11 research outputs found
Inhibition of Cardiac RIP3 Mitigates Early Reperfusion Injury and Calcium-Induced Mitochondrial Swelling without Altering Necroptotic Signalling
Receptor-interacting protein kinase 3 (RIP3) is a convergence point of multiple signalling pathways, including necroptosis, inflammation and oxidative stress; however, it is completely unknown whether it underlies acute myocardial ischemia/reperfusion (I/R) injury. Langendorff-perfused rat hearts subjected to 30 min ischemia followed by 10 min reperfusion exhibited compromised cardiac function which was not abrogated by pharmacological intervention of RIP3 inhibition. An immunoblotting analysis revealed that the detrimental effects of I/R were unlikely mediated by necroptotic cell death, since neither the canonical RIP3–MLKL pathway (mixed lineage kinase-like pseudokinase) nor the proposed non-canonical molecular axes involving CaMKIIδ–mPTP (calcium/calmodulin-dependent protein kinase IIδ–mitochondrial permeability transition pore), PGAM5–Drp1 (phosphoglycerate mutase 5–dynamin-related protein 1) and JNK–BNIP3 (c-Jun N-terminal kinase–BCL2-interacting protein 3) were activated. Similarly, we found no evidence of the involvement of NLRP3 inflammasome signalling (NOD-, LRR- and pyrin domain-containing protein 3) in such injury. RIP3 inhibition prevented the plasma membrane rupture and delayed mPTP opening which was associated with the modulation of xanthin oxidase (XO) and manganese superoxide dismutase (MnSOD). Taken together, this is the first study indicating that RIP3 regulates early reperfusion injury via oxidative stress- and mitochondrial activity-related effects, rather than cell loss due to necroptosis
METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy
Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research. Yet, a massive lack of annotations prevents the broad use of deep learning to analyze such data. So far, existing generative models fail to mitigate this problem because of frequent labeling errors. In this paper, we introduce a novel generative method which leverages real anatomical information to generate realistic image-label pairs of tumours. We construct a dual-pathway generator, for the anatomical image and label, trained in a cycle-consistent setup, constrained by an independent, pretrained segmentor. The generated images yield significant quantitative improvement compared to existing methods. To validate the quality of synthesis, we train segmentation networks on a dataset augmented with the synthetic data, substantially improving the segmentation over baseline
Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging
Novel methods for quantitative, transient-state multiparametric imaging are
increasingly being demonstrated for assessment of disease and treatment
efficacy. Here, we build on these by assessing the most common Non-Cartesian
readout trajectories (2D/3D radials and spirals), demonstrating efficient
anti-aliasing with a k-space view-sharing technique, and proposing novel
methods for parameter inference with neural networks that incorporate the
estimation of proton density. Our results show good agreement with gold
standard and phantom references for all readout trajectories at 1.5T and 3T.
Parameters inferred with the neural network were within 6.58% difference from
the parameters inferred with a high-resolution dictionary. Concordance
correlation coefficients were above 0.92 and the normalized root mean squared
error ranged between 4.2% - 12.7% with respect to gold-standard phantom
references for T1 and T2. In vivo acquisitions demonstrate sub-millimetric
isotropic resolution in under five minutes with reconstruction and inference
times < 7 minutes. Our 3D quantitative transient-state imaging approach could
enable high-resolution multiparametric tissue quantification within clinically
acceptable acquisition and reconstruction times.Comment: 43 pages, 12 Figures, 5 Table
Whole-body cellular mapping in mouse using standard IgG antibodies
Whole-body imaging techniques play a vital role in exploring the interplay of physiological systems in maintaining health and driving disease. We introduce wildDISCO, a new approach for whole-body immunolabeling, optical clearing and imaging in mice, circumventing the need for transgenic reporter animals or nanobody labeling and so overcoming existing technical limitations. We identified heptakis(2,6-di-O-methyl)-beta-cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep, homogeneous penetration of standard antibodies without aggregation. WildDISCO facilitates imaging of peripheral nervous systems, lymphatic vessels and immune cells in whole mice at cellular resolution by labeling diverse endogenous proteins. Additionally, we examined rare proliferating cells and the effects of biological perturbations, as demonstrated in germ-free mice. We applied wildDISCO to map tertiary lymphoid structures in the context of breast cancer, considering both primary tumor and metastases throughout the mouse body. An atlas of high-resolution images showcasing mouse nervous, lymphatic and vascular systems is accessible at
blob loss: instance imbalance aware loss functions for semantic segmentation
Deep convolutional neural networks have proven to be remarkably effective in
semantic segmentation tasks. Most popular loss functions were introduced
targeting improved volumetric scores, such as the Sorensen Dice coefficient. By
design, DSC can tackle class imbalance; however, it does not recognize instance
imbalance within a class. As a result, a large foreground instance can dominate
minor instances and still produce a satisfactory Sorensen Dice coefficient.
Nevertheless, missing out on instances will lead to poor detection performance.
This represents a critical issue in applications such as disease progression
monitoring. For example, it is imperative to locate and surveil small-scale
lesions in the follow-up of multiple sclerosis patients. We propose a novel
family of loss functions, nicknamed blob loss, primarily aimed at maximizing
instance-level detection metrics, such as F1 score and sensitivity. Blob loss
is designed for semantic segmentation problems in which the instances are the
connected components within a class. We extensively evaluate a DSC-based blob
loss in five complex 3D semantic segmentation tasks featuring pronounced
instance heterogeneity in terms of texture and morphology. Compared to soft
Dice loss, we achieve 5 percent improvement for MS lesions, 3 percent
improvement for liver tumor, and an average 2 percent improvement for
Microscopy segmentation tasks considering F1 score.Comment: 23 pages, 7 figures // corrected one mistake where it said beta
instead of alpha in the tex
Deciphering sources of PET signals in the tumor microenvironment of glioblastoma at cellular resolution
Various cellular sources hamper interpretation of positron emission tomography (PET) biomarkers in the tumor microenvironment (TME). We developed an approach of immunomagnetic cell sorting after in vivo radiotracer injection (scRadiotracing) with three-dimensional (3D) histology to dissect the cellular allocation of PET signals in the TME. In mice with implanted glioblastoma, translocator protein (TSPO) radiotracer uptake per tumor cell was higher compared to tumor-associated microglia/macrophages (TAMs), validated by protein levels. Translation of in vitro scRadiotracing to patients with glioma immediately after tumor resection confirmed higher single-cell TSPO tracer uptake of tumor cells compared to immune cells. Across species, cellular radiotracer uptake explained the heterogeneity of individual TSPO-PET signals. In consideration of cellular tracer uptake and cell type abundance, tumor cells were the main contributor to TSPO enrichment in glioblastoma;however, proteomics identified potential PET targets highly specific for TAMs. Combining cellular tracer uptake measures with 3D histology facilitates precise allocation of PET signals and serves to validate emerging novel TAM-specific radioligands
Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging
Novel methods for quantitative, transient-state multiparametric imaging are increasingly being demonstrated for assessment of disease and treatment efficacy. Here, we build on these by assessing the most common Non-Cartesian readout trajectories (2D/3D radials and spirals), demonstrating efficient anti-aliasing with a k-space view-sharing technique, and proposing novel methods for parameter inference with neural networks that incorporate the estimation of proton density. Our results show good agreement with gold standard and phantom references for all readout trajectories at 1.5 T and 3 T. Parameters inferred with the neural network were within 6.58% difference from the parameters inferred with a high-resolution dictionary. Concordance correlation coefficients were above 0.92 and the normalized root mean squared error ranged between 4.2 and 12.7% with respect to gold-standard phantom references for T1 and T2. In vivo acquisitions demonstrate sub-millimetric isotropic resolution in under five minutes with reconstruction and inference times < 7 min. Our 3D quantitative transient-state imaging approach could enable high-resolution multiparametric tissue quantification within clinically acceptable acquisition and reconstruction times
Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings
Human ratings are abstract representations of segmentation quality. To
approximate human quality ratings on scarce expert data, we train surrogate
quality estimation models. We evaluate on a complex multi-class segmentation
problem, specifically glioma segmentation following the BraTS annotation
protocol. The training data features quality ratings from 15 expert
neuroradiologists on a scale ranging from 1 to 6 stars for various
computer-generated and manual 3D annotations. Even though the networks operate
on 2D images and with scarce training data, we can approximate segmentation
quality within a margin of error comparable to human intra-rater reliability.
Segmentation quality prediction has broad applications. While an understanding
of segmentation quality is imperative for successful clinical translation of
automatic segmentation quality algorithms, it can play an essential role in
training new segmentation models. Due to the split-second inference times, it
can be directly applied within a loss function or as a fully-automatic dataset
curation mechanism in a federated learning setting.Comment: 11 pages, 5 figure