolbox as described and deposited (Lohse et al., 2020).
T310 7570-7691 Sentence denotes Importantly, both CTF and NL-CTF implementations can be augmented by imposing support and range constraints, when needed.
T311 7692-7850 Sentence denotes When available, projections recorded at several defocus distances were first aligned with sub-pixel accuracy and then used for multi-distance phase retrieval.
T312 7851-8019 Sentence denotes For these purposes, the HoloTomoToolbox provides auxiliary functions, which also help to refine the Fresnel number or to correct for drift in the illumination function.
T313 8020-8324 Sentence denotes After phase reconstruction of all projections, the tomographic reconstruction was carried out with the MATLAB implemented iradon-function (Ram-Lak filter) for the parallel geometry and with the FDK-function of the ASTRA toolbox (van Aarle et al., 2015; van Aarle et al., 2016) for the cone beam geometry.
T314 8325-8652 Sentence denotes Hot pixel and detector sensitivity variations as well as strong phase features in the parallel beam illumination resulting from upstream window materials, which persist after empty beam correction, can all result in ring artifacts in the tomographic reconstruction, in particular as these flaws can increase by phase retrieval.
T315 8653-8821 Sentence denotes To correct for this, the extra information provided by 360° scans was used to mask out the corresponding pixels and replace them with values of the opposing projection.
T316 8822-8929 Sentence denotes Stitching of reconstructions from different tomographic scans was performed using (Miettinen et al., 2019).
T317 8930-8997 Sentence denotes Resolution estimates were obtained by FSC analysis, see Appendix 2.
T318 8999-9036 Sentence denotes Image segmentation and quantification
T319 9037-9138 Sentence denotes For each patient the stitched overview scans were analyzed with regard to structural characteristics.
T320 9139-9361 Sentence denotes The 3D-reconstructions were first binned (2 × 2 × 2), and the tissue was then segmented from the surrounding paraffin using the segmentation software Ilastik (Berg et al., 2019), which was then further refined with MATLAB.
T321 9362-9500 Sentence denotes In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map.
T322 9501-9616 Sentence denotes Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block.
T323 9617-9712 Sentence denotes Individual self-contained areas of paraffin (not connected to air) were excluded from the mask.
T324 9713-9830 Sentence denotes Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel.
T325 9831-9903 Sentence denotes The tissue volume V is given by the sum of all voxels containing tissue.
T326 9904-9994 Sentence denotes The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air.
T327 9995-10100 Sentence denotes From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio.
T328 10101-10209 Sentence denotes Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample.
T329 10210-10345 Sentence denotes Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated.
T330 10346-10484 Sentence denotes Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA).
T331 10485-10640 Sentence denotes Beside hyaline membranes and the capillary network, different cell types can be readily identified based on the 3D reconstructions of the electron density.
T332 10641-10751 Sentence denotes In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished.
T333 10752-10865 Sentence denotes To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany).
T334 10866-11009 Sentence denotes Based on its segmentation output, the amount and position of the lymphocytes in the 3D-reconstructions from parallel beam scans was calculated.
T335 11010-11082 Sentence denotes The algorithm is able to identify roundish structures with a given size.
T336 11083-11166 Sentence denotes For the segmentation of the lymphocytes, we chose a characteristic size of 6.5⁢μ⁢m.
T337 11167-11265 Sentence denotes The structures identified in this step also include macrophages and parts of the capillary system.
T338 11266-11414 Sentence denotes For the unbinned datasets, a distinction between lymphocytes and the nuclei of the macrophages was made based on the difference in electron density.
T339 11415-11523 Sentence denotes In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages.
T340 11524-11664 Sentence denotes Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape.
T341 11665-11730 Sentence denotes Only structures with a sphericity higher than 0.55 were included.
T342 11731-11908 Sentence denotes Based on the segmentation of lymphocytes, the total number of lymphocytes Nl was obtained and the mean concentration of lymphocytes within the lung tissue cl=Nl/V was estimated.