Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 63
Filter
1.
Nat Methods ; 19(4): 479-485, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1764194

ABSTRACT

The recent development of solvent- and polymer-based brain-clearing techniques has advanced our ability to visualize the mammalian nervous system in three dimensions. However, it remains challenging to image the mammalian body en bloc. Here we developed HYBRiD (hydrogel-based reinforcement of three-dimensional imaging solvent-cleared organs (DISCO)), by recombining components of organic- and polymer-based clearing pipelines. We achieved high transparency and protein retention, as well as compatibility with direct fluorescent imaging and immunostaining in cleared mammalian bodies. Using parvalbumin- and somatostatin-Cre models, we demonstrated the utility of HYBRiD for whole-body imaging of genetically encoded fluorescent reporters without antibody enhancement of signals in newborn and juvenile mice. Using K18-hACE2 transgenic mice, HYBRiD enabled perfusion-free clearing and visualization of SARS-CoV-2 infection in a whole mouse chest, revealing macroscopic and microscopic features of viral pathology in the same sample. HYBRiD offers a simple and universal solution to visualize large heterogeneous body parts or entire animals for basic and translational research.


Subject(s)
COVID-19 , Hydrogels , Animals , Imaging, Three-Dimensional/methods , Mammals , Mice , Polymers , SARS-CoV-2 , Solvents
2.
Sci Rep ; 12(1): 4025, 2022 03 07.
Article in English | MEDLINE | ID: covidwho-1730321

ABSTRACT

Computational fluid dynamics (CFD) modelling and 3D simulations of the air flow and dispersion of droplets or drops in semi-confined ventilated spaces have found topical applications with the unfortunate development of the Covid-19 pandemic. As an illustration of this scenario, we have considered the specific situation of a railroad coach containing a seated passenger infected with the SARS-CoV-2 virus (and not wearing a face mask) who, by breathing and coughing, releases droplets and drops that contain the virus and that present aerodynamic diameters between 1 and 1000 µm. The air flow is generated by the ventilation in the rail coach. While essentially 3D, the flow is directed from the bottom to the top of the carriage and comprises large to small eddies visualised by means of streamlines. The space and time distribution of the droplets and drops is computed using both an Eulerian model and a Lagrangian model. The results of the two modelling approaches are fully consistent and clearly illustrate the different behaviours of the drops, which fall down close to the infected passenger, and the droplets, which are carried along with the air flow and invade a large portion of the rail coach. This outcome is physically sound and demonstrates the relevance of CFD for simulating the transport and dispersion of droplets and drops with any diameter in enclosed ventilated spaces. As coughing produces drops and breathing produces droplets, both modes of transmission of the SARS-CoV-2 virus in human secretions have been accounted for in our 3D numerical study. Beyond the specific, practical application of the rail coach, this study offers a much broader scope by demonstrating the feasibility and usefulness of 3D numerical simulations based on CFD. As a matter of fact, the same computational approach that has been implemented in our study can be applied to a huge variety of ventilated indoor environments such as restaurants, performance halls, classrooms and open-plan offices in order to evaluate if their occupation could be critical with respect to the transmission of the SARS-CoV-2 virus or to other airborne respiratory infectious agents, thereby enabling relevant recommendations to be made.


Subject(s)
COVID-19/transmission , Railroads , SARS-CoV-2/metabolism , COVID-19/virology , Computer Simulation , Disease Transmission, Infectious/statistics & numerical data , Humans , Imaging, Three-Dimensional
3.
Med Mol Morphol ; 55(1): 60-67, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1712248

ABSTRACT

SARS-CoV-2 is the cause of COVID-19. The three-dimensional morphology of viral particles existing and multiplying in infected cells has not been established by electron tomography, which is different from cryo-electron tomography using frozen samples. In this study, we establish the morphological structure of SARS-CoV-2 particles by three-dimensional reconstruction of images obtained by electron tomography and transmission electron microscopy of biological samples embedded in epoxy resin. The characteristic roots of spike structures were found to be arranged at the surface of a virion covered with an envelope. A high-electron-density structure that appears to be a nucleocapsid was observed inside the envelope of the virion on three-dimensional images reconstructed by electron tomography. The SARS-CoV-2 particles that budded in the vacuoles in the cytoplasm were morphologically identical to those found outside the cells, suggesting that mature and infectious SARS-CoV-2 particles were already produced in the vacuoles. Here, we show the three-dimensional morphological structure of SARS-CoV-2 particles reconstructed by electron tomography. To control infection, inhibition of viral release from vacuoles would be a new target in the development of prophylactic agents against SARS-CoV-2.


Subject(s)
Electron Microscope Tomography , SARS-CoV-2 , COVID-19 , Humans , Imaging, Three-Dimensional , SARS-CoV-2/ultrastructure , Virion/ultrastructure
4.
Sci Rep ; 12(1): 1847, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1671622

ABSTRACT

Automatic segmentation of infected lesions from computed tomography (CT) of COVID-19 patients is crucial for accurate diagnosis and follow-up assessment. The remaining challenges are the obvious scale difference between different types of COVID-19 lesions and the similarity between the lesions and normal tissues. This work aims to segment lesions of different scales and lesion boundaries correctly by utilizing multiscale and multilevel features. A novel multiscale dilated convolutional network (MSDC-Net) is proposed against the scale difference of lesions and the low contrast between lesions and normal tissues in CT images. In our MSDC-Net, we propose a multiscale feature capture block (MSFCB) to effectively capture multiscale features for better segmentation of lesions at different scales. Furthermore, a multilevel feature aggregate (MLFA) module is proposed to reduce the information loss in the downsampling process. Experiments on the publicly available COVID-19 CT Segmentation dataset demonstrate that the proposed MSDC-Net is superior to other existing methods in segmenting lesion boundaries and large, medium, and small lesions, and achieves the best results in Dice similarity coefficient, sensitivity and mean intersection-over-union (mIoU) scores of 82.4%, 81.1% and 78.2%, respectively. Compared with other methods, the proposed model has an average improvement of 10.6% and 11.8% on Dice and mIoU. Compared with the existing methods, our network achieves more accurate segmentation of lesions at various scales and lesion boundaries, which will facilitate further clinical analysis. In the future, we consider integrating the automatic detection and segmentation of COVID-19, and conduct research on the automatic diagnosis system of COVID-19.


Subject(s)
COVID-19/diagnostic imaging , Neural Networks, Computer , Radiography, Thoracic/methods , Tomography, X-Ray Computed/methods , Datasets as Topic , Female , Humans , Imaging, Three-Dimensional/methods , Male
6.
Biochim Biophys Acta Mol Basis Dis ; 1868(4): 166347, 2022 04 01.
Article in English | MEDLINE | ID: covidwho-1636951

ABSTRACT

As epitomised by the COVID-19 pandemic, diseases caused by viruses are one of the greatest health and economic burdens to human society. Viruses are 'nanostructures', and their small size (typically less than 200 nm in diameter) can make it challenging to obtain images of their morphology and structure. Recent advances in fluorescence microscopy have given rise to super-resolution techniques, which have enabled the structure of viruses to be visualised directly at a resolution in the order of 20 nm. This mini-review discusses how recent state-of-the-art super-resolution imaging technologies are providing new nanoscale insights into virus structure.


Subject(s)
Microscopy, Fluorescence , Viruses/chemistry , Humans , Imaging, Three-Dimensional , Virion/chemistry
7.
Elife ; 102021 12 21.
Article in English | MEDLINE | ID: covidwho-1597375

ABSTRACT

For the first time, we have used phase-contrast X-ray tomography to characterize the three-dimensional (3d) structure of cardiac tissue from patients who succumbed to Covid-19. By extending conventional histopathological examination by a third dimension, the delicate pathological changes of the vascular system of severe Covid-19 progressions can be analyzed, fully quantified and compared to other types of viral myocarditis and controls. To this end, cardiac samples with a cross-section of 3.5mm were scanned at a laboratory setup as well as at a parallel beam setup at a synchrotron radiation facility the synchrotron in a parallel beam configuration. The vascular network was segmented by a deep learning architecture suitable for 3d datasets (V-net), trained by sparse manual annotations. Pathological alterations of vessels, concerning the variation of diameters and the amount of small holes, were observed, indicative of elevated occurrence of intussusceptive angiogenesis, also confirmed by high-resolution cone beam X-ray tomography and scanning electron microscopy. Furthermore, we implemented a fully automated analysis of the tissue structure in the form of shape measures based on the structure tensor. The corresponding distributions show that the histopathology of Covid-19 differs from both influenza and typical coxsackie virus myocarditis.


Subject(s)
COVID-19/complications , Myocarditis/pathology , Myocarditis/virology , Myocardium/pathology , SARS-CoV-2/isolation & purification , Artificial Intelligence , COVID-19/pathology , Heart/diagnostic imaging , Heart/virology , Humans , Imaging, Three-Dimensional , Myocarditis/diagnostic imaging , Myocarditis/etiology , Synchrotrons , Tomography, X-Ray Computed
8.
Sci Rep ; 11(1): 23688, 2021 12 08.
Article in English | MEDLINE | ID: covidwho-1561240

ABSTRACT

The global virtual reality (VR) market is significantly expanding and being challenged with an increased demand owing to COVID-19. Unfortunately, VR is not useful for everyone due to large interindividual variability existing in VR suitability. To understand the neurobiological basis of this variability, we obtained neural structural and functional data from the participants using 3T magnetic resonance imaging. The participants completed one of two tasks (sports training or cognitive task) using VR, which differed in the time scale (months/minutes) and domain (motor learning/attention task). Behavioral results showed that some participants improved their motor skills in the real world after 1-month training in the virtual space or obtained high scores in the 3D attention task (high suitability for VR), whereas others did not (low suitability for VR). Brain structure analysis revealed that the structural properties of the superior and inferior parietal lobes contain information that can predict an individual's suitability for VR.


Subject(s)
Parietal Lobe/anatomy & histology , Virtual Reality , Adolescent , Algorithms , Female , Humans , Image Processing, Computer-Assisted , Imaging, Three-Dimensional , Magnetic Resonance Imaging , Male , Parietal Lobe/diagnostic imaging , Young Adult
9.
Med Mol Morphol ; 55(1): 60-67, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1536314

ABSTRACT

SARS-CoV-2 is the cause of COVID-19. The three-dimensional morphology of viral particles existing and multiplying in infected cells has not been established by electron tomography, which is different from cryo-electron tomography using frozen samples. In this study, we establish the morphological structure of SARS-CoV-2 particles by three-dimensional reconstruction of images obtained by electron tomography and transmission electron microscopy of biological samples embedded in epoxy resin. The characteristic roots of spike structures were found to be arranged at the surface of a virion covered with an envelope. A high-electron-density structure that appears to be a nucleocapsid was observed inside the envelope of the virion on three-dimensional images reconstructed by electron tomography. The SARS-CoV-2 particles that budded in the vacuoles in the cytoplasm were morphologically identical to those found outside the cells, suggesting that mature and infectious SARS-CoV-2 particles were already produced in the vacuoles. Here, we show the three-dimensional morphological structure of SARS-CoV-2 particles reconstructed by electron tomography. To control infection, inhibition of viral release from vacuoles would be a new target in the development of prophylactic agents against SARS-CoV-2.


Subject(s)
Electron Microscope Tomography , SARS-CoV-2 , COVID-19 , Humans , Imaging, Three-Dimensional , SARS-CoV-2/ultrastructure , Virion/ultrastructure
10.
Comput Math Methods Med ; 2021: 7259414, 2021.
Article in English | MEDLINE | ID: covidwho-1533111

ABSTRACT

In this paper, based on the improved convolutional neural network, in-depth analysis of the CT image of the new coronary pneumonia, using the U-Net series of deep neural networks to semantically segment the CT image of the new coronary pneumonia, to obtain the new coronary pneumonia area as the foreground and the remaining areas as the background of the binary image, provides a basis for subsequent image diagnosis. Secondly, the target-detection framework Faster RCNN extracts features from the CT image of the new coronary pneumonia tumor, obtains a higher-level abstract representation of the data, determines the lesion location of the new coronary pneumonia tumor, and gives its bounding box in the image. By generating an adversarial network to diagnose the lesion area of the CT image of the new coronary pneumonia tumor, obtaining a complete image of the new coronary pneumonia, achieving the effect of the CT image diagnosis of the new coronary pneumonia tumor, and three-dimensionally reconstructing the complete new coronary pneumonia model, filling the current the gap in this aspect, provide a basis to produce new coronary pneumonia prosthesis and improve the accuracy of diagnosis.


Subject(s)
Algorithms , COVID-19/diagnostic imaging , Neural Networks, Computer , Tomography, X-Ray Computed/statistics & numerical data , COVID-19/diagnosis , Computational Biology , Databases, Factual , Deep Learning , Diagnosis, Computer-Assisted/statistics & numerical data , Humans , Imaging, Three-Dimensional/statistics & numerical data , Pandemics , Radiographic Image Interpretation, Computer-Assisted/statistics & numerical data , SARS-CoV-2
11.
Sci Rep ; 11(1): 22612, 2021 11 19.
Article in English | MEDLINE | ID: covidwho-1526106

ABSTRACT

This paper proposes an investigating SARS-CoV-2 inactivation on surfaces with UV-C LED irradiation using our in-house-developed ray-tracing simulator. The results are benchmarked with experiments and Zemax OpticStudio commercial software simulation to demonstrate our simulator's easy accessibility and high reliability. The tool can input the radiant profile of the flexible LED source and accurately yield the irradiance distribution emitted from an LED-based system in 3D environments. The UV-C operating space can be divided into the safe, buffer, and germicidal zones for setting up a UV-C LED system. Based on the published measurement data, the level of SARS-CoV-2 inactivation has been defined as a function of UV-C irradiation. A realistic case of public space, i.e., a food court in Singapore, has been numerically investigated to demonstrate the relative impact of environmental UV-C attenuation on the SARS-CoV-2 inactivation. We optimise a specific UV-C LED germicidal system and its corresponding exposure time according to the simulation results. These ray-tracing-based simulations provide a useful guideline for safe deployment and efficient design for germicidal UV-C LED technology.


Subject(s)
SARS-CoV-2/radiation effects , Ultraviolet Rays , Virus Inactivation/radiation effects , Computer Simulation , Disinfection/instrumentation , Imaging, Three-Dimensional , Singapore , Sterilization/instrumentation
12.
Magn Reson Med ; 87(4): 1784-1798, 2022 04.
Article in English | MEDLINE | ID: covidwho-1525480

ABSTRACT

PURPOSE: To develop an isotropic high-resolution stack-of-spirals UTE sequence for pulmonary imaging at 0.55 Tesla by leveraging a combination of robust respiratory-binning, trajectory correction, and concomitant-field corrections. METHODS: A stack-of-spirals golden-angle UTE sequence was used to continuously acquire data for 15.5 minutes. The data was binned to a stable respiratory phase based on superoinferior readout self-navigator signals. Corrections for trajectory errors and concomitant field artifacts, along with image reconstruction with conjugate gradient SENSE, were performed inline within the Gadgetron framework. Finally, data were retrospectively reconstructed to simulate scan times of 5, 8.5, and 12 minutes. Image quality was assessed using signal-to-noise, image sharpness, and qualitative reader scores. The technique was evaluated in healthy volunteers, patients with coronavirus disease 2019 infection, and patients with lung nodules. RESULTS: The technique provided diagnostic quality images with parenchymal lung SNR of 3.18 ± 0.0.60, 4.57 ± 0.87, 5.45 ± 1.02, and 5.89 ± 1.28 for scan times of 5, 8.5, 12, and 15.5 minutes, respectively. The respiratory binning technique resulted in significantly sharper images (p < 0.001) as measured with relative maximum derivative at the diaphragm. Concomitant field corrections visibly improved sharpness of anatomical structures away from iso-center. The image quality was maintained with a slight loss in SNR for simulated scan times down to 8.5 minutes. Inline image reconstruction and artifact correction were achieved in <5 minutes. CONCLUSION: The proposed pulmonary imaging technique combined efficient stack-of-spirals imaging with robust respiratory binning, concomitant field correction, and trajectory correction to generate diagnostic quality images with 1.75 mm isotropic resolution in 8.5 minutes on a high-performance 0.55 Tesla system.


Subject(s)
COVID-19 , Imaging, Three-Dimensional , Artifacts , Humans , Lung/diagnostic imaging , Magnetic Resonance Imaging , Retrospective Studies , SARS-CoV-2
13.
Nat Methods ; 18(12): 1532-1541, 2021 12.
Article in English | MEDLINE | ID: covidwho-1504972

ABSTRACT

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)'s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).


Subject(s)
COVID-19/pathology , Image Processing, Computer-Assisted/methods , Imaging, Three-Dimensional/methods , Lung/pathology , SARS-CoV-2 , Tomography, X-Ray Computed/methods , Humans , Kidney/anatomy & histology , Synchrotrons
14.
Interv Neuroradiol ; 26(5): 557-565, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-1455862

ABSTRACT

BACKGROUND: The Low-profile Visualized Intraluminal Support device (LVIS) has been successfully used to treat cerebral aneurysm, and the push-pull technique has been used clinically to compact the stent across aneurysm orifice. Our aim was to exhibit the hemodynamic effect of the compacted LVIS stent. METHODS: Two patient-specific aneurysm models were constructed from three-dimensional angiographic images. The uniform LVIS stent, compacted LVIS and Pipeline Embolization Device (PED) with or without coil embolization were virtually deployed into aneurysm models to perform hemodynamic analysis. Intra-aneurysmal flow parameters were calculated to assess hemodynamic differences among different models. RESULTS: The compacted LVIS had the highest metal coverage across the aneurysm orifice (case 1, 46.37%; case 2, 67.01%). However, the PED achieved the highest pore density (case 1, 19.56 pores/mm2; case 2, 18.07 pores/mm2). The compacted LVIS produced a much higher intra-aneurysmal flow reduction than the uniform LVIS. The PED showed a higher intra-aneurysmal flow reduction than the compacted LVIS in case 1, but the results were comparable in case 2. After stent placement, the intra-aneurysmal flow was further reduced as subsequent coil embolization. The compacted LVIS stent with coils produced a similar reduction in intra-aneurysmal flow to that of the PED. CONCLUSIONS: The combined characteristics of stent metal coverage and pore density should be considered when assessing the flow diversion effects of stents. More intra-aneurysmal flow reductions could be introduced by compacted LVIS stent than the uniform one. Compared with PED, compacted LVIS stent may exhibit a flow-diverting effect comparable to that of the PED.


Subject(s)
Embolization, Therapeutic/methods , Intracranial Aneurysm/therapy , Stents , Subarachnoid Hemorrhage/therapy , Angiography, Digital Subtraction , Cerebral Angiography , Computer Simulation , Hemodynamics , Humans , Hydrodynamics , Imaging, Three-Dimensional , Intracranial Aneurysm/diagnostic imaging , Magnetic Resonance Angiography , Prosthesis Design , Subarachnoid Hemorrhage/diagnostic imaging
15.
Laryngoscope ; 131(6): E1971-E1979, 2021 06.
Article in English | MEDLINE | ID: covidwho-1453618

ABSTRACT

OBJECTIVE/HYPOTHESIS: To assess the ability of ultra-short echo time (UTE)-MRI to detect subglottic stenosis (SGS) and evaluate response to balloon dilation. To correlate measurements from UTE-MRI with endotracheal-tube (ETT)-sizing and to investigate whether SGS causes change in airway dynamics. STUDY DESIGN: Animal research study. METHODS: Eight adult New-Zealand white rabbits were used as they approximate neonatal airway-size. The airways were measured using ETT-sizing and 3D UTE-MRI at baseline, 2 weeks post-cauterization induced SGS injury, and post-balloon dilation treatment. UTE-MR images were acquired to determine airway anatomy and motion. Airways were segmented from MR images. Cross-sectional area (CSA), major and minor diameters (Dmajor and Dminor ), and eccentricity were measured. RESULTS: Post-injury CSA at SGS was significantly reduced (mean 38%) compared to baseline (P = .003) using UTE-MRI. ETT-sizing correlated significantly with MRI-measured CSA at the SGS location (r = 0.6; P < .01), particularly at the post-injury timepoint (r = 0.93; P < .01). Outer diameter from ETT-sizing (OD) correlated significantly with Dmajor (r = 0.63; P < .01) from UTE-MRI at the SGS location, especially for the post-injury timepoint (r = 0.91; P < .01). Mean CSA of upper trachea did not change significantly between end-expiration and end-inspiration at any timepoint (all P > .05). Eccentricity of the upper trachea increased significantly post-balloon dilation (P < .05). CONCLUSIONS: UTE-MRI successfully detected SGS and treatment response in the rabbit model, with good correlation to ETT-sizing. Balloon dilation increased CSA at SGS, but not to baseline values. SGS did not alter dynamic motion for the trachea in this rabbit model; however, tracheas were significantly eccentric post-balloon dilation. UTE-MRI can detect SGS without sedation or ionizing radiation and may be a non-invasive alternative to ETT-sizing. LEVEL OF EVIDENCE: NA Laryngoscope, 131:E1971-E1979, 2021.


Subject(s)
Laryngostenosis/diagnostic imaging , Magnetic Resonance Imaging/methods , Animals , Disease Models, Animal , Female , Imaging, Three-Dimensional , Intubation, Intratracheal , Laryngoscopy , Rabbits
16.
Blood ; 138(22): 2256-2268, 2021 12 02.
Article in English | MEDLINE | ID: covidwho-1443788

ABSTRACT

SARS-CoV-2 vaccine ChAdOx1 nCoV-19 (AstraZeneca) causes a thromboembolic complication termed vaccine-induced immune thrombotic thrombocytopenia (VITT). Using biophysical techniques, mouse models, and analysis of VITT patient samples, we identified determinants of this vaccine-induced adverse reaction. Super-resolution microscopy visualized vaccine components forming antigenic complexes with platelet factor 4 (PF4) on platelet surfaces to which anti-PF4 antibodies obtained from VITT patients bound. PF4/vaccine complex formation was charge-driven and increased by addition of DNA. Proteomics identified substantial amounts of virus production-derived T-REx HEK293 proteins in the ethylenediaminetetraacetic acid (EDTA)-containing vaccine. Injected vaccine increased vascular leakage in mice, leading to systemic dissemination of vaccine components known to stimulate immune responses. Together, PF4/vaccine complex formation and the vaccine-stimulated proinflammatory milieu trigger a pronounced B-cell response that results in the formation of high-avidity anti-PF4 antibodies in VITT patients. The resulting high-titer anti-PF4 antibodies potently activated platelets in the presence of PF4 or DNA and polyphosphate polyanions. Anti-PF4 VITT patient antibodies also stimulated neutrophils to release neutrophil extracellular traps (NETs) in a platelet PF4-dependent manner. Biomarkers of procoagulant NETs were elevated in VITT patient serum, and NETs were visualized in abundance by immunohistochemistry in cerebral vein thrombi obtained from VITT patients. Together, vaccine-induced PF4/adenovirus aggregates and proinflammatory reactions stimulate pathologic anti-PF4 antibody production that drives thrombosis in VITT. The data support a 2-step mechanism underlying VITT that resembles the pathogenesis of (autoimmune) heparin-induced thrombocytopenia.


Subject(s)
Antigen-Antibody Complex/immunology , Autoantibodies/immunology , COVID-19/prevention & control , Capsid Proteins/adverse effects , Drug Contamination , Genetic Vectors/adverse effects , HEK293 Cells/immunology , Immunoglobulin G/immunology , Platelet Factor 4/immunology , Purpura, Thrombocytopenic, Idiopathic/etiology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/adverse effects , Adenoviridae/immunology , Animals , Antigen-Antibody Complex/ultrastructure , Autoantibodies/biosynthesis , Capillary Leak Syndrome/etiology , Capsid Proteins/immunology , Cell Line, Transformed , /immunology , Dynamic Light Scattering , Epitopes/chemistry , Epitopes/immunology , Extracellular Traps/immunology , Extravasation of Diagnostic and Therapeutic Materials/etiology , Genetic Vectors/immunology , HEK293 Cells/chemistry , Humans , Imaging, Three-Dimensional , Immunoglobulin G/biosynthesis , Inflammation , Mice , Microscopy/methods , Platelet Activation , Proteomics , Purpura, Thrombocytopenic, Idiopathic/blood , Purpura, Thrombocytopenic, Idiopathic/immunology , Sinus Thrombosis, Intracranial/diagnostic imaging , Sinus Thrombosis, Intracranial/immunology , Spike Glycoprotein, Coronavirus/immunology , Virus Cultivation
17.
Comput Med Imaging Graph ; 92: 101957, 2021 09.
Article in English | MEDLINE | ID: covidwho-1330724

ABSTRACT

Lung cancer is one of the most common and deadly malignant cancers. Accurate lung tumor segmentation from CT is therefore very important for correct diagnosis and treatment planning. The automated lung tumor segmentation is challenging due to the high variance in appearance and shape of the targeting tumors. To overcome the challenge, we present an effective 3D U-Net equipped with ResNet architecture and a two-pathway deep supervision mechanism to increase the network's capacity for learning richer representations of lung tumors from global and local perspectives. Extensive experiments on two real medical datasets: the lung CT dataset from Liaoning Cancer Hospital in China with 220 cases and the public dataset of TCIA with 422 cases. Our experiments demonstrate that our model achieves an average dice score (0.675), sensitivity (0.731) and F1-score (0.682) on the dataset from Liaoning Cancer Hospital, and an average dice score (0.691), sensitivity (0.746) and F1-score (0.724) on the TCIA dataset, respectively. The results demonstrate that the proposed 3D MSDS-UNet outperforms the state-of-the-art segmentation models for segmenting all scales of tumors, especially for small tumors. Moreover, we evaluated our proposed MSDS-UNet on another challenging volumetric medical image segmentation task: COVID-19 lung infection segmentation, which shows consistent improvement in the segmentation performance.


Subject(s)
COVID-19/diagnostic imaging , Imaging, Three-Dimensional , Lung Neoplasms/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Radiographic Image Interpretation, Computer-Assisted/methods , Supervised Machine Learning , Tomography, X-Ray Computed , China , Humans , Pneumonia, Viral/virology , SARS-CoV-2
18.
J Clin Invest ; 131(8)2021 04 15.
Article in English | MEDLINE | ID: covidwho-1291498

ABSTRACT

BACKGROUNDThe coronavirus disease 2019 (COVID-19) rapidly progressed to a global pandemic. Although some patients totally recover from COVID-19 pneumonia, the disease's long-term effects on the brain still need to be explored.METHODSWe recruited 51 patients with 2 subtypes of COVID-19 (19 mild and 32 severe) with no specific neurological manifestations at the acute stage and no obvious lesions on the conventional MRI 3 months after discharge. Changes in gray matter morphometry, cerebral blood flow (CBF), and white matter (WM) microstructure were investigated using MRI. The relationship between brain imaging measurements and inflammation markers was further analyzed.RESULTSCompared with healthy controls, the decrease in cortical thickness/CBF and the changes in WM microstructure were more severe in patients with severe disease than in those with mild disease, especially in the frontal and limbic systems. Furthermore, changes in brain microstructure, CBF, and tract parameters were significantly correlated (P < 0.05) with the inflammatory markers C-reactive protein, procalcitonin, and interleukin 6.CONCLUSIONIndirect injury related to inflammatory storm may damage the brain, altering cerebral volume, CBF, and WM tracts. COVID-19-related hypoxemia and dysfunction of vascular endothelium may also contribute to neurological changes. The abnormalities in these brain areas need to be monitored during recovery, which could help clinicians understand the potential neurological sequelae of COVID-19.FUNDINGNatural Science Foundation of China.


Subject(s)
COVID-19/diagnostic imaging , Cerebrovascular Circulation/physiology , SARS-CoV-2 , Aged , Brain/blood supply , Brain/diagnostic imaging , Brain/pathology , C-Reactive Protein/metabolism , COVID-19/epidemiology , COVID-19/physiopathology , Case-Control Studies , China/epidemiology , Diffusion Tensor Imaging , Echo-Planar Imaging , Female , Follow-Up Studies , Gray Matter/diagnostic imaging , Gray Matter/pathology , Humans , Imaging, Three-Dimensional , Inflammation Mediators/blood , Interleukin-6/blood , Male , Middle Aged , Neuroimaging , Pandemics , Procalcitonin/blood , Severity of Illness Index , Time Factors , White Matter/diagnostic imaging , White Matter/pathology
19.
Int J Mol Sci ; 22(13)2021 Jun 25.
Article in English | MEDLINE | ID: covidwho-1285390

ABSTRACT

During this global pandemic, cryo-EM has made a great impact on the structure determination of COVID-19 proteins. However, nearly all high-resolution results are based on data acquired on state-of-the-art microscopes where their availability is restricted to a number of centers across the globe with the studies on infectious viruses being further regulated or forbidden. One potential remedy is to employ multipurpose microscopes. Here, we investigated the capability of 200 kV multipurpose microscopes equipped with a direct electron camera in determining the structures of infectious particles. We used 30 nm particles of the grouper nerve necrosis virus as a test sample and obtained the cryo-EM structure with a resolution as high as ∼2.7 Šfrom a setting that used electron counting. For comparison, we tested a high-end cryo-EM (Talos Arctica) using a similar virus (Macrobrachium rosenbergii nodavirus) to obtain virtually the same resolution. Those results revealed that the resolution is ultimately limited by the depth of field. Our work updates the density maps of these viruses at the sub-3Šlevel to allow for building accurate atomic models from de novo to provide structural insights into the assembly of the capsids. Importantly, this study demonstrated that multipurpose TEMs are capable of the high-resolution cryo-EM structure determination of infectious particles and is thus germane to the research on pandemics.


Subject(s)
Cryoelectron Microscopy , Microscopy, Electron, Transmission , SARS-CoV-2/physiology , Virion/chemistry , COVID-19/pathology , COVID-19/virology , Humans , Imaging, Three-Dimensional , Models, Molecular , SARS-CoV-2/chemistry , SARS-CoV-2/isolation & purification
20.
PLoS One ; 16(6): e0252143, 2021.
Article in English | MEDLINE | ID: covidwho-1270947

ABSTRACT

The use of face masks by the general population during viral outbreaks such as the COVID-19 pandemic, although at times controversial, has been effective in slowing down the spread of the virus. The extent to which face masks mitigate the transmission is highly dependent on how well the mask fits each individual. The fit of simple cloth masks on the face, as well as the resulting perimeter leakage and face mask efficacy, are expected to be highly dependent on the type of mask and facial topology. However, this effect has, to date, not been adequately examined and quantified. Here, we propose a framework to study the efficacy of different mask designs based on a quasi-static mechanical model of the deployment of face masks onto a wide range of faces. To illustrate the capabilities of the proposed framework, we explore a simple rectangular cloth mask on a large virtual population of subjects generated from a 3D morphable face model. The effect of weight, age, gender, and height on the mask fit is studied. The Centers for Disease Control and Prevention (CDC) recommended homemade cloth mask design was used as a basis for comparison and was found not to be the most effective design for all subjects. We highlight the importance of designing masks accounting for the widely varying population of faces. Metrics based on aerodynamic principles were used to determine that thin, feminine, and young faces were shown to benefit from mask sizes smaller than that recommended by the CDC. Besides mask size, side-edge tuck-in, or pleating, of the masks as a design parameter was also studied and found to have the potential to cause a larger localized gap opening.


Subject(s)
COVID-19/prevention & control , Face/anatomy & histology , Masks/standards , SARS-CoV-2/isolation & purification , Textiles/standards , Adolescent , Adult , Algorithms , COVID-19/epidemiology , COVID-19/virology , Child , Cohort Studies , Computer Simulation , Female , Humans , Imaging, Three-Dimensional , Male , Masks/classification , Middle Aged , Models, Theoretical , Pandemics , SARS-CoV-2/physiology , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL