Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the ...Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.
•A novel conditional GAN for synthesizing realistic histopathology images.•Selective synthetic data augmentation with model and image selection.•Extensive experiments show superior results on two ...histopathology image datasets.•Proposed method can be adapted to other histopathology image analysis tasks.
Histopathological analysis is the present gold standard for precancerous lesion diagnosis. The goal of automated histopathological classification from digital images requires supervised training, which requires a large number of expert annotations that can be expensive and time-consuming to collect. Meanwhile, accurate classification of image patches cropped from whole-slide images is essential for standard sliding window based histopathology slide classification methods. To mitigate these issues, we propose a carefully designed conditional GAN model, namely HistoGAN, for synthesizing realistic histopathology image patches conditioned on class labels. We also investigate a novel synthetic augmentation framework that selectively adds new synthetic image patches generated by our proposed HistoGAN, rather than expanding directly the training set with synthetic images. By selecting synthetic images based on the confidence of their assigned labels and their feature similarity to real labeled images, our framework provides quality assurance to synthetic augmentation. Our models are evaluated on two datasets: a cervical histopathology image dataset with limited annotations, and another dataset of lymph node histopathology images with metastatic cancer. Here, we show that leveraging HistoGAN generated images with selective augmentation results in significant and consistent improvements of classification performance (6.7% and 2.8% higher accuracy, respectively) for cervical histopathology and metastatic cancer datasets.
Oxytocin (Oxt) neurons regulate diverse physiological responses via direct connections with different neural circuits. However, the lack of comprehensive input-output wiring diagrams of Oxt neurons ...and their quantitative relationship with Oxt receptor (Oxtr) expression presents challenges to understanding circuit-specific Oxt functions. Here, we establish a whole-brain distribution and anatomic connectivity map of Oxt neurons, and their relationship with Oxtr expression using high-resolution 3D mapping methods in adult male and female mice. We use a flatmap to describe Oxt neuronal expression in four hypothalamic domains including under-characterized Oxt neurons in the tuberal nucleus (TU). Oxt neurons in the paraventricular hypothalamus (PVH) broadly project to nine functional circuits that control cognition, brain state, and somatic visceral response. In contrast, Oxt neurons in the supraoptic (SO) and accessory (AN) nuclei have limited central projection to a small subset of the nine circuits. Surprisingly, quantitative comparison between Oxt output and Oxtr expression showed no significant correlation across the whole brain, suggesting abundant indirect Oxt signaling in Oxtr-expressing areas. Unlike output, Oxt neurons in both the PVH and SO receive similar monosynaptic inputs from a subset of the nine circuits mainly in the thalamic, hypothalamic, and cerebral nuclei areas. Our results suggest that PVH-Oxt neurons serve as a central modulator to integrate external and internal information via largely reciprocal connection with the nine circuits while the SO-Oxt neurons act mainly as unidirectional Oxt hormonal output. In summary, our Oxt wiring diagram provides anatomic insights about distinct behavioral functions of Oxt signaling in the brain.
Oxytocin (Oxt) neurons regulate diverse physiological functions from prosocial behavior to pain sensation via central projection in the brain. Thus, understanding detailed anatomic connectivity of Oxt neurons can provide insight on circuit-specific roles of Oxt signaling in regulating different physiological functions. Here, we use high-resolution mapping methods to describe the 3D distribution, monosynaptic input and long-range output of Oxt neurons, and their relationship with Oxt receptor (Oxtr) expression across the entire mouse brain. We found Oxt connections with nine functional circuits controlling cognition, brain state, and somatic visceral response. Furthermore, we identified a quantitatively unmatched Oxt-Oxtr relationship, suggesting broad indirect Oxt signaling. Together, our comprehensive Oxt wiring diagram advances our understanding of circuit-specific roles of Oxt neurons.
The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species
. However, studies in ...zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how ...synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
Decreased growth hormone (GH) and thyroid hormone (TH) signaling are associated with longevity and metabolic fitness. The mechanisms underlying these benefits are poorly understood, but may overlap ...with those of dietary restriction (DR), which imparts similar benefits. Recently we discovered that hydrogen sulfide (H2S) is increased upon DR and plays an essential role in mediating DR benefits across evolutionary boundaries. Here we found increased hepatic H2S production in long-lived mouse strains of reduced GH and/or TH action, and in a cell-autonomous manner upon serum withdrawal in vitro. Negative regulation of hepatic H2S production by GH and TH was additive and occurred via distinct mechanisms, namely direct transcriptional repression of the H2S-producing enzyme cystathionine γ-lyase (CGL) by TH, and substrate-level control of H2S production by GH. Mice lacking CGL failed to downregulate systemic T4 metabolism and circulating IGF-1, revealing an essential role for H2S in the regulation of key longevity-associated hormones.
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•Hepatic H2S production capacity is elevated in long-lived hypopituitary mouse models•Growth hormone (GH) represses hepatic H2S production post-transcriptionally•Thyroid hormone (TH) acts via TRβ to repress cystathionine γ-lyase and H2S levels•H2S negatively regulates circulating TH and IGF-1 levels
Reduced thyroid hormone (TH) and growth hormone (GH) activity are hallmarks of genetic models of longevity in mice. Here, Hine et al. find that TH and GH negatively regulate hepatic production of the longevity-associated gas hydrogen sulfide, which feeds back to negatively regulate circulating TH and IGF-1 levels.
Background The prevalence of chronic kidney disease (CKD) is increasing in the United States, caused in part by older age and increasing prevalences of hypertension and type 2 diabetes. CKD is silent ...and undetected until advanced stages. The study of populations with earlier stages of kidney disease may improve outcomes of CKD. Methods The Kidney Early Evaluation Program (KEEP), a National Kidney Foundation program, is a targeted community-based health-screening program enrolling individuals 18 years and older with diabetes, hypertension, or family history of kidney disease, diabetes, or hypertension. Participants who had received transplants or were on regular dialysis treatment were excluded from this analysis. The National Health and Nutrition Examination Survey (NHANES) 1999-2004 was a nationally representative cross-sectional survey; participants were interviewed in their homes and/or received standardized medical examinations in mobile examination centers. Results Of the 61,675 KEEP participants, 16,689 (27.1%) were found to have CKD. In the NHANES sample of 14,632 participants, 2,734 (15.3%) had CKD. Older age, smoking, obesity, diabetes, hypertension, and cardiovascular disease were associated significantly with CKD in both KEEP and NHANES ( P < 0.05 for all). Of note, the likelihood for CKD in African Americans differed between KEEP (odds ratio, 0.81; P < 0.001) and NHANES (odds ratio, 1.10; P = 0.2). Conclusion A greater prevalence of CKD was detected in the KEEP screening than in the NHANES data. KEEP has the limitations common to population-screening studies and conclusions for population-attributable risk may be limited. The targeted nature of the KEEP screening program and the large sample size with clinical characteristics comparable to NHANES validates KEEP as a valuable cohort to explore health associations for the CKD and at-risk-for-CKD populations in the United States.
Ideal three‐dimensional imaging of complex samples made up of micron‐scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For ...existing optics and detectors used for micro‐CT (computed tomography) imaging, sub‐micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field‐of‐view image circle and 0.5 µm pixel size that can be used in micro‐CT units utilizing both synchrotron and commercial X‐ray sources. A resolution‐test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist‐limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro‐CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.
A custom wide‐field lens and a new‐generation megapixel camera enabled micro‐CT scanning over a 3.5 mm × 5 mm field of view at 1 µm resolution/0.5 µm pixel size at Lawrence Berkeley Laboratory's Advanced Light Source and Argonne National Laboratory's Advanced Photon Source using a phantom with micron‐scale features. This novel combination of resolution and field of view was designed for broad applicability to any setting in which micron‐scale structures need to be characterized comprehensively in three dimensions over mm to cm.
Reduced angular sampling is a key strategy for increasing scanning efficiency of micron-scale computed tomography (micro-CT). Despite boosting throughput, this strategy introduces noise and ...extrapolation artifacts due to undersampling. In this work, we present a solution to this issue, by proposing a novel Dense Residual Hierarchical Transformer (DRHT) network to recover high-quality sinograms from 2×, 4× and 8× undersampled scans. DRHT is trained to utilize limited information available from sparsely angular sampled scans and once trained, it can be applied to recover higher-resolution sinograms from shorter scan sessions. Our proposed DRHT model aggregates the benefits of a hierarchical- multi-scale structure along with the combination of local and global feature extraction through dense residual convolutional blocks and non-overlapping window transformer blocks respectively. We also propose a novel noise-aware loss function named KL-L1 to improve sinogram restoration to full resolution. KL-L1, a weighted combination of pixel-level and distribution-level cost functions, leverages inconsistencies in noise distribution and uses learnable spatial weight maps to improve the training of the DRHT model. We present ablation studies and evaluations of our method against other state-of-the-art (SOTA) models over multiple datasets. Our proposed DRHT network achieves an average increase in peak signal to noise ratio (PSNR) of 17.73 dB and a structural similarity index (SSIM) of 0.161, for 8× upsampling, across the three diverse datasets, compared to their respective Bicubic interpolated versions. This novel approach can be utilized to decrease radiation exposure to patients and reduce imaging time for large-scale CT imaging projects.
•We present a novel sinogram restoration method to accurately restore full angular resolution from under-sampled versions.•We propose a dense-residual hierarchical transformer with window attention and multi-scale blocks to remove artifacts and improve SNR.•We improve training with a “KL-L1” loss using sinogram spatial attention, emphasizing relevant areas during optimization.•Our model with KL-L1 loss outperforms SOTA models across three datasets, achieving significant gains over the Bicubic baseline.
ABSTRACT
Model organism (MO) research provides a basic understanding of biology and disease due to the evolutionary conservation of the molecular and cellular language of life. MOs have been used to ...identify and understand the function of orthologous genes, proteins, cells and tissues involved in biological processes, to develop and evaluate techniques and methods, and to perform whole-organism-based chemical screens to test drug efficacy and toxicity. However, a growing richness of datasets and the rising power of computation raise an important question: How do we maximize the value of MOs? In-depth discussions in over 50 virtual presentations organized by the National Institutes of Health across more than 10 weeks yielded important suggestions for improving the rigor, validation, reproducibility and translatability of MO research. The effort clarified challenges and opportunities for developing and integrating tools and resources. Maintenance of critical existing infrastructure and the implementation of suggested improvements will play important roles in maintaining productivity and facilitating the validation of animal models of human biology and disease.
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