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Relating brain activity associated with a complex stimulus to different properties of that stimulus is a powerful approach for constructing functional brain maps. However, when stimuli are naturalistic, their properties are often correlated (e.g., visual and semantic features of natural images, or different layers of a convolutional neural network that are used as features of images). Correlated properties can act as confounders for each other and complicate the interpretability of brain maps, and can impact the robustness of statistical estimators. Here, we present an approach for brain mapping based on two proposed methods: stacking different encoding models and structured variance partitioning. Our stacking algorithm combines encoding models that each uses as input a feature space that describes a different stimulus attribute. The algorithm learns to predict the activity of a voxel as a linear combination of the outputs of different encoding models. We show that the resulting combined model can predict held-out brain activity better or at least as well as the individual encoding models. Further, the weights of the linear combination are readily interpretable; they show the importance of each feature space for predicting a voxel. We then build on our stacking models to introduce structured variance partitioning, a new type of variance partitioning that takes into account the known relationships between features. Our approach constrains the size of the hypothesis space and allows us to ask targeted questions about the similarity between feature spaces and brain regions even in the presence of correlations between the feature spaces. We validate our approach in simulation, showcase its brain mapping potential on fMRI data, and release a Python package. Our methods can be useful for researchers interested in aligning brain activity with different layers of a neural network, or with other types of correlated feature spaces. [Display omitted] •Naturalistic stimuli have correlated features that can lead to confounding.•Our first method estimates encoding models reliably using multiple feature spaces.•Our second method factors in feature dependence to create interpretable brain maps.•We test our approach in simulation and using a large-scale fMRI dataset.•We provide a GitHub repository: https://github.com/brainML/Stacking.

Background Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal-to-noise ratio (SNR), large volume and high content complexity within cells, it remains difficult and time-consuming to localize and identify different components in cellular cryo-ET. To automatically localize and recognize in situ cellular structures of interest captured by cryo-ET, we proposed a simple yet effective automatic image analysis approach based on Faster-RCNN. Results Our experimental results were validated using in situ cyro-ET-imaged mitochondria data. Our experimental results show that our algorithm can accurately localize and identify important cellular structures on both the 2D tilt images and the reconstructed 2D slices of cryo-ET. When ran on the mitochondria cryo-ET dataset, our algorithm achieved Average Precision >0.95. Moreover, our study demonstrated that our customized pre-processing steps can further improve the robustness of our model performance. Conclusions In this paper, we proposed an automatic Cryo-ET image analysis algorithm for localization and identification of different structure of interest in cells, which is the first Faster-RCNN based method for localizing an cellular organelle in Cryo-ET images and demonstrated the high accuracy and robustness of detection and classification tasks of intracellular mitochondria. Furthermore, our approach can be easily applied to detection tasks of other cellular structures as well.

Visual cortex contains regions of selectivity for domains of ecological importance. Food is an evolutionarily critical category whose visual heterogeneity may make the identification of selectivity more challenging. We investigate neural responsiveness to food using natural images combined with large-scale human fMRI. Leveraging the improved sensitivity of modern designs and statistical analyses, we identify two food-selective regions in the ventral visual cortex. Our results are robust across 8 subjects from the Natural Scenes Dataset (NSD), multiple independent image sets and multiple analysis methods. We then test our findings of food selectivity in an fMRI “localizer” using grayscale food images. These independent results confirm the existence of food selectivity in ventral visual cortex and help illuminate why earlier studies may have failed to do so. Our identification of food-selective regions stands alongside prior findings of functional selectivity and adds to our understanding of the organization of knowledge within the human visual system. Neural responsiveness to food images was measured in healthy participants using fMRI, establishing food-selective regions using both data- and hypothesis-driven methods. Further analyses illuminate the organization of food within the visual system.

Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular Electron Cryo-Tomography (CECT) 3D imaging technology, it is now possible for researchers to gain accesses to fully study and understand the macromolecular structures single cells. However, systematic recovery of macromolecular structures from CECT is very difficult due to high degree of structural complexity and practical imaging limitations. Specifically, we proposed a deep learning-based image classification approach for large-scale systematic macromolecular structure separation from CECT data. However, our previous work was only a very initial step toward exploration of the full potential of deep learning-based macromolecule separation. In this paper, we focus on improving classification performance by proposing three newly designed individual CNN models: an extended version of (Deep Small Receptive Field) DSRF3D, donated as DSRF3D-v2, a 3D residual block-based neural network, named as RB3D, and a convolutional 3D (C3D)-based model, CB3D. We compare them with our previously developed model (DSRF3D) on 12 datasets with different SNRs and tilt angle ranges. The experiments show that our new models achieved significantly higher classification accuracies. The accuracies are not only higher than 0.9 on normal datasets, but also demonstrate potentials to operate on datasets with high levels of noises and missing wedge effects presented.

Relating brain activity associated with a complex stimulus to different properties of that stimulus is a powerful approach for constructing functional brain maps. However, when stimuli are naturalistic, their properties are often correlated (e.g., visual and semantic features of natural images, or different layers of a convolutional neural network that are used as features of images). Correlated properties can act as confounders for each other and complicate the interpretability of brain maps, and can impact the robustness of statistical estimators. Here, we present an approach for brain mapping based on two proposed methods: different encoding models and . Our stacking algorithm combines encoding models that each use as input a feature space that describes a different stimulus attribute. The algorithm learns to predict the activity of a voxel as a linear combination of the outputs of different encoding models. We show that the resulting combined model can predict held-out brain activity better or at least as well as the individual encoding models. Further, the weights of the linear combination are readily interpretable; they show the importance of each feature space for predicting a voxel. We then build on our stacking models to introduce structured variance partitioning, a new type of variance partitioning that takes into account the known relationships between features. Our approach constrains the size of the hypothesis space and allows us to ask targeted questions about the similarity between feature spaces and brain regions even in the presence of correlations between the feature spaces. We validate our approach in simulation, showcase its brain mapping potential on fMRI data, and release a Python package. Our methods can be useful for researchers interested in aligning brain activity with different layers of a neural network, or with other types of correlated feature spaces.

Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular electron cryo tomography (CECT) 3D imaging technology, it is now possible for researchers to gain accesses to fully study and understand the macromolecular structures single cells. However, systematic recovery of macromolecular structures from CECT is very difficult due to high degree of structural complexity and practical imaging limitations. Specifically, we proposed a deep learning based image classification approach for large-scale systematic macromolecular structure separation from CECT data. However, our previous work was only a very initial step towards exploration of the full potential of deep learning based macromolecule separation. In this paper, we focus on improving classification performance by proposing three newly designed individual CNN models: an extended version of (Deep Small Receptive Field) DSRF3D, donated as DSRF3D-v2, a 3D residual block based neural network, named as RB3D and a convolutional 3D(C3D) based model, CB3D. We compare them with our previously developed model (DSRF3D) on 12 datasets with different SNRs and tilt angle ranges. The experiments show that our new models achieved significantly higher classification accuracies. The accuracies are not only higher than 0.9 on normal datasets, but also demonstrate potentials to operate on datasets with high levels of noises and missing wedge effects presented.

Ventral visual cortex contains regions of selectivity for domains of ecological importance. Food is an ecologically and evolutionarily important category whose high degree of visual variability may make the identification of selectivity more challenging. First, we investigated neural responsiveness to food using natural images combined with large-scale human fMRI. Leveraging the improved sensitivity of modern designs and statistical analysis methods, we identify two food-selective regions in the ventral visual cortex. Our results were robust across 8 subjects from the Natural Scenes Dataset (NSD), multiple independent sets of images and multiple analysis methods. Second, we tested our findings regarding visual food selectivity by designing and running an fMRI ''localizer'' experiment that included grayscale food images. Our independent localizer results confirm the existence of food selectivity in human ventral visual cortex and help illuminate why earlier studies may have failed to do so. The identification of food-selective regions stands alongside prior findings of functional selectivity and provides an important addition to our understanding of the organization of knowledge within the human visual system.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Add additional analyses and refer to repo.* https://github.com/brainML/food4thought

In this paper, we propose a new correlated and individual multi-modal deep learning (CIMDL) method for RGB-D object recognition. Unlike most conventional RGB-D object recognition methods which extract features from the RGB and depth channels individually, our CIMDL jointly learns feature representations from raw RGB-D data with a pair of deep neural networks, so that the sharable and modal-specific information can be simultaneously exploited. Specifically, we construct a pair of deep convolutional neural networks (CNNs) for the RGB and depth data, and concatenate them at the top layer of the network with a loss function which learns a new feature space where both correlated part and the individual part of the RGB-D information are well modelled. The parameters of the whole networks are updated by using the back-propagation criterion. Experimental results on two widely used RGB-D object image benchmark datasets clearly show that our method outperforms state-of-the-arts.

Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and their spatial organization inside single cells. However, due to the high degree of structural complexity and practical imaging limitations, systematic macromolecular structural recovery inside CECT images remains challenging. Particularly, the recovery of a macromolecule is likely to be biased by its neighbor structures due to the high molecular crowding. To reduce the bias, here we introduce a novel 3D convolutional neural network inspired by Fully Convolutional Network and Encoder-Decoder Architecture for the supervised segmentation of macromolecules of interest in subtomograms. The tests of our models on realistically simulated CECT data demonstrate that our new approach has significantly improved segmentation performance compared to our baseline approach. Also, we demonstrate that the proposed model has generalization ability to segment new structures that do not exist in training data.

Background and Purpose: In clinical application of dental implants, the functional state of dendritic cells (DCs) has been suggested to have a close relationship with the implant survival rate or speed of osseointegration. Although microscale surfaces have a stable osteogenesis property, they also incline to trigger unfavorable DCs activation and threaten the osseointegration process. Nanoscale structures have an advantage in regulating cell immune response through orchestrating cell adhesion, indicating the potential of hierarchical micro/nanostructured surface in regulation of DCs’ activation without sacrificing the advantage of microscale topography. Materials and Methods: Two micro/nanostructures were fabricated based on microscale rough surfaces through anodization or alkali treatment, the sand-blasted and acid-etched (SA) surface served as control. The surface characteristics, in vitro and in vivo DC immune reactions and β 2 integrin-FAK signal expression were systematically investigated. The DC responses to different surface topographies after FAK inhibition were also tested. Results: Both micro/nano-modified surfaces exhibited unique composite structures, with higher hydrophilicity and lower roughness compared to the SA surface. The DCs showed relatively immature functional states with round morphologies and significantly downregulated β 2 integrin-FAK levels on micro/nanostructures. Implant surfaces with micro/nano-topographies also triggered lower levels of DC inflammatory responses than SA surfaces in vivo. The inhibited FAK activation effectively reduced the differences in topography-caused DC activation and narrowed the differences in DC activation among the three groups. Conclusion: Compared to the SA surface with solely micro-scale topography, titanium surfaces with hybrid micro/nano-topographies reduced DC inflammatory response by influencing their adhesion states. This regulatory effect was accompanied by the modulation of β 2 integrin-FAK signal expression. The β 2 integrin-FAK-mediated adhesion plays a critical role in topography-induced DC activation, which represents a potential target for material–cell interaction regulation. Graphical Abstract: