High-resolution MRI of the human palatine tonsil and its schematic anatomic 3D reconstruction.
Ontology highlight
ABSTRACT:
SUBMITTER: Herrmann KH
PROVIDER: S-EPMC8655163 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Palatine tonsils (PT) are B cell-predominant lymphoid organs that provide primary immune responses to airborne and dietary pathogens. Numerous histopathological and immunological studies have been conducted on PT, yet no investigations have been conducted on its metabolic profile. We performed high-resolution magic angle spinning nuclear magnetic resonance spectroscopy-based metabolic profiling in 35 pediatric and 28 adult human palatine tonsillar tissue samples. A total of 36 metabolites were identified, and the levels of 10 metabolites were significantly different depending on age. Among them, partial correlation analysis shows that glucose levels increased with age, whereas glycine, phosphocholine, phosphoethanolamine, and ascorbate levels decreased with age. We confirmed the decrease in immunometabolic activity in adults through metabolomic analysis, which had been anticipated from previous histological and immunological studies on the PT. These results improve our understanding of metabolic changes in the PT with aging and serve as a basis for future tonsil-related metabolomic studies.
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Project description:?-Amyloid (A?) accumulation and aggregation are hallmarks of Alzheimer's disease (AD). High-resolution three-dimensional (HR-3D) volumetric imaging allows for better analysis of fluorescence confocal microscopy and 3D visualization of A? pathology in brain. Early intraneuronal A? pathology was studied in AD transgenic mouse brains by HR-3D volumetric imaging. To better visualize and analyze the development of A? pathology, thioflavin S staining and immunofluorescence using antibodies against A?, fibrillar A?, and structural and synaptic neuronal proteins were performed in the brain tissue of Tg19959, wild-type, and Tg19959-YFP mice at different ages. Images obtained by confocal microscopy were reconstructed into three-dimensional volumetric datasets. Such volumetric imaging of CA1 hippocampus of AD transgenic mice showed intraneuronal onset of A?42 accumulation and fibrillization within cell bodies, neurites, and synapses before plaque formation. Notably, early fibrillar A? was evident within individual synaptic compartments, where it was associated with abnormal morphology. In dendrites, increasing intraneuronal thioflavin S correlated with decreases in neurofilament marker SMI32. Fibrillar A? aggregates could be seen piercing the cell membrane. These data support that A? fibrillization begins within AD vulnerable neurons, leading to disruption of cytoarchitecture and degeneration of spines and neurites. Thus, HR-3D volumetric image analysis allows for better visualization of intraneuronal A? pathology and provides new insights into plaque formation in AD.
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Project description:The egg plays a pivotal role in the reproduction of our species. Nevertheless, its fundamental biology remains elusive. Transmission electron microscopy is traditionally used to inspect the ultrastructure of female gametes. However, two-dimensional micrographs contain only fragmentary information about the spatial organization of the complex oocyte cytoplasm. Here, we employed the Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) to explore human oocyte intracellular morphology in three dimensions (3D). Volume reconstruction of generated image stacks provided an unprecedented view of ooplasmic architecture. Organelle distribution patterns observed in nine donor oocytes, representing three maturational stages, documented structural changes underlying the process by which the egg acquires developmental competence. 3D image segmentation was performed to extract information about distinct organelle populations, and the following quantitative analysis revealed that the mitochondrion occupies ∼ 4.26% of the maturing oocyte cytoplasm. In summary, this proof-of-concept study demonstrates the potential of large volume electron microscopy to study rare samples of delicate female gametes and paves the way for applying the FIB-SEM technique in human oocyte research.
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Project description:The purposes of the study were to determine whether there are differences in texture analysis parameters between tonsil cancers and normal tonsils, and to correlate texture analysis with 18F-FDG PET/CT to investigate the relationship between texture analysis and metabolic parameters. Sixty-four patients with squamous cell carcinoma of the palatine tonsil were included. A ROI was drawn, including all slices, to involve the entire tumor. The contralateral normal tonsil was used for comparison with the tumors. Texture analysis parameters, mean, standard deviation (SD), entropy, mean positive pixels, skewness, and kurtosis were obtained using commercially available software. Parameters were compared between the tumor and the normal palatine tonsils. Comparisons were also performed among early tonsil cancer, advanced tonsil cancer, and normal tonsils. An ROC curve analysis was performed to assess discrimination of tumor from normal tonsils. Correlation between texture analysis and 18F-FDG PET/CT was performed. Compared to normal tonsils, the tumors showed a significantly lower mean, higher SD, higher entropy, lower skewness, and higher kurtosis on most filters (p<0.001). On comparisons among normal tonsils, early cancers, and advanced tonsil cancers, SD and entropy showed significantly higher values on all filters (p<0.001) between early cancers and normal tonsils. The AUC from the ROC analysis was 0.91, obtained from the entropy. A mild correlation was shown between texture parameters and metabolic parameters. The texture analysis parameters, especially entropy, showed significant differences in contrast-enhanced CT results between tumor and normal tonsils, and between early tonsil cancers and normal tonsils. Texture analysis can be useful as an adjunctive tool for the diagnosis of tonsil cancers.
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Project description:PurposeHigh-resolution three-dimensional (3D) structural MRI is useful for delineating complex or small structures of the body. However, it requires long acquisition times and high SAR, limiting its clinical use. The purpose of this work is to accelerate the acquisition of high-resolution images by combining compressed sensing and parallel imaging (CSPI) on a 3D-GRASE sequence and to compare it with a (CS)PI 3D-FSE sequence. Several sampling patterns were investigated to assess their influence on image quality.MethodsThe proposed k-space sampling patterns are based on two undersampled k-space grids, variable density (VD) Poisson-disc, and VD pseudo-random Gaussian, and five different trajectories described in the literature. Bloch simulations are performed to obtain the transform point spread function and evaluate the coherence of each sampling pattern. Image resolution was assessed by the full-width at half-maximum (FWHM). Prospective CSPI 3D-GRASE phantom and in vivo experiments in knee and brain are carried out to assess image quality, SNR, SAR, and acquisition time compared to PI 3D-GRASE, PI 3D-FSE, and CSPI 3D-FSE acquisitions.ResultsSampling patterns with VD Poisson-disc obtain the lowest coherence for both PD-weighted and T2 -weighted acquisitions. VD pseudo-random Gaussian obtains lower FWHM, but higher sidelobes than VD Poisson-disc. CSPI 3D-GRASE reduces acquisition time (43% for PD-weighted and 40% for T2 -weighted) and SAR (∼45% for PD-weighted and T2 -weighted) compared to CSPI 3D-FSE.ConclusionsCSPI 3D-GRASE reduces acquisition time compared to a CSPI 3DFSE acquisition, preserving image quality. The design of the sampling pattern is crucial for image quality in CSPI 3D-GRASE image acquisitions.
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Project description:Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality high-resolution 3D models is still challenging with existing methods. Hence, we designed a hierarchical algorithm, called Hierarchical3DGenome, to reconstruct 3D chromosome models at high resolution (<=5 Kilobase (KB)). The algorithm first reconstructs high-resolution 3D models at TAD level. The TAD models are then assembled to form complete high-resolution chromosomal models. The assembly of TAD models is guided by a complete low-resolution chromosome model. The algorithm is successfully used to reconstruct 3D chromosome models at 5 KB resolution for the human B-cell (GM12878). These high-resolution models satisfy Hi-C chromosomal contacts well and are consistent with models built at lower (i.e. 1 MB) resolution, and with the data of fluorescent in situ hybridization experiments. The Java source code of Hierarchical3DGenome and its user manual are available here https://github.com/BDM-Lab/Hierarchical3DGenome .
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Project description:ObjectiveTo demonstrate lateral pharyngeal wall collapse and increased apnea-hypopnea index in a child posttonsillectomy.BackgroundSome children have worsening of their sleep symptoms after tonsillectomy for obstructive sleep apnea. This case report demonstrates an open airway on drug-induced sleep endoscopy (DISE) in a child with tonsillar hypertrophy followed by more pronounced airway obstruction related to lateral pharyngeal wall collapse after tonsillectomy.Case presentationA 7-year-old boy presented with obstructive sleep apnea and underwent workup with DISE. Following adenotonsillectomy and subsequent lingual tonsillectomy with epiglottopexy, the patient's sleep apnea symptoms and polysomnogram results worsened. Subsequent DISE showed a more narrowed oropharyngeal airway space as compared to his preoperative DISE.DiscussionPalatine tonsillar tissue may splint open the airway and prevent airway obstruction in a subset of pediatric patients. Further clinical studies are necessary to determine which children experience this phenomenon. Clinical examination using DISE can be useful in making clinical decisions prior to tonsillectomy.
| S-EPMC6311753 | biostudies-literature
Project description:BackgroundMicrobial flora in several organs of HIV-infected individuals have been characterized; however, the palatine tonsil bacteriome and mycobiome and their relationship with each other remain unclear. Determining the palatine tonsil microbiome may provide a better understanding of the pathogenesis of oral and systemic complications in HIV-infected individuals. We conducted a cross-sectional study to characterize the palatine tonsil microbiome in HIV-infected individuals.ResultsPalatine tonsillar swabs were collected from 46 HIV-infected and 20 HIV-uninfected individuals. The bacteriome and mycobiome were analyzed by amplicon sequencing using Illumina MiSeq. The palatine tonsil bacteriome of the HIV-infected individuals differed from that of HIV-uninfected individuals in terms of the decreased relative abundances of the commensal genera Neisseria and Haemophilus. At the species level, the relative abundances and presence of Capnocytophaga ochracea, Neisseria cinerea, and Selenomonas noxia were higher in the HIV-infected group than those in the HIV-uninfected group. In contrast, fungal diversity and composition did not differ significantly between the two groups. Microbial intercorrelation analysis revealed that Candida and Neisseria were negatively correlated with each other in the HIV-infected group. HIV immune status did not influence the palatine tonsil microbiome in the HIV-infected individuals.ConclusionsHIV-infected individuals exhibit dysbiotic changes in their palatine tonsil bacteriome, independent of immunological status.
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Project description:The use of MRI for prostate cancer diagnosis and treatment is increasing rapidly. However, identifying the presence and extent of cancer on MRI remains challenging, leading to high variability in detection even among expert radiologists. Improvement in cancer detection on MRI is essential to reducing this variability and maximizing the clinical utility of MRI. To date, such improvement has been limited by the lack of accurately labeled MRI datasets. Data from patients who underwent radical prostatectomy enables the spatial alignment of digitized histopathology images of the resected prostate with corresponding pre-surgical MRI. This alignment facilitates the delineation of detailed cancer labels on MRI via the projection of cancer from histopathology images onto MRI. We introduce a framework that performs 3D registration of whole-mount histopathology images to pre-surgical MRI in three steps. First, we developed a novel multi-image super-resolution generative adversarial network (miSRGAN), which learns information useful for 3D registration by producing a reconstructed 3D MRI. Second, we trained the network to learn information between histopathology slices to facilitate the application of 3D registration methods. Third, we registered the reconstructed 3D histopathology volumes to the reconstructed 3D MRI, mapping the extent of cancer from histopathology images onto MRI without the need for slice-to-slice correspondence. When compared to interpolation methods, our super-resolution reconstruction resulted in the highest PSNR relative to clinical 3D MRI (32.15 dB vs 30.16 dB for BSpline interpolation). Moreover, the registration of 3D volumes reconstructed via super-resolution for both MRI and histopathology images showed the best alignment of cancer regions when compared to (1) the state-of-the-art RAPSODI approach, (2) volumes that were not reconstructed, or (3) volumes that were reconstructed using nearest neighbor, linear, or BSpline interpolations. The improved 3D alignment of histopathology images and MRI facilitates the projection of accurate cancer labels on MRI, allowing for the development of improved MRI interpretation schemes and machine learning models to automatically detect cancer on MRI.
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Project description:Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iterates between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.
| S-EPMC5585178 | biostudies-literature