100 research outputs found
An Efficient Cervical Whole Slide Image Analysis Framework Based on Multi-scale Semantic and Spatial Deep Features
Digital gigapixel whole slide image (WSI) is widely used in clinical
diagnosis, and automated WSI analysis is key for computer-aided diagnosis.
Currently, analyzing the integrated descriptor of probabilities or feature maps
from massive local patches encoded by ResNet classifier is the main manner for
WSI-level prediction. Feature representations of the sparse and tiny lesion
cells in cervical slides, however, are still challengeable for the
under-promoted upstream encoders, while the unused spatial representations of
cervical cells are the available features to supply the semantics analysis. As
well as patches sampling with overlap and repetitive processing incur the
inefficiency and the unpredictable side effect. This study designs a novel
inline connection network (InCNet) by enriching the multi-scale connectivity to
build the lightweight model named You Only Look Cytopathology Once (YOLCO) with
the additional supervision of spatial information. The proposed model allows
the input size enlarged to megapixel that can stitch the WSI without any
overlap by the average repeats decreased from to
for collecting features and predictions at two scales. Based on Transformer for
classifying the integrated multi-scale multi-task features, the experimental
results appear AUC score better and faster than the best
conventional method in WSI classification on multicohort datasets of 2,019
slides from four scanning devices.Comment: 16 pages, 8 figures, already submitted to Medical Image Analysi
Detection of MMP activity in living cells by a genetically encoded surface-displayed FRET sensor
AbstractMatrix metalloproteinases (MMPs) are secretory endopeptidases. They have been associated with invasion by cancer-cell and metastasis. Previous studies have demonstrated that proteolytic activity could be detected using fluorescence resonance energy transfer (FRET) with mutants of GFP. To monitor MMP activity, we constructed vectors that encoded a MMP Substrate Site (MSS) between YFP and CFP. In vitro, YFPâMSSâCFP can be used to detect MMP activity and 1,10-phenathroline inhibition of MMP activity. In living cells, MMPs are secreted proteins and act outside of the cell, and therefore YFPâMSSâCFPdisplay was anchored on the cellular surface to detect extracellular MMP. A pDisplay-YC vector expressing the YFPâMSSâCFPdisplay on the cellular surface was transfected into MCF-7 cells that expressed low levels of MMP. Efficient transfer of energy from excited CFP to YFP within the YFPâMSSâCFPdisplay molecule was observed, and real-time FRET was declined when MCF-7 was incubated with MMP2. However, no such transfer of energy was detected in the YFPâMSSâCFPdisplay expressing MDA-MB 435s cells, in which high secretory MMP2 were expressed. The FRET sensor YFPâMSSâCFPdisplay can sensitively and reliably monitor MMP activation in living cells and can be used for high-throughput screening of MMP inhibitors for anti-cancer treatments
Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions
To better understand the dynamic regulation of optimality in metabolic networks under perturbed conditions, we reconstruct the energetic-metabolic network in mammalian myocardia using dynamic flux balance analysis (DFBA). Additionally, we modified the optimal objective from the maximization of ATP production to the minimal fluctuation of the profile of metabolite concentration under ischemic conditions, extending the hypothesis of original minimization of metabolic adjustment to create a composite modeling approach called M-DFBA. The simulation results are more consistent with experimental data than are those of the DFBA model, particularly the retentive predominant contribution of fatty acid to oxidative ATP synthesis, the exact mechanism of which has not been elucidated and seems to be unpredictable by the DFBA model. These results suggest that the systemic states of metabolic networks do not always remain optimal, but may become suboptimal when a transient perturbation occurs. This finding supports the relevance of our hypothesis and could contribute to the further exploration of the underlying mechanism of dynamic regulation in metabolic networks
Optimization of Traced Neuron Skeleton Using Lasso-Based Model
Reconstruction of neuronal morphology from images involves mainly the extraction of neuronal skeleton points. It is an indispensable step in the quantitative analysis of neurons. Due to the complex morphology of neurons, many widely used tracing methods have difficulties in accurately acquiring skeleton points near branch points or in structures with tortuosity. Here, we propose two models to solve these problems. One is based on an L1-norm minimization model, which can better identify tortuous structure, namely, a local structure with large curvature skeleton points; the other detects an optimized branch point by considering the combination patterns of all neurites that link to this point. We combined these two models to achieve optimized skeleton detection for a neuron. We validate our models in various datasets including MOST and BigNeuron. In addition, we demonstrate that our method can optimize the traced skeletons from large-scale images. These characteristics of our approach indicate that it can reduce manual editing of traced skeletons and help to accelerate the accurate reconstruction of neuronal morphology
DeepBouton: Automated Identification of Single-Neuron Axonal Boutons at the Brain-Wide Scale
Fine morphological reconstruction of individual neurons across the entire brain is essential for mapping brain circuits. Inference of presynaptic axonal boutons, as a key part of single-neuron fine reconstruction, is critical for interpreting the patterns of neural circuit wiring schemes. However, automated bouton identification remains challenging for current neuron reconstruction tools, as they focus mainly on neurite skeleton drawing and have difficulties accurately quantifying bouton morphology. Here, we developed an automated method for recognizing single-neuron axonal boutons in whole-brain fluorescence microscopy datasets. The method is based on deep convolutional neural networks and density-peak clustering. High-dimensional feature representations of bouton morphology can be learned adaptively through convolutional networks and used for bouton recognition and subtype classification. We demonstrate that the approach is effective for detecting single-neuron boutons at the brain-wide scale for both long-range pyramidal projection neurons and local interneurons
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations
Brain circuits comprise vast numbers of interconnected neurons with diverse molecular, anatomical and physiological properties. To allow targeting of individual neurons for structural and functional studies, we created light-inducible site-specific DNA recombinases based on Cre, Dre and Flp (RecVs). RecVs can induce genomic modifications by one-photon or two-photon light induction in vivo. They can produce targeted, sparse and strong labeling of individual neurons by modifying multiple loci within mouse and zebrafish genomes. In combination with other genetic strategies, they allow intersectional targeting of different neuronal classes. In the mouse cortex they enable sparse labeling and whole-brain morphological reconstructions of individual neurons. Furthermore, these enzymes allow single-cell two-photon targeted genetic modifications and can be used in combination with functional optical indicators with minimal interference. In summary, RecVs enable spatiotemporally precise optogenomic modifications that can facilitate detailed single-cell analysis of neural circuits by linking genetic identity, morphology, connectivity and function
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations
Brain circuits comprise vast numbers of interconnected neurons with diverse molecular, anatomical and physiological properties. To allow targeting of individual neurons for structural and functional studies, we created light-inducible site-specific DNA recombinases based on Cre, Dre and Flp (RecVs). RecVs can induce genomic modifications by one-photon or two-photon light induction in vivo. They can produce targeted, sparse and strong labeling of individual neurons by modifying multiple loci within mouse and zebrafish genomes. In combination with other genetic strategies, they allow intersectional targeting of different neuronal classes. In the mouse cortex they enable sparse labeling and whole-brain morphological reconstructions of individual neurons. Furthermore, these enzymes allow single-cell two-photon targeted genetic modifications and can be used in combination with functional optical indicators with minimal interference. In summary, RecVs enable spatiotemporally precise optogenomic modifications that can facilitate detailed single-cell analysis of neural circuits by linking genetic identity, morphology, connectivity and function
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