Histological Sections Research Articles

Adipose-derived stem cells apoptosis rejuvenate radiation-impaired skin in mice via remodeling and rearranging dermal collagens matrix

BackgroundChronic radiation dermatitis (CRD) is a late consequence of radiation with high incidence in patients receiving radiotherapy. Conventional therapies often yield unsatisfactory results. Therefore, this study aimed to explore the therapeutic potential and mechanism of adipose-derived stem cells (ADSCs) for CRD, paving the way for novel regenerative therapies in clinical practice.MethodsClinical CRD skin biopsies were analyzed to character the pathological changes of CRD skin and guided the animal modeling scheme. Subsequently, an in vivo analysisusing mouse CRD models was conducted to explore their effects of ADSCs on CRD, monitoring therapeutic impact for up to 8 weeks. Transcriptome sequencing and histologic sections analysis were performed to explore the potential therapeutic mechanism of ADSCs. Following observing extensive apoptosis of transplanted ADSCs, the therapeutic effect of ADSCs were compared with those of apoptosis-inhibited ADSCs. Multiphoton imaging and analysis of collagen morphologic features were employed to explain how translated ADSCs promote collagen remodeling at the microscopic level based on the contrast of morphology of collagen fibers.ResultsFollowing injection into CRD-afflicted skin, ADSCs therapy effectively mitigated symptoms of CRD, including acanthosis of the epidermis, fibrosis, and irregular collagen deposition, consistent with the possible therapeutic mechanism suggested by transcriptome sequencing. Notably, in vivo tracking revealed a significant reduction in ADSCs number due to extensive apoptosis. Inhibiting apoptosis in ADSCs partially tempered their therapeutic effects. Mechanically, analysis of collagen morphologic features indicated that translated ADSCs might promote dermal extracellular matrix remodeling through enlarging, lengthening, crimping, and evening collagen, counteracting the atrophy and rupture caused by irradiation.ConclusionsThis study demonstrated that ADSCs underwent substantial apoptosis upon local skin transplantation, and paradoxically, this apoptosis is essential for their efficacy in promoting the regeneration of late radiation-impaired skin. Mechanically, transplanted ADSCs could promote the remodeling and rearrangement of radiation-damaged dermal collagen matrix.

Age and growth rate estimated by skeletochronology in loggerhead sea turtles from French Mediterranean waters

Abstract Skeletochronology was used to determine the ages of 30 loggerhead sea turtles (Caretta caretta) found in French Mediterranean waters. Histological sections were performed with 30 humeri collected on stranded C. caretta on the coast of Provence and the Gulf of Lion. Lines of arrested growth (LAGs) were used to evaluate age, considering only one period of arrested growth per year. Two successive LAGs delimit an interval that is proportional to the individual’s body growth. In a first step, we created a skeletogram for each individual that identified its LAGs. Secondly, we measured the areas delineating successive intervals to determine individual growth patterns over the years. Two methods were used to deduce sea turtle age from histological sections: the correction factor (CF) method and the growth rate (GR) method, the latter using Von Bertalanffy growth function. Age estimations varied from 4.3 to 24.7 years (mean ± SD = 10.1 ± 4.8) with the CF method and from 6.2 to 25.6 years (mean ± SD = 12.2 ± 5.2) with the GR method, with no significant difference between the methods. The study sample was thus mostly composed of juveniles, which is also the most frequent life stage observed in the study area. The annual curved carapace length growth rate calculated with every LAG interval varied from 1.0 to 6.9 cm/year (mean ± SD = 3.5 ± 1.4, ). High variability in interindividual growth rates were observed, which is of interest in understanding the complex lifecycle of these long-lived marine reptiles.

The expressions of nr0b1/2 genes in the Chinese giant salamander and their response to estradiol benzoate/17α-methyltestosterone treatment

Previously, the nr0b1 and nr0b2 genes have been identified in various animals and found to be closely associated with sex determination. In order to investigate the regulatory roles of nr0b1 and nr0b2 genes in the sex determination of Chinese giant salamander (CGS, Andrias davidianus), we obtained the full-length cDNA sequences of nr0b1 and nr0b2 through cloning, determined the characteristics of their tissue expressions and the responses of nr0b1 and nr0b2 to estradiol benzoate (EB) and 17α-methyltestosterone (MT) by using quantitative real-time PCR (qRT-PCR), and evaluated gonad development through histological sections. The full-lengths of cDNA of nr0b1/2 in C GS are separately 1278bp and 789bp. They have complete open reading frames (ORF) of 864bp and 774bp and encode 287 and 257 amino acids respectively. The 3' untranslated regions (UTR) are 276bp and 15bp, and the 5' UTR of nr0b1 is 138bp. In the 3' UTR of nr0b1, a putative polyadenylation signal (AATAAA) is identified. Tissue distribution analysis indicates that nr0b1 is mainly expressed in the pituitary, kidney, and testes, with significant differences between females (ZW-F) and males (ZZ-M) expression in the testes. On the other hand, nr0b2 is mainly expressed in the liver, followed by gonadal tissues. After immersion and feeding with EB and MT, EB's promotion on nr0b1 expression in CGS ovaries and testes is shown, by contrast MT only has a positive effect on nr0b2 in CGS testes. Histological sections show that after EB treatment, both genetic females (ZW-F) and sex-reversed females (ZZ-F) of CGS contain oogonia, indicating that EB can cause sex reversal in CGS; however, after MT treatment, no cellular morphological changes are observed either in genetic females (ZW-F) or in genetic males (ZW-M), indicating that this concentration cannot induce a shift in the sex ratio of CGS. These findings lay the foundation for further investigating the molecular mechanisms by which nr0b1/2 influence the differentiation and maintenance of CGS gonads.

Photobiological response of mast cells to green and red light-emitting diodes (LEDs) in cutaneous burns.

This study assessed the effects of red and green LEDs on mast cells (MCs) in third-degree burns in 75 Wistar rats, divided into control, red LED (RED), and green LED (GREEN) groups. Animals were irradiated daily with RED (630 nm, 300 mW, 0.779 W/cm2, 9 J/cm2, 30 s) and GREEN (520 nm, 180 mW, 0.467 W/cm2, 60 J/cm2, 30 s). Histological sections stained with toluidine blue were analyzed for total and subtype MCs. Standardized MC counting was performed across the viable lesion area, considering lesion margins, through intact connective tissue and the integrity of skin appendages. No statistically significant differences in MCs 2 (with released granules and intact cell border) were found between groups. Irradiated groups showed increased total MCs at 7, 14, and 21 days (p < 0.05), with a decrease in MCs 1 (intact MCs) at all time points compared to control (p < 0.05). Significant changes in MCs 3 (with massive degranulation and partial or complete disintegration of the cell border) degranulation were noted in RED at 7, 14, and 21 days (p < 0.009) and in GREEN at 14 (p < 0.009) and 32 days (p < 0.028). Results suggest red and green LEDs modulate MC recruitment and degranulation in third-degree burns.

Fetal Vertebral Chondrostasis—Significance of Excessive Cartilage in Vertebral Bodies of Newborns

Introduction: We describe an abnormality in fetal and neonatal vertebral bodies whose most conspicuous characteristic is an increase in cartilaginous matrix within cancellous osseous trabeculae. We have termed this finding fetal chondrostasis (FC). Methods: We initiated a retrospective review of autopsy reports in which this condition had been prospectively diagnosed during a 36-year period. The Chalkley point counting method was applied to histologic sections of vertebral bodies to assess the relative components of cartilage, bone, and bone marrow. The results were compared to those of three control groups whose causes of death were prematurity, birth trauma, and infection. Results: We found that on average, the cartilaginous content in the FC group was considerably greater in both preterm and term infants when compared to controls. FC seemed to evolve from diminished activity in the cartilaginous growth zone resulting in formation of excessively broad cartilaginous columns. These subsequently suffered from delayed resorption following their incorporation within cancellous bony trabeculae. Conclusion: Excess cartilage within cancellous bone of vertebral centra in newborns is merely one aspect of disturbed intrauterine osseous development but is seemingly more readily discernible than other features at this site. The most common clinical correlates for FC were multiple congenital anomalies, congenital heart disease, intrauterine growth retardation, prematurity, and certain maternal factors.

Efficacy of Jasminum subtriplinerve Extract against 7,12-Dimethylbenz[a]anthracene-Induced Cancer in Mice.

Jasminum subtriplinerve Blume tea is a traditional Vietnamese medicine used to treat impetigo, menstruation issues, and painful menstrual hematometra. Previous studies have shown that extracts and isolated compounds from J. subtriplinerve possess diverse pharmacological properties, such as antioxidant, antibacterial, and antidiabetic effects. However, their potential anticancer effects and underlying mechanisms of action have not been clear. Here, we examined the effects of J. subtriplinerve extracts against three human cancer cell lines. We also conducted in vivo analyses using a mouse model of 7,12-dimethylbenz[a]anthracene-induced breast cancer, including an investigation of changes in histological sections. The effect of the J. subtriplinerve ethyl acetate fraction on cytokine levels (IL-2, PGE2, TNF-α) in serum was determined using ELISA kits. Results showed that the EtOAc fraction had the highest anti-proliferative activity (IC50 = 13.7 mg/ml) against the breast cancer (MCF-7) cell line, while the BuOH and water fractions did not show any anticancer effects. Additionally, the EtOAc fraction at a dose of 14.4 mg/kg was able to elevate IL-2 levels and suppress the expression of PGE2 in the serum of mice. A remarkable decrease in the percentage of death and tumor incidence in mice was achieved following treatment with the EtOAc fraction at a dose of 14.4 mg/kg. No abnormal parameters in blood were observed in the J. subtriplinerve treatment groups. These results suggest that J. subtriplinerve, when used as tea or a functional food, is nontoxic and has clear chemopreventive effects against breast cancer.

Characteristics of the Integument of Phyllomedusa burmeisteri (Anura, Phyllomedusidae) and Boana semilineata (Anura, Hylidae) Males Can Contribute to Understanding its Relation to Habitat.

The integument of anurans plays vital physiological roles, crucial for understanding the species' survival in their environment. Despite its significance, there are few studies describing the cutaneous morphology of anurans from the Brazilian Atlantic Forest. This study aimed to characterize the integument of Phyllomedusa burmeisteri and Boana semilineata in males using microscopic and histochemical approaches. Histological sections were stained with various dyes, and additional fragments underwent electron microscopy and energy-dispersive X-ray spectroscopy. Results showed different projections on the dorsal and ventral regions of males from these species, without the Eberth-Katschenko layer. Differences in the arrangement of chromatophore cells in regions with varying solar incidence were observed in the spongy dermis. Various gland types were identified, aiding taxonomic differentiation and validation of behavioral data. Both species had seromucous and granular glands, while only P. burmeisteri displayed lipid glands. Histochemical analysis revealed higher production of polysaccharides and proteins, contributing to the integument's moisture and protection. Lipid secretions in P. burmeisteri helped waterproof the integument more effectively against desiccation. This study concludes that analyzing anuran integument provides valuable insights into their behavior, with integument composition potentially influenced by habitat choice among different species.

Distribution of mechanical properties of native human ligamentum flavum depending on histopathological changes

This study aimed to characterize the mechanical properties of native human ligamentum flavum (LF) and correlate them with histopathological changes. Mechanical property gradients across the cranial, medial, and caudal regions of LF were mapped and compared with histological sections. We also compared lumbar spinal stenosis (LSS) samples with disc herniation (DH) samples as reference material to identify differences in mechanical properties and histopathological features. Our results revealed significant heterogeneity in LF mechanical properties, with local variations correlating with specific histopathological changes such as chondroid metaplasia and loss of elastic fibers. These findings underscore the importance of considering LF heterogeneity in mechanical characterization and provide insights into its behavior under pathological conditions.

Fatal exulceratio simplex (dieulafoy lesion) – a case report and review

AbstractA 64-year-old man involved in a low-speed vehicle crash was found at autopsy to have altered blood extending from his stomach to his rectum. Within the stomach a small arterial vessel opened onto the mucosa of the posterior wall of the antrum adjacent to the pylorus with no adjacent mucosal ulceration or malignancy. Histologic sections showed the typical appearances of a Dieulafoy lesion with a tortuous small arteriole within the submucosa extending to the gastric lumen with an overlying cap of recently formed clot. There were no injuries attributable to the vehicle collision. Death was due to a bleeding Dieulafoy lesion of the stomach with a background of cardiomegaly. Dieulafoy lesion of the stomach is a rare disorder accounting for only 1–2% of cases of acute gastrointestinal hemorrhage. Although its pathogenesis is poorly understood it is capable of producing life-threatening bleeding, as in the present case. The small size of the lesion may make it difficult to identify at the time of autopsy.

In Vivo visualization of white matter fiber tracts in the brainstem using low flip angle double echo 3D gradient echo imaging at 3T

BackgroundWhite matter (WM) fiber tracts in the brainstem communicate with various regions in the cerebrum, cerebellum, and spinal cord. Clinically, small lesions, malformations, or histopathological changes in the brainstem can cause severe neurological disorders. A direct and non-invasive assessment approach could bring valuable information about the intricate anatomical variations of the white matter fiber tracts and nuclei. Although tractography from diffusion tensor imaging has been commonly used to map the WM fiber tracts connectivity, it is difficult to differentiate the complex WM tracts anatomically. Both high field MRI methods and ultrahigh-field MRI methods at 7T and 11.7 T have been used to enhance the contrast of WM fiber tracts. Despite their promising results, it is still challenging to achieve wide clinical adoption at 3T. In this study, we explored a clinically feasible method using a proton density weighted (PDW) 3D gradient echo (GRE) sequence to directly image the WM fiber tracts in the brainstem at 3T in vivo. MethodsWe optimized a 3D high resolution, double echo, short TR, PDW GRE sequence on 5 healthy volunteers using a clinical 3T scanner to visualize the complicated anatomy of WM fiber tracts in the brain stem. Tissue properties including T1, proton density and T2* from in vivo quantitative MRI data were used for simulations to determine the optimal flip angle for the sequence. The visualization of multiple WM fiber tracts in the brainstem was assessed qualitatively and quantitatively using relative contrast and contrast-to-noise ratio (CNR). To improve the CNR, the final images were created by averaging over all echoes from two consecutive scans at the optimal flip angle. The results were compared to anatomical atlases and histology sections to identify the major fiber tracts. All the identified major fiber tracts were labeled on axial, sagittal and coronal slices. ResultsThe WM fiber tracts were found to have distinct hypointense signal throughout the brainstem and most of the major WM fiber tracts, such as the corticospinal tract, medial lemniscus, medial longitudinal fasciculus, and central tegmental tract, in the brainstem up to and including the thalamus were identified in all subjects. Both qualitative and quantitative evaluations showed that the 3° scan offered the best contrast for WM fiber tracts for a TR of 20 ms. The average over the first two echo times and two consecutive 3° scans gave a CNR of 47.8 ± 6.2 for the pyramidal tracts in particular and CNRs values greater than 6.5 ± 2.4 for the rest of the fiber tracts. ConclusionsAll the major fiber tracts in the brainstem could be visualized. Given the reasonably short scan time of 10 min at 3T, double echo PDW GRE sequence is a very practical approach for clinical adoption.

Integrated multiomics revealed adenosine signaling predict immunotherapy response and regulate tumor ecosystem of melanoma

Extracellular adenosine is extensively involved in regulating the tumor microenvironment. Given the disappointing results of adenosine-targeted therapy trials, personalized treatment might be necessary, tailored to the microenvironment status of individual patients. Here, we introduce the adenosine signaling score (ADO-score) model using non-negative matrix fraction identified patient subtypes using publicly available melanoma dataset, which aimed to profile adenosine signaling-related genes and construct a model to predict prognosis. We analyzed 580 malignant melanoma samples and demonstrated its robust value for prognosis. Further investigation in immune checkpoint inhibitor dataset suggests its potential as a stratified factor of immune checkpoint inhibitor efficacy. We validated the power of the ADO-score at the protein level immunofluorescence in a melanoma cohort from Xiangya Hospital. More importantly, single-cell and spatial transcriptomic data highlighted the cell-specific expression patterns of adenosine signaling-related genes and the existence of adenosine signaling-mediated crosstalk between tumor cells and immune cells in melanoma. Our study reveals a robust connection between adenosine signaling and clinical benefits in melanoma patients and proposes a universally applicable adenosine signaling model, the ADO-score, in gene expression profiles and histological sections. This model enables us to more precisely and conveniently select patients who are likely to benefit from immunotherapy.

Impact of anatomic variability and other vascular factors on lamina cribrosa hypoxia.

Insufficient oxygenation in the lamina cribrosa (LC) may contribute to axonal damage and glaucomatous vision loss. To understand the range of susceptibilities to glaucoma, we aimed to identify key factors influencing LC oxygenation and examine if these factors vary with anatomical differences between eyes. We reconstructed 3D, eye-specific LC vessel networks from histological sections of four healthy monkey eyes. For each network, we generated 125 models varying vessel radius, oxygen consumption rate, and arteriole perfusion pressure. Using hemodynamic and oxygen supply modeling, we predicted blood flow distribution and tissue oxygenation in the LC. ANOVA assessed the significance of each parameter. Our results showed that vessel radius had the greatest influence on LC oxygenation, followed by anatomical variations. Arteriole perfusion pressure and oxygen consumption rate were the third and fourth most influential factors, respectively. The LC regions are well perfused under baseline conditions. These findings highlight the importance of vessel radius and anatomical variation in LC oxygenation, providing insights into LC physiology and pathology. Pathologies affecting vessel radius may increase the risk of LC hypoxia, and anatomical variations could influence susceptibility. Conversely, increased oxygen consumption rates had minimal effects, suggesting that higher metabolic demands, such as those needed to maintain intracellular transport despite elevated intraocular pressure, have limited impact on LC oxygenation.

Assessment of anticoagulant potential of Halocnemum strobilaceum (Pall.) against black rat (Rattus rattus Lin.) from Algeria

BackgroundBlack rats (Rattus rattus; Rodentia: Muridae) cause significant damage to agricultural and human health, and they are considered a reservoir for a variety of diseases. ObjectivesThe current study aimed to evaluate the toxicity of oral anticoagulants derived from Halocnemum strobilaceum (Pall.) M. Bieb. to these dangerous animals. MethodFour selected doses (100, 150, 200 and 300 mg/day/kg of individual weight) and one control were utilized, with 10 repetitions of each dose (5 ♂ and 5 ♀). The extract was powdered on dates as bait. ResultsUPLC-ESI/MS-MS chromatography identified three distinct coumarins (coumaric acid, p-coumaric acid and 4-hydroxycoumarin). The results showed that the fourth dose used caused the highest number of deaths (100 % after three days of treatment). In contrast, after 48 h of therapy, all rats examined showed lethargy, anorexia and unconsciousness, followed by rapid death at 72 h in the treated individuals. The LD50 was recorded at 146.4 mg.kg−1 with a LT50 of 59.37 h. At the end of the experiment, the autopsies of all deceased individuals allowed us to observe the bleeding of their internal organs. The analysis of PT and aPTT demonstrated that the halophyte under investigation possesses anticoagulant activity that increased with the concentration. Histological sections of the liver revealed cellular alteration and significant necrosis. As well, the kidneys had vascular occlusion with an inflammatory filtrate. ConclusionsTo reduce food losses and wastes caused by these pests, H. strobilaceum will be an important plant for use in protecting against invasive rodents, especially in environmental and stored product programs focused at eradicating rodent pests.

Three-dimensional virtual histology of the rat uterus musculature using micro-computed tomography.

Contractions of the uterus play an important role in menstruation and fertility, and contractile dysfunction can lead to chronic diseases such as endometriosis. However, the structure and function of the uterus are difficult to interrogate in humans, and thus animal studies are often employed to understand its function. In rats, anatomical studies of the uterus have typically been based on histological assessment, have been limited to small segments of the uterine structure, and have been time-consuming to reconstruct at the organ scale. This study used micro-computed tomography imaging to visualise the muscle structures in the entire non-pregnant rat uterus and assess its use for 3D virtual histology. An assessment of the rodent uterus is presented to (i) quantify muscle thickness variations along the horns, (ii) identify predominant fibre orientations of the muscles and (iii) demonstrate how the anatomy of the uterus can be mapped to 3D volumetric meshes via virtual histology. Micro-computed tomography measurements were validated against measurements from histological sections. The average thickness of the myometrium was found to be 0.33 ± 0.11 mm and 0.31 ± 0.09 mm in the left and right horns, respectively. The micro-computed tomography and histology thickness calculations were found to correlate strongly at different locations in the uterus: at the cervix, r = 0.87, and along the horn from the cervical end to the ovarian end, respectively, r = 0.77, r = 0.89 and r = 0.54, with p < 0.001 in every location. This study shows that micro-computed tomography can be used to quantify the musculature in the whole non-pregnant uterus and can be used for 3D virtual histology.

MetFinder: A Tool for Automated Quantitation of Metastatic Burden in Histological Sections From PreclinicalModels.

As efforts to study the mechanisms of melanoma metastasis and novel therapeutic approaches multiply, researchers need accurate, high-throughput methods to evaluate the effects on tumor burden resulting from specific interventions. We show that automated quantification of tumor content from whole slide images is a compelling solution to assess invivo experiments. In order to increase the outflow of data collection from preclinical studies, we assembled a large dataset with annotations and trained a deep neural network for the quantitative analysis of melanoma tumor content on histopathological sections of murine models. After assessing its performance in segmenting these images, the tool obtained consistent results with an orthogonal method (bioluminescence) of measuring metastasis in an experimental setting. This AI-based algorithm, made freely available to academic laboratories through a web-interface called MetFinder, promises to become an asset for melanoma researchers and pathologists interested in accurate, quantitative assessment of metastasis burden.

Impact of elevated IOP on lamina cribrosa oxygenation; A combined experimental-computational study on monkeys.

Our goal is to evaluate how lamina cribrosa (LC) oxygenation is affected by the tissue distortions resulting from elevated IOP. Experimental study on monkeys. Four healthy monkey eyes with OCT scans with IOP of 10 to 50 mmHg, and then with histological sections of LC. Since in-vivo LC oxygenation measurement is not yet possible, we used 3D eye-specific numerical models of the LC vasculature which we subjected to experimentally-derived tissue deformations. We reconstructed 3D models of the LC vessel networks of 4 healthy monkey eyes from histological sections. We also obtained in-vivo IOP-induced tissue deformations from a healthy monkey using OCT images and digital volume correlation analysis techniques. The extent that LC vessels distort under a given OCT-derived tissue strain remains unknown. We biomechanics-based mapping techniques: cross-sectional and isotropic. The hemodynamics and oxygenations of the four vessel networks were simulated for deformations at several IOPs up to 60mmHg. The results were used to determine the effects of IOP on LC oxygen supply, assorting the extent of tissue mild and severe hypoxia. IOP-induced deformation, vasculature structure, blood supply, and oxygen supply for LC region. IOP-induced deformations reduced LC oxygenation significantly. More than 20% of LC tissue suffered from mild hypoxia when IOP reached 30 mmHg. Extreme IOP(>50mmHg) led to large severe hypoxia regions (>30%) in the isotropic mapping cases. Our models predicted that moderately elevated IOP can lead to mild hypoxia in a substantial part of the LC, which, if sustained chronically, may contribute to neural tissue damage. For extreme IOP elevations, severe hypoxia was predicted, which would potentially cause more immediate damage. Our findings suggest that despite the remarkable LC vascular robustness, IOP-induced distortions can potentially contribute to glaucomatous neuropathy.

Chalkbrood Disease Caused by Ascosphaera apis in Honey Bees (Apis mellifera)-Morphological and Histological Changes in Infected Larvae.

Chalkbrood is a mycological brood disease of the Western honey bee (Apis mellifera), caused by the fungus Ascosphaera apis. The aim of this study was the investigation of the pathology of artificially reared Apis mellifera larvae, experimentally infected with A. apis spores (1.0 × 103 spores/larva). Non-infected larvae served as control. Five living larvae and every dead larva were collected daily (day 1-7 p.i.). All larvae were macroscopically measured, photographed, formalin-fixed, and histologically processed (hematoxylin-eosin stain, Grocott silvering). Histological sections were digitized, and the size of the larvae was measured (mouth-after length, area) and statistically analyzed. Twenty-six larvae from the collected larvae (n = 64; 23 dead, 3 alive) showed histological signs of infection from 3 d p.i. onwards. The dead larvae showed macroscopically white/brown deposits, indistinct segmentation, and a lack of body elongation. Infected larvae were significantly smaller than the controls on days 3 p.i. (p < 0.05), 4 p.i. (p < 0.001), and 6 p.i. (p < 0.05). The early time of death, the low number of transitional stages, and the strong penetration of the larval carcass with fungal mycelium indicate a rapid and fulminant infection process, which is probably relevant for spreading the disease within the colony.

A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation.

Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo. In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison of neuroanatomy from different subjects in a common coordinate frame. High-resolution, digital atlases derived from histology (e.g., Allen atlas [7], BigBrain [13], Julich [15]), are currently the state of the art and provide exquisite 3D cytoarchitectural maps, but lack probabilistic labels throughout the whole brain. Here we present NextBrain, a next-generation probabilistic atlas of human brain anatomy built from serial 3D histology and corresponding highly granular delineations of five whole brain hemispheres. We developed AI techniques to align and reconstruct ~10,000 histological sections into coherent 3D volumes with joint geometric constraints (no overlap or gaps between sections), as well as to semi-automatically trace the boundaries of 333 distinct anatomical ROIs on all these sections. Comprehensive delineation on multiple cases enabled us to build the first probabilistic histological atlas of the whole human brain. Further, we created a companion Bayesian tool for automated segmentation of the 333 ROIs in any in vivo or ex vivo brain MRI scan using the NextBrain atlas. We showcase two applications of the atlas: automated segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimer's disease and healthy brain ageing based on ~4,000 publicly available in vivo MRI scans. We publicly release: the raw and aligned data (including an online visualisation tool); the probabilistic atlas; the segmentation tool; and ground truth delineations for a 100 μm isotropic ex vivo hemisphere (that we use for quantitative evaluation of our segmentation method in this paper). By enabling researchers worldwide to analyse brain MRI scans at a superior level of granularity without manual effort or highly specific neuroanatomical knowledge, NextBrain holds promise to increase the specificity of MRI findings and ultimately accelerate our quest to understand the human brain in health and disease.

Association of quantitative histopathology measurements with antemortem medial temporal lobe cortical thickness in the Alzheimer’s disease continuum

The medial temporal lobe (MTL) is a hotspot for neuropathology, and measurements of MTL atrophy are often used as a biomarker for cognitive decline associated with neurodegenerative disease. Due to the aggregation of multiple proteinopathies in this region, the specific relationship of MTL atrophy to distinct neuropathologies is not well understood. Here, we develop two quantitative algorithms using deep learning to measure phosphorylated tau (p-tau) and TDP-43 (pTDP-43) pathology, which are both known to accumulate in the MTL and are associated with MTL neurodegeneration. We focus on these pathologies in the context of Alzheimer’s disease (AD) and limbic predominant age-related TDP-43 encephalopathy (LATE) and apply our deep learning algorithms to distinct histology sections, on which MTL subregions were digitally annotated. We demonstrate that both quantitative pathology measures show high agreement with expert visual ratings of pathology and discriminate well between pathology stages. In 140 cases with antemortem MR imaging, we compare the association of semi-quantitative and quantitative postmortem measures of these pathologies in the hippocampus with in vivo structural measures of the MTL and its subregions. We find widespread associations of p-tau pathology with MTL subregional structural measures, whereas pTDP-43 pathology had more limited associations with the hippocampus and entorhinal cortex. Quantitative measurements of p-tau pathology resulted in a significantly better model of antemortem structural measures than semi-quantitative ratings and showed strong associations with cortical thickness and volume. By providing a more granular measure of pathology, the quantitative p-tau measures also showed a significant negative association with structure in a severe AD subgroup where semi-quantitative ratings displayed a ceiling effect. Our findings demonstrate the advantages of using quantitative neuropathology to understand the relationship of pathology to structure, particularly for p-tau, and motivate the use of quantitative pathology measurements in future studies.

Volumetric changes of the enteric nervous system under physiological and pathological conditions measured using x-ray phase-contrast tomography.

Full-thickness biopsies of the intestinal wall may be used to study and assess damage to the neurons of the enteric nervous system (ENS), that is, enteric neuropathy. The ENS is difficult to examine due to its localization deep in the intestinal wall and its organization with several connections in diverging directions. Histological sections used in clinical practice only visualize the sample in a two-dimensional way. X-ray phase-contrast micro-computed tomography (PC-μCT) has shown potential to assess the cross-sectional thickness and volume of the ENS in three dimensions (3D). The aim of this study was to explore the potential of PC-μCT to evaluate its use to determine the size of the ENS. Full-thickness biopsies of ileum obtained during surgery from five controls and six patients clinically diagnosed with enteric neuropathy and dysmotility were included. Punch biopsies of 1 mm in diameter and 1 cm in length, from an area containing myenteric plexus, were extracted from paraffin blocks, and scanned with synchrotron-based PC-μCT without any staining. The microscopic volumetric structure of the neural tissue (consisting of both ganglia and fascicles) could be determined in all samples. The ratio of neural tissue volume/total tissue volume was higher in controls than in patients with enteric neuropathy (P = 0.013). The patient with the longest disease duration had the lowest ratio. The assessment of neural tissue can be performed in an objective, standardized way, to ensure reproducibility and comparison under physiological and pathological conditions. Further evaluation is needed to examine the role of this method in the diagnosis of enteric neuropathy.