Traditional staining for routine diagnostic pathology including the role of tannic acid. 1. Value and limitations of the hematoxylin-eosin stain

Advisory on delayed fading caused by the use of a xylene substitute for frozen tissue specimen staining in micrographic surgery

BACKGROUND

The use of xylene substitutes is becoming more common in the setting of micrographic surgery frozen tissue section staining, and dermatologic surgeons need to be aware of possible undesirable delayed effects of using these agents and the possibility of modifying H&E staining protocols to prevent delayed fading. This report demonstrates an undesirable outcome of using an isoparaffinic aliphatic hydrocarbon as a xylene substitute, implementation of a quality improvement intervention to eliminate frozen section slide fading in the setting of micrographic surgery tissue processing, and recommendations for the modification of protocol when using a xylene substitute.

CLINICAL AND LABORATORY INFORMATION

Frozen section slides processed with xylene and xylene substitute were analyzed by histotechnicians, a dermatopathologist, and a micrographic surgery surgeon at 1-week and 1-month intervals. The use of a standard H&E protocol resulted in zero stains fading when using xylene as a clearing agent, but delayed fading when using a xylene substitute.

DISCUSSION

Using an isoparaffinic aliphatic hydrocarbon as a xylene substitute can lead to excess water carryover, which may result in delayed hematoxylin fading in micrographic surgery tissue staining, so using this xylene substitute likely requires modification to the dehydration phase and tap water immersion phase to prevent fading.

Image Analysis in Histopathology and Cytopathology: From Early Days to Current Perspectives

Both pathology and cytopathology still rely on recognizing microscopical morphologic features, and image analysis plays a crucial role, enabling the identification, categorization, and characterization of different tissue types, cell populations, and disease states within microscopic images. Historically, manual methods have been the primary approach, relying on expert knowledge and experience of pathologists to interpret microscopic tissue samples. Early image analysis methods were often constrained by computational power and the complexity of biological samples. The advent of computers and digital imaging technologies challenged the exclusivity of human eye vision and brain computational skills, transforming the diagnostic process in these fields. The increasing digitization of pathological images has led to the application of more objective and efficient computer-aided analysis techniques. Significant advancements were brought about by the integration of digital pathology, machine learning, and advanced imaging technologies. The continuous progress in machine learning and the increasing availability of digital pathology data offer exciting opportunities for the future. Furthermore, artificial intelligence has revolutionized this field, enabling predictive models that assist in diagnostic decision making. The future of pathology and cytopathology is predicted to be marked by advancements in computer-aided image analysis. The future of image analysis is promising, and the increasing availability of digital pathology data will invariably lead to enhanced diagnostic accuracy and improved prognostic predictions that shape personalized treatment strategies, ultimately leading to better patient outcomes.

Salmonella Typhimurium screen identifies shifts in mixed-acid fermentation during gut colonization

How enteric pathogens adapt their metabolism to a dynamic gut environment is not yet fully understood. To investigate how Salmonella enterica Typhimurium (S.Tm) colonizes the gut, we conducted an in vivo transposon mutagenesis screen in a gnotobiotic mouse model. Our data implicate mixed-acid fermentation in efficient gut-luminal growth and energy conservation throughout infection. During initial growth, the pathogen utilizes acetate fermentation and fumarate respiration. After the onset of gut inflammation, hexoses appear to become limiting, as indicated by carbohydrate analytics and the increased need for gluconeogenesis. In response, S.Tm adapts by ramping up ethanol fermentation for redox balancing and supplying the TCA cycle with α-ketoglutarate for additional energy. Our findings illustrate how S.Tm flexibly adapts mixed fermentation and its use of the TCA cycle to thrive in the changing gut environment. Similar metabolic wiring in other pathogenic Enterobacteriaceae may suggest a broadly conserved mechanism for gut colonization.

PST-Diff: Achieving High-Consistency Stain Transfer by Diffusion Models With Pathological and Structural Constraints

Histopathological examinations heavily rely on hematoxylin and eosin (HE) and immunohistochemistry (IHC) staining. IHC staining can offer more accurate diagnostic details but it brings significant financial and time costs. Furthermore, either re-staining HE-stained slides or using adjacent slides for IHC may compromise the accuracy of pathological diagnosis due to information loss. To address these challenges, we develop PST-Diff, a method for generating virtual IHC images from HE images based on diffusion models, which allows pathologists to simultaneously view multiple staining results from the same tissue slide. To maintain the pathological consistency of the stain transfer, we propose the asymmetric attention mechanism (AAM) and latent transfer (LT) module in PST-Diff. Specifically, the AAM can retain more local pathological information of the source domain images, while ensuring the model's flexibility in generating virtual stained images that highly confirm to the target domain. Subsequently, the LT module transfers the implicit representations across different domains, effectively alleviating the bias introduced by direct connection and further enhancing the pathological consistency of PST-Diff. Furthermore, to maintain the structural consistency of the stain transfer, the conditional frequency guidance (CFG) module is proposed to precisely control image generation and preserve structural details according to the frequency recovery process. To conclude, the pathological and structural consistency constraints provide PST-Diff with effectiveness and superior generalization in generating stable and functionally pathological IHC images with the best evaluation score. In general, PST-Diff offers prospective application in clinical virtual staining and pathological image analysis.

MicroRNA expression profiles reveal wool development and fineness regulation in Gansu alpine fine-wool sheep

The development of wool has a complex regulatory mechanism both influenced by genetic and environmental factors. MicroRNAs (miRNA) were involved in various biological processes of animals, and may play an important role in the regulation of wool development. In this study, we comprehensively analyzed and identified the histological parameters of hair follicles, as well as the miRNAs, target genes, pathways, and Gene Ontology terms related to wool fineness regulation and wool growth and development using HE staining and RNA-Seqs methods. Both coarse (group C, mean fiber diameter (MFD) = 22.26 ± 0.69 μm, n = 6) and fine (group F, MFD = 16.91 ± 0.29 μm, n = 6) of Gansu alpine fine-wool sheep with different wool fineness were used in this study. The results showed that the primary follicle diameter and secondary wool fiber diameter in group C were significantly higher than those in group F (P < 0.05). And the number of primary and secondary hair follicles in group C was significantly lower than that in group F (P < 0.05). Furthermore, a total of 67 DE miRNAs and 290 potential DE miRNAs target genes were screened in the skin tissues of sheep from groups F and C, and some potential target genes related to wool fineness regulation were screened, such as CDH2, KRT82, FOXN1, LOC101106296, KRT20, MCOLN3, KRT71, and TERT. These genes were closely related to Glutathione metabolism, epidermal cell differentiation, keratinization, and regulation of hair cycle. Moreover, the regulatory network of miRNAs-mRNAs suggested that miRNAs (miR-129-x, novel m0079-3p, miR-2484-z, novel m0025-5P, etc.) may play a key role in the wool development and wool fineness regulation of Gansu alpine fine-wool sheep. In summary, this study expands the existing miRNAs database and provides new information for studying the regulation of wool development in Gansu alpine fine wool sheep.

Added Value of Histological Evaluation of Muscle Biopsies in Porcine Vascularized Composite Allografts

Background: Machine perfusion (MP) offers extended preservation of vascularized complex allografts (VCA), but the diagnostic value of histology using hematoxylin and eosin (H&E) in detecting ischemia-reperfusion injury (IRI) in muscle cells remains unclear. This study aims to document the application of the Histology Injury Severity Score (HISS) and to assess whether additional staining for nicotinamide adenine dinucleotide (NADH) and membrane attack complex (MAC) improves IRI detection in a porcine limb replantation model. Methods: The forelimbs of 16 Dutch Landrace pigs were amputated and preserved for 24 h using hypothermic MP (n = 8) with Histidine-Tryptophan-Ketoglutarate (HTK) or for 4 h with SCS (n = 8) before heterotopic replantation and 7 days of follow-up. Muscle damage was assessed via biochemical markers and light microscopy using H&E, NADH, and MAC at baseline, post-intervention, and post-operative day (POD) 1, 3, and 7 timepoints, using the HISS and a self-developed NADH and MAC score. Results: H&E effectively identified damaged muscle fibers and contributed to IRI assessment in porcine limbs (p < 0.05). The highest HISS was measured on POD 3 between MP (4.9) and SCS (3.5) (p = 0.029). NADH scores of both preservation groups varied over the 7-day follow-up and were statistically insignificant compared with baseline measurements (p > 0.05). MAC revealed no to minimal necrotic tissue across the different timepoints. Conclusions: This study documents the application of the HISS with H&E to detect IRI in muscle fibers. NADH and MAC showed no significant added diagnostic utility. The 24 h MP showed similar muscle alterations using the HISS compared to that of the 4 h SCS after a 7-day follow up.

ResSAT: Enhancing Spatial Transcriptomics Prediction from H&E- Stained Histology Images with Interactive Spot Transformer

Spatial transcriptomics (ST) revolutionizes RNA quantification with high spatial resolution. Hematoxylin and eosin (H&E) images, the gold standard in medical diagnosis, offer insights into tissue structure, correlating with gene expression patterns. Current methods for predicting spatial gene expression from H&E images often overlook spatial relationships. We introduce ResSAT (Residual networks - Self-Attention Transformer), a framework generating spatially resolved gene expression profiles from H&E images by capturing tissue structures and using a self-attention transformer to enhance prediction.Benchmarking on 10× Visium datasets, ResSAT significantly outperformed existing methods, promising reduced ST profiling costs and rapid acquisition of numerous profiles.

Cost-Effective Staining Alternatives to Immunohistochemistry for Keratin Demonstration in Oral Epithelial Pathologies

Background

Demonstrating keratin is crucial in diagnosing various epithelial pathologies and is typically done through histological and immunohistochemical (IHC) methods. While IHC staining for keratin is highly specific, it can be costly and time-consuming. Therefore, common histological staining methods for keratin, suitable for routine histotechniques labs, are gaining importance.

Methodology

Twenty formalin-fixed, paraffin-embedded tissue blocks, each representing histologically confirmed normal oral mucosa (NOM), hyperorthokeratosis (HOK), and well-differentiated squamous cell carcinoma (WDSCC), were retrieved. Five histological sections of 4-μ thickness from each block were stained using routine hematoxylin and eosin (H and E), modified pap stain (mPap), Ayoub-Shklar (AS), Dane-Herman (DH), and Alcian blue-PAS stains (AB-PAS). Two independent observers evaluated the stained sections and scored staining specificity and intensity. Statistical comparisons were made.

Results

All sections of NOM, HOK, and WDSCC showed positive staining for keratin with each of the five stains used. The staining specificity and intensity scores were highest with the AS stain and lowest with the AB-PAS stain.

Conclusion

Routine H and E, mPap, AS, and DH stains effectively stained keratin with adequate intensity in NOM, HOK, and WDSCC. However, while AB-PAS stain also positively stained keratin, its staining intensity was poor across all three tissue types.

Advances in cellular and tissue-based imaging techniques for sarcoid granulomas

Sarcoidosis embodies a complex inflammatory disorder spanning multiple systems, with its origin remaining elusive. It manifests as the infiltration of inflammatory cells that coalesce into distinctive noncaseous granulomas within afflicted organs. Unraveling this disease necessitates the utilization of cellular or tissue-based imaging methods to both visualize and characterize the biochemistry of these sarcoid granulomas. Although hematoxylin and eosin stain, standard in routine use alongside cytological stains have found utility in diagnosis within clinical contexts, special stains such as Masson's trichrome, reticulin, methenamine silver, and Ziehl-Neelsen provide additional varied perspectives of sarcoid granuloma imaging. Immunohistochemistry aids in pinpointing specific proteins and gene expressions further characterizing these granulomas. Finally, recent advances in spatial transcriptomics promise to divulge profound insights into their spatial orientation and three-dimensional (3-D) molecular mapping. This review focuses on a range of preexisting imaging methods employed for visualizing sarcoid granulomas at the cellular level while also exploring the potential of the latest cutting-edge approaches like spatial transcriptomics and matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI), with the overarching goal of shedding light on the trajectory of sarcoidosis research.

Skin substitutes based on gellan gum with mechanical and penetration compatibility to native human skin

The study reports on a simple system to fabricate skin substitutes consisting of a naturally occurring bacterial polysaccharide gellan gum. Gelation was driven by the addition of a culture medium whose cations induced gellan gum crosslinking at physiological temperature, resulting in hydrogels. Human dermal fibroblasts were incorporated in these hydrogels and their mechanical, morphological, and penetration characteristics were studied. The mechanical properties were determined by means of oscillatory shear rheology, and a short linear viscoelastic regime was noted up to less than 1% of strain amplitude. The storage modulus increased with an increasing polymer concentration. The moduli were in the range noted for native human skin. After 2 weeks of fibroblast cultivation, the storage moduli showed signs of deterioration, so that a culture time of 2 weeks was proposed for further studies. Microscopic and fluorescent staining observations were documented. These depicted a crosslinked network structure in the hydrogels with a homogeneous distribution of cells and an assured cell viability of 2 weeks. H&E staining was also performed, which showed some traces of ECM formation in a few sections. Finally, caffeine penetration experiments were carried out with Franz diffusion cells. The hydrogels with a higher concentration of polymer containing cells showed an improved barrier function against caffeine compared to previously studied multicomponent hydrogels as well as commercially available 3D skin models. Therefore, these hydrogels displayed both mechanical and penetration compatibility with the ex vivo native human skin.

Suberosin Alleviates Thiazolidinedione-Induced Cardiomyopathy in Diabetic Rats by Inhibiting Ferroptosis via Modulation of ACSL4-LPCAT3 and PI3K-AKT Signaling Pathways

Thiazolidinediones are useful antidiabetic medications. However, their use is associated with adverse side effects like edema, heart failure and bone fractures. In this study, we investigated the anti-ferroptosis effects of suberosin (SBR; a prenylated coumarin) in diabetic Sprague Dawley rats. Further, we assessed the effects of co-administration of SBR (30 and 90 mg/kg/day) with thiazolidinedione (TZ at 15 mg/kg) to mitigate TZ-induced cardiomyopathy in diabetic rats. Our results showed that cardiac output, stroke volume, left ventricle systolic and diastolic pressures were aggravated in diabetic rats treated with TZ alone after 4 weeks. TZ treatments induced ferroptosis as well as marked histoarchitecture disarrangements in rat cardiomyocytes. The study found that optimizing volume overload alleviated cardiac hypertrophy and mitigated left ventricular dysfunction in diabetic rats co-treated with SBR. SBR co-administration with TZ reduced MDA levels in heart tissue and serum iron concentration (biomarkers of ferroptosis), downregulated mRNA expressions of LOX, ACSL4, LPCAT3, and promoted GPX4 activity as well as upregulated mRNA levels of AKT/PI3K/GSK3β as compared to the group administered with TZ at 15 mg/kg. SBR co-administration also helped to retain the normal histoarchitecture of cardiomyocytes in diabetic rats. Hence, our results suggested that SBR is an effective supplement and could be prescribed to diabetic patients along with TZ but this requires further clinical trials.

The sound of blood: photoacoustic imaging in blood analysis

Blood analysis is a ubiquitous and critical aspect of modern medicine. Analyzing blood samples requires invasive techniques, various testing systems, and samples are limited to relatively small volumes. Photoacoustic imaging (PAI) is a novel imaging modality that utilizes non-ionizing energy that shows promise as an alternative to current methods. This paper seeks to review current applications of PAI in blood analysis for clinical use. Furthermore, we discuss obstacles to implementation and future directions to overcome these challenges. Firstly, we discuss three applications to cellular analysis of blood: sickle cell, bacteria, and circulating tumor cell detection. We then discuss applications to the analysis of blood plasma, including glucose detection and anticoagulation quantification. As such, we hope this article will serve as inspiration for PAI's potential application in blood analysis and prompt further studies to ultimately implement PAI into clinical practice.

Mass spectrometry imaging as an emerging tool for studying metabolism in human brain organoids

Human brain organoids are emerging models to study human brain development and pathology as they recapitulate the development and characteristics of major neural cell types, and enable manipulation through an in vitro system. Over the past decade, with the advent of spatial technologies, mass spectrometry imaging (MSI) has become a prominent tool for metabolic microscopy, providing label-free, non-targeted molecular and spatial distribution information of the metabolites within tissue, including lipids. This technology has never been used for studies of brain organoids and here, we set out to develop a standardized protocol for preparation and mass spectrometry imaging of human brain organoids. We present an optimized and validated sample preparation protocol, including sample fixation, optimal embedding solution, homogenous deposition of matrices, data acquisition and processing to maximize the molecular information derived from mass spectrometry imaging. We focus on lipids in organoids, as they play critical roles during cellular and brain development. Using high spatial and mass resolution in positive- and negative-ion modes, we detected 260 lipids in the organoids. Seven of them were uniquely localized within the neurogenic niches or rosettes as confirmed by histology, suggesting their importance for neuroprogenitor proliferation. We observed a particularly striking distribution of ceramide-phosphoethanolamine CerPE 36:1; O2 which was restricted within rosettes and of phosphatidyl-ethanolamine PE 38:3, which was distributed throughout the organoid tissue but not in rosettes. This suggests that ceramide in this particular lipid species might be important for neuroprogenitor biology, while its removal may be important for terminal differentiation of their progeny. Overall, our study establishes the first optimized experimental pipeline and data processing strategy for mass spectrometry imaging of human brain organoids, allowing direct comparison of lipid signal intensities and distributions in these tissues. Further, our data shed new light on the complex processes that govern brain development by identifying specific lipid signatures that may play a role in cell fate trajectories. Mass spectrometry imaging thus has great potential in advancing our understanding of early brain development as well as disease modeling and drug discovery.

Frozen Block Tissue Staining for Eye Structure of Zebrafish Embryo

Histology is a technique used to study the morphology of cell structures by cutting samples into thin sections. Histological cross-section and staining are the techniques needed to visualize the morphology of cell tissues. A suitable tissue staining experiment was created to observe changes in the retinal layer in zebrafish embryos. Zebrafish have a human-like visual system, retina, and eye structures. Due to the small size of zebrafish and undeveloped bones in the embryonic stage, the resistance through cross-section is inevitably small. Here, we present optimized protocol changes in eye tissue of zebrafish using frozen blocks.

StainCUT: Stain Normalization with Contrastive Learning

In recent years, numerous deep-learning approaches have been developed for the analysis of histopathology Whole Slide Images (WSI). A recurrent issue is the lack of generalization ability of a model that has been trained with images of one laboratory and then used to analyze images of a different laboratory. This occurs mainly due to the use of different scanners, laboratory procedures, and staining variations. This can produce strong color differences, which change not only the characteristics of the image, such as the contrast, brightness, and saturation, but also create more complex style variations. In this paper, we present a deep-learning solution based on contrastive learning to transfer from one staining style to another: StainCUT. This method eliminates the need to choose a reference frame and does not need paired images with different staining to learn the mapping between the stain distributions. Additionally, it does not rely on the CycleGAN approach, which makes the method efficient in terms of memory consumption and running time. We evaluate the model using two datasets that consist of the same specimens digitized with two different scanners. We also apply it as a preprocessing step for the semantic segmentation of metastases in lymph nodes. The model was trained on data from one of the laboratories and evaluated on data from another. The results validate the hypothesis that stain normalization indeed improves the performance of the model. Finally, we also investigate and compare the application of the stain normalization step during the training of the model and at inference.

Maximal Activation of Apoptosis Signaling by Cotargeting Antiapoptotic Proteins in BH3 Mimetic-Resistant AML and AML Stem Cells

MCL-1 is known to play a major role in resistance to BCL-2 inhibition, but the contribution of other BCL-2 family proteins has not been fully explored. We, here, demonstrate the ineffectiveness of MCL-1 inhibitor AMG176 in venetoclax-resistant, and conversely, of venetoclax in AMG176-resistant acute myelogenous leukemia (AML). Like cells with acquired resistance to venetoclax, cells with acquired resistance to AMG176 express increased MCL-1. Both cells with acquired resistance to venetoclax and to AMG176 express increased levels of BCL-2 and BCL-2A1, decreased BAX, and/or altered levels of other BCL-2 proteins. Cotargeting BCL-2 and MCL-1 was highly synergistic in AML cell lines with intrinsic or acquired resistance to BH3 mimetics or engineered to genetically overexpress BCL-2 or BCL-2A1 or downregulate BAX. The combination effectively eliminated primary AML blasts and stem/progenitor cells resistant to or relapsed after venetoclax-based therapy irrespective of mutations and cytogenetic abnormalities. Venetoclax and AMG176 combination markedly suppressed antiapoptotic BCL-2 proteins and AML stem/progenitor cells and dramatically extended mouse survival (median 336 vs. control 126 days; P < 0.0001) in a patient-derived xenograft (PDX) model developed from a venetoclax/hypomethylating agent therapy-resistant patient with AML. However, decreased BAX levels in the bone marrow residual leukemia cells after 4-week combination treatment may represent a resistance mechanism that contributed to their survival. Enhanced antileukemia activity was also observed in a PDX model of monocytic AML, known to be resistant to venetoclax therapy. Our results support codependence on multiple antiapoptotic BCL-2 proteins and suppression of BAX as mechanisms of AML resistance to individual BH3 mimetics. Cotargeting of MCL-1 and BCL-2 eliminates otherwise apoptosis-resistant cells.

Polarized Microscopic Analysis of Picrosirius Red Stained Salivary Gland Pathologies: An Observational Study

OBJECTIVE

 Salivary gland diseases and their pathologies may affect the glandular structure including collagen, a major stromal component, in response to tissue damage or diseases. This study aimed to examine the changes in collagens in different salivary gland diseases using polarized picrosirius red staining.

MATERIALS AND METHODS

 The submandibular gland samples diagnosed as sialadenitis, chronic sclerosing sialadenitis, pleomorphic adenoma, adenoid cystic carcinoma, and mucoepidermoid carcinoma were stained with picrosirius red, Masson's trichrome, and anticollagen I staining. The quantity of collagens was examined and reported as a percentage of positive picrosirius red area. The maturity of collagens was studied with polarized light microscope and reported as a percentage of orange-red and yellow-green polarized collagens, representing the mature and immature collagens, respectively.

STATISTICAL ANALYSIS

 The % positive areas for picrosirius red representing the collagen amount among salivary gland diseases were analyzed by one-way analysis of variance with Tukey's test. The % orange-red and % yellow-green polarized areas representing the collagen maturity were analyzed by Kruskal-Wallis test and Mann-Whitney U test.

RESULTS

 The malignant tumors, adenoid cystic carcinoma (29.92) and mucoepidermoid carcinoma (26.59), had higher significant percentage of positive picrosirius red area, compared with the benign tumor (14.56), chronic sclerosing sialadenitis (10.61), and sialadenitis (7.22) (p < 0.05). The percentages of orange-red polarized areas are 48.07, 39.6, 62.67, 83.75, and 76.05 in sialadenitis, chronic sclerosing sialadenitis, pleomorphic adenoma, adenoid cystic carcinoma, and mucoepidermoid carcinoma, respectively. This percentage tended to increase in the benign and malignant lesions with statistical difference, compared with the inflammatory lesions (p < 0.05). There was no statistical difference in the percentages of yellow-green polarized areas among various salivary gland diseases. In addition, the results of Masson's trichrome and anticollagen I staining are corresponding to that of picrosirius red among various salivary gland diseases.

CONCLUSIONS

 Polarized picrosirius red demonstrated the most amounts of collagen in the malignant lesion, and represented the different maturity of collagens in each lesion group. Studying the amounts and maturity of collagen with picrosirius red for extracellular matrix alteration in salivary gland diseases along with routine hematoxylin and eosin, Masson's trichrome, and immunohistochemistry may provide a better understanding in different salivary gland pathologies.

Physiology and Transcriptomics Analysis Reveal the Contribution of Lungs on High-Altitude Hypoxia Adaptation in Tibetan Sheep

The Tibetan sheep is an indigenous species on the Tibetan plateau with excellent adaptability to high-altitude hypoxia and is distributed at altitudes of 2500–5000 m. The high-altitude hypoxia adaptation of Tibetan sheep requires adaptive reshaping of multiple tissues and organs, especially the lungs. To reveal the mechanisms of adaptation at the tissue and molecular levels in the lungs of Tibetan sheep under hypoxic conditions at different altitudes, we performed light and electron microscopic observations, transcriptomic sequencing, and enzyme-linked immunosorbent assay studies on the lungs of Tibetan sheep from three altitudes (2500, 3500, and 4500 m). The results showed that in addition to continuous increase in pulmonary artery volume, thickness, and elastic fiber content with altitude, Tibetan sheep increase the hemoglobin concentration at an altitude of 3500 m, while they decrease the Hb concentration and increase the surface area of gas exchange and capacity of the blood at an altitude of 4500 m. Other than that, some important differentially expressed genes related to angiogenesis (FNDC1, HPSE, and E2F8), vasomotion and fibrogenesis (GJA4, FAP, COL1A1, COL1A2, COL3A1, and COL14A1), and gas transport (HBB, HBA1, APOLD1, and CHL1) were also identified; these discoveries at the molecular level explain to some extent the physiological findings. In conclusion, the lungs of Tibetan sheep adopt different strategies when adapting to different altitudes, and these findings are valuable for understanding the basis of survival of indigenous species on the Tibetan plateau.

A low-cost pathological image digitalization method based on 5 times magnification scanning

BACKGROUND

Digital pathology has aroused widespread interest in modern pathology. The key to digitalization is to scan the whole slide image (WSI) at high magnification. The file size of each WSI at 40 times magnification (40×) may range from 1 gigabyte (GB) to 5 GB depending on the size of the specimen, which leads to huge storage capacity, very slow scanning and network exchange, seriously increasing time and storage costs for digital pathology.

METHODS

We design a strategy to scan slides with low resolution (LR) (5×), and a superresolution (SR) method is proposed to restore the image details during diagnosis. The method is based on a multiscale generative adversarial network, which can sequentially generate three high-resolution (HR) images: 10×, 20×, and 40×. A dataset consisting of 100,000 pathological images from 10 types of human body systems is used for training and testing. The differences between the generated images and the real images have been extensively evaluated using quantitative evaluation, visual inspection, medical scoring, and diagnosis.

RESULTS

The file size of each 5× WSI is approximately 15 Megabytes. The peak-signal-to-noise ratios (PSNRs) of 10× to 40× generated images are 24.167±3.734 dB, 22.272±4.272 dB, and 20.436±3.845 dB, and the structural similarity (SSIM) index values are 0.845±0.089, 0.680±0.150, and 0.559±0.179, which are better than those of other SR networks and conventional digital zoom methods. Visual inspections show that the generated images have details similar to the real images. Visual scoring average with 0.95 confidence interval from three pathologists are 3.630±1.024, 3.700±1.126, and 3.740±1.095, respectively, and the P value of analysis of variance is 0.367, indicating the pathologists confirm that generated images include sufficient information for diagnosis. The average value of the Kappa test of the diagnoses of paired generated and real images is 0.990, meaning the diagnosis of generated images is highly consistent with that of the real images.

CONCLUSIONS

The proposed method can generate high-quality 10×, 20×, 40× images from 5× images, which can effectively reduce the time and storage costs of digitalization up to 1/64 of the previous costs, which shows the potential for clinical applications and is expected to be an alternative digitalization method after large-scale evaluation.

HEPATOCELLULAR TOXICITY OF THE METABOLITE EMODIN PRODUCED BY THE COMMON BUCKTHORN (RHAMNUS CATHARTICA) IN GREEN FROG (LITHOBATES CLAMITANS) TADPOLES

The secondary metabolite emodin, produced by the widely distributed invasive shrub known as the common buckthorn (Rhamnus cathartica), has been shown to produce deformities and mortality in invertebrates, fish, and amphibian larvae. Here, we describe the effects on the liver of green frog (Lithobates clamitans) tadpoles after 21 d of exposure to high concentrations of emodin in a controlled environment. Histopathologic analysis showed fibrosis, bile duct proliferation, hepatocellular swelling, and accumulations of flocculent material consistent with emodin within the gall bladder and bile ducts of exposed individuals. The extensive fibrosis produced probably impeded the blood flow within the portal triads, limiting the detoxification function of the liver and resulting in hepatocellular necrosis and premature death for the individuals exposed. Exposure to emodin in the environment could represent a significant threat to developing amphibian larvae and contribute to local declines of populations.

GasHisSDB: A new gastric histopathology image dataset for computer aided diagnosis of gastric cancer

BACKGROUND AND OBJECTIVE

Gastric cancer is the fifth most common cancer globally, and early detection of gastric cancer is essential to save lives. Histopathological examination of gastric cancer is the gold standard for the diagnosis of gastric cancer. However, computer-aided diagnostic techniques are challenging to evaluate due to the scarcity of publicly available gastric histopathology image datasets.

METHODS

In this paper, a noble publicly available Gastric Histopathology Sub-size Image Database (GasHisSDB) is published to identify classifiers' performance. Specifically, two types of data are included: normal and abnormal, with a total of 245,196 tissue case images. In order to prove that the methods of different periods in the field of image classification have discrepancies on GasHisSDB, we select a variety of classifiers for evaluation. Seven classical machine learning classifiers, three Convolutional Neural Network classifiers, and a novel transformer-based classifier are selected for testing on image classification tasks.

RESULTS

This study performed extensive experiments using traditional machine learning and deep learning methods to prove that the methods of different periods have discrepancies on GasHisSDB. Traditional machine learning achieved the best accuracy rate of 86.08% and a minimum of just 41.12%. The best accuracy of deep learning reached 96.47% and the lowest was 86.21%. Accuracy rates vary significantly across classifiers.

CONCLUSIONS

To the best of our knowledge, it is the first publicly available gastric cancer histopathology dataset containing a large number of images for weakly supervised learning. We believe that GasHisSDB can attract researchers to explore new algorithms for the automated diagnosis of gastric cancer, which can help physicians and patients in the clinical setting.

Low concentration Phloxine B staining for high chemical contrast, nonlinear microscope mosaic imaging of skin alterations in pseudoxanthoma elasticum

Pseudoxanthoma elasticum (PXE) is an autosomal recessive metabolic disorder characterized by ectopic mineralization of soft connective tissue. Histopathology findings include fragmented, mineralized elastic fibers and calcium deposits in the mid-dermis. Nonlinear microscopy (NLM) can be used for visualization of these histopathological alterations of the mid-dermis in PXE-affected skin sections. Upon introducing a normalized 3D color vector representation of emission spectra of three of the main tissue components (collagen, elastin and calcification) we found that due to their broad, overlapping emission spectra, spectral separation of emission from elastin and calcification is practically impossible in fresh-frozen or unstained, deparaffinized PXE sections. However, we found that the application of a low concentration Phloxine B staining after the deparaffinization process creates an imaging contrast for these two tissue components, which enables spectral decomposition of their fluorescence images. The obtained concentration maps for calcium deposits can be well suited for the determination of illness severity by quantitative analysis.

Integration of deep learning-based image analysis and genomic data in cancer pathology: A systematic review

BACKGROUND

Over the past decade, the development of molecular high-throughput methods (omics) increased rapidly and provided new insights for cancer research. In parallel, deep learning approaches revealed the enormous potential for medical image analysis, especially in digital pathology. Combining image and omics data with deep learning tools may enable the discovery of new cancer biomarkers and a more precise prediction of patient prognosis. This systematic review addresses different multimodal fusion methods of convolutional neural network-based image analyses with omics data, focussing on the impact of data combination on the classification performance.

METHODS

PubMed was screened for peer-reviewed articles published in English between January 2015 and June 2021 by two independent researchers. Search terms related to deep learning, digital pathology, omics, and multimodal fusion were combined.

RESULTS

We identified a total of 11 studies meeting the inclusion criteria, namely studies that used convolutional neural networks for haematoxylin and eosin image analysis of patients with cancer in combination with integrated omics data. Publications were categorised according to their endpoints: 7 studies focused on survival analysis and 4 studies on prediction of cancer subtypes, malignancy or microsatellite instability with spatial analysis.

CONCLUSIONS

Image-based classifiers already show high performances in prognostic and predictive cancer diagnostics. The integration of omics data led to improved performance in all studies described here. However, these are very early studies that still require external validation to demonstrate their generalisability and robustness. Further and more comprehensive studies with larger sample sizes are needed to evaluate performance and determine clinical benefits.

Modulation of SOD3 Levels Is Detrimental to Retinal Homeostasis

Retinal oxidative stress is a common secondary feature of many retinal diseases. Though it may not be the initial insult, it is a major contributor to the pathogenesis of highly prevalent retinal dystrophic diseases like macular degeneration, diabetic retinopathy, and retinitis pigmentosa. We explored the role of superoxide dismutase 3 (SOD3) in retinal homeostasis since SOD3 protects the extracellular matrix (ECM) from oxidative injury. We show that SOD3 is mainly extracellularly localized and is upregulated as a result of environmental and pathogenic stress. Ablation of SOD3 resulted in reduced functional electroretinographic responses and number of photoreceptors, which is exacerbated with age. By contrast, overexpression showed increased electroretinographic responses and increased number of photoreceptors at young ages, but appears deleterious as the animal ages, as determined from the associated functional decline. Our exploration shows that SOD3 is vital to retinal homeostasis but its levels are tightly regulated. This suggests that SOD3 augmentation to combat oxidative stress during retinal degenerative changes may only be effective in the short-term.

In-Silico Analysis of Chromatin Modifiers and Profiling of Histone Deacetylases (HDAC's) in Human Oral Cancer

Histone modifications have been demonstrated to play a significant role in oral squamous cell carcinoma (OSCC) epigenetic regulation. An in-silico analysis of The Cancer Genome Atlas (TCGA) of various histone acetyl transferases (HATs) and histone deacetylases (HDACs) suggested that HATs do not differ between normal and tumor samples whereas HDAC2 and HDAC1 change maximally and marginally respectively between normal and tumor patients with no change being noted in HDAC6 expression. Hence, this investigation was carried out to validate the expression states of HDAC 1, 2 and 6 mRNAs in buccal mucosa and tongue SCC samples in an Indian cohort. Buccal mucosa and tongue squamous cell carcinoma tissues with intact histopathology were processed for RNA isolation followed by cDNA synthesis which was then subjected to q-PCR for HDACs. The average RNA yield of the tongue tissue sample was ∼2 µg/mg of tissue and the A_260/280 ratios were between 2.03 and 2.06. The average RNA yield of buccal mucosa tissue sample was ∼1 µg/mg of tissue and the A_260/280 ratio were between 2.00 and 2.08. We have demonstrated that HDAC2 was overexpressed in tongue and buccal mucosa samples. Over-expression of HDAC2 imply potential use of HDACi along with standard chemotherapeutic drug in oral cancer treatment.

Optical Metabolic Imaging of Mitochondrial Dysfunction on HADH Mutant Newborn Rat Hearts

BACKGROUND

Mitochondrial [Formula: see text]-oxidation of fatty acids is the primary energy source for the heart and carried out by Hydroxy Acyl-CoA Dehydrogenase (HADH) encoded trifunctional protein. Mutations in the genes encoding mitochondrial proteins result in functionally defective protein complexes that contribute to energy deficiencies, excessive reactive oxygen species (ROS) production, and accumulation of damaged mitochondria. We hypothesize that a dramatic alternation in redox state and associated mitochondrial dysfunction is the underlying cause of Fatty Acid Oxidation (FAO) deficiency mutant, resulting in heart failure. Mitochondrial co-enzymes, NADH and FAD, are autofluorescent metabolic indices of cells when imaged, yield a quantitative assessment of the cells' redox status and, in turn, that of the tissue and organ.

METHOD

We utilized an optical cryo-imager to quantitively evaluate the three-dimensional distribution of mitochondrial redox state in newborn rats' hearts and kidneys. Redox ratio (RR) assessment shows that mitochondrial dysfunction is extreme and could contribute to severe heart problems and eventual heart failure in the mutants.

RESULTS

Three-dimensional redox ratio (NADH/FAD) rendering, and the volumetric mean value calculations confirmed significantly decreased cardiac RR in mutants by 31.90% and 12.32%, in renal mitochondrial RR compared to wild-type control. Further, histological assessment of newborn heart myocardial tissue indicated no significant difference in myocardial tissue architecture in both control and severe (HADHAe4-/-) conditions.

CONCLUSION

These results demonstrate that optical imaging can accurately estimate the redox state changes in newborn rat organs. It is also apparent that the FAO mutant's heart tissue with a low redox ratio is probably more vulnerable to cumulative damages than kidneys and fails prematurely, contributing to sudden death.

Gut micobiota alteration by Lactobacillus rhamnosus reduces pro-inflammatory cytokines and glucose level in the adult model of Zebrafish

Objective

Type 2 diabetes mellitus (T2DM) is still a challenge for physicians to manage patient’s circumstances. It is assumed that alterations in the normal flora may be involved in the pathogenesis of T2DM through inducing chronic inflammation. To investigate the effect of Lactobacillus rhamnosus as a common probiotic on T2DM, we induced an experimental model of T2DM in adult male Zebrafish by gradient hyper-glucose accumulation methodology.

Results

In this trial 3-month old male adult Zebrafish were divided in to four groups including two control groups and T2DM induced groups with or without probiotic treatment. After 5 days of acclimation, T2DM was induced by a gradient hyper-glucose accumulation methodology. Diabetic fishes had statistically abnormal blood glucose and pro-inflammatory cytokine levels compared to control group (p = 0.0001). These results suggest that probiotic intervention decreased the blood glucose level in the T2DM-P group by decreasing pro-inflammatory cytokines responsible for signaling in T2DM therapeutic modalities.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05706-5.

Training of computational algorithms to predict NAFLD activity score and fibrosis stage from liver histopathology slides

BACKGROUND

The incidence of non-alcoholic fatty liver disease (NAFLD) and its progressive form, non-alcoholic steatohepatitis (NASH), has been increasing for decades. Since the mainstay is lifestyle modification in this mainly asymptomatic condition, there is a need for accurate diagnostic methods.

OBJECTIVES

This study proposes a method with a computer-aided diagnosis (CAD) system to predict NAFLD Activity score (NAS scores-steatosis, lobular inflammation, and ballooning) and fibrosis stage from histopathology slides.

METHODS

A total of 87 pathology slides pairs (H&E and Trichrome-stained) were used for the study. Ground-truth NAS scores and fibrosis stages were previously identified by a pathologist. Each slide was split into 224 × 224 patches and fed into a feature extraction network to generate local features. These local features were processed and aggregated to obtain a global feature to predict the slide's scores. The effects of different training strategies, as well as training data with different staining and magnifications were explored. Four-fold cross validation was performed due to the small data size. Area Under the Receiver Operating Curve (AUROC) was utilized to evaluate the prediction performance of the machine-learning algorithm.

RESULTS

Predictive accuracy for all subscores was high in comparison with pathologist assessment. There was no difference among the 3 magnifications (5x, 10x, 20x) for NAS-steatosis and fibrosis stage tasks. A larger magnification (20x) achieved better performance for NAS-lobular scores. Middle-level magnification was best for NAS-ballooning task. Trichrome slides are better for fibrosis stage prediction and NAS-ballooning score prediction task. NAS-steatosis prediction had the best performance (AUC 90.48%) in the model. A good performance was observed with fibrosis stage prediction (AUC 83.85%) as well as NAS-ballooning prediction (AUC 81.06%).

CONCLUSIONS

These results were robust. The method proposed proved to be effective in predicting NAFLD Activity score and fibrosis stage from histopathology slides. The algorithms are an aid in having an accurate and systematic diagnosis in a condition that affects hundreds of millions of patients globally.

Examining lysyl oxidase-like modulation of collagen architecture in 3D spheroid models of idiopathic pulmonary fibrosis via second-harmonic generation microscopy

SIGNIFICANCE

Idiopathic pulmonary fibrosis (IPF) patients have a poor prognosis with short lifespan following diagnosis as there are limited effective treatment options. Despite matrix stiffening being the hallmark of the disease there remains a lack of knowledge surrounding the underlying collagen alterations in the disease. Specifically, while increased collagen crosslinking has been implicated, the resulting effects on collagen macro/supramolecular changes have not been explored.

AIM

We sought to determine if second-harmonic generation (SHG) microscopy could characterize differences in the collagen architecture in 3D spheroid models of IPF grown under different crosslinking modulation conditions (promotion and inhibition).

APPROACH

We used SHG metrics based on the fiber morphology, relative SHG brightness, and macro/supramolecular structure by SHG polarization analyses to compare the structure of the IPF spheroids.

RESULTS

Comparison of the fiber morphology of the spheroids showed that the control group had the longest, straightest, and thickest fibers. The spheroids with crosslink enhancement and inhibition had the highest and lowest SHG conversion efficiencies, respectively, consistent with the resulting harmonophore density. SHG polarization analyses showed that the peptide pitch angle, alignment of collagen molecules, and overall chirality were altered upon crosslink modulation and were also consistent with reduced organization relative to the control group.

CONCLUSIONS

While no single SHG signature is associated with crosslinking, we show that the suite of metrics used here is effective in delineating alterations across the collagen architecture sizescales. The results largely mirror those of human tissues and demonstrate that the combination of 3D spheroid models and SHG analysis is a powerful approach for hypothesis testing the roles of operative cellular and molecular factors in IPF.

Toward developing natural histologic stains using anthocyanins: A novel approach

Introduction:

In the present-day scenario, wherein histotechnological laboratory personnel come into contact with numerous hazardous chemicals every day, laboratories are emphasizing on development of safer and environment-friendly alternatives globally which are easily available and feasible. In this context, we have attempted to utilize anthocyanins, a family of pigments naturally occurring in fruits and flowers and which are already used as natural food colorants, for assessing their utility as histological stains.

Materials and methods:

Juices of thin consistency from well-ripened pomegranates were obtained by using a juicer with blender functions. Formalin-fixed paraffin-embedded 4 μm thin sections were immersed in this solution for 2 h, during which the solution was periodically monitored. Several modifications were attempted such as the addition of Citrus limon (lemon) extract or acetic acid, change in orientation of the slides and refrigeration of the solution during the staining procedure.

Results:

A peculiar pattern of reasonably diagnostic staining was observed in which the basal and suprabasal cells, basement membrane, inflammatory cells and collagen fibers stained prominently with a magenta color. The addition of lemon, horizontal orientation of slides and refrigeration each separately led to an improvement in staining characteristics. The addition of 4% acetic acid and refrigeration of the solution each led to an improvement in longevity of the staining solution.

Conclusion:

Anthocyanins could potentially be used as viable histological stains having advantages of availability, feasibility, color stability and nontoxicity, although numerous modifications to improve longevity of staining solution and staining characteristics are warranted by further research for which the present study could serve as a pretext.

Heart development in two populations of Atlantic killifish (Fundulus heteroclitus) following exposure to a polycyclic aromatic hydrocarbon mixture

Historic industrial pollution of the Elizabeth River, Virginia resulted in polycyclic aromatic hydrocarbon (PAH) contamination in sediments. Atlantic killifish (Fundulus heteroclitus) inhabiting the Atlantic Wood (AW) industrial site adapted to complex PAH mixture at this Superfund site. Their embryos have proved highly resistant to cardiac abnormalities indicative of PAH toxicity. In this study, embryos spawned from adults collected at AW and King's Creek (KC), a reference site, were exposed at 24 h post fertilization (hpf) to Elizabeth River Sediment Extract (ERSE), a complex PAH mixture, in a range of concentrations (0, 5.04, 50.45, 100.90, 151.35, or 252.25 µg/L total PAHs). Embryos were processed for histology at 144 hpf to enable evaluations of hearts at tissue and cellular levels. Morphometry and severity scoring were used to evaluate the extent of alterations. Unexposed embryos were similar in both populations. ERSE exposure resulted in multiple changes to hearts of KC embryos but not AW. Alterations were particularly evident in KC embryos exposed to concentrations above 1% ERSE (50.45 µg/L), which had thinner ventricular walls and larger pericardial edema. Individuals with moderate pericardial edema maintained arrangement and proximity of heart chambers, but changes were seen in ventricular myocytes. Severe pericardial edema was prevalent in exposed KC embryos and typically resulted in tube heart formation. Ventricles of tube hearts had very thin walls composed of small, basophilic cells and lacked trabeculae. Edematous pericardial fluid contained small amounts of proteinaceous material, as did controls, and was free of cells. This fluid was primarily unstained, suggesting water influx due to increased permeability. The use of histological approaches provided more specific detail for tissue and cellular effects in hearts of embryos exposed to PAHs and enabled understanding of potential links to later life effects of early life exposure.

A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate

X-ray microtomography (microCT) enables histological-scale 3D imaging of many types of biological samples, but it has yet to rival traditional histology for differentiation of tissue types and cell components. This report presents prima facie results indicating that a simple lead(II) acetate staining solution can impart preferential X-ray contrast to cell nuclei. While not strictly selective for nuclei, the staining reflects local cell-density differences. It can be applied in a single overnight treatment and does not require hematoxylin staining or drying of the sample. The stain is removable with EDTA, and it may enhance early calcifications. A basic protocol is given as a guide for further testing and optimization.

Specialized Histological and Histomorphometrical Analytical Methods for Biocompatibility Testing of Biomaterials for Maxillofacial Surgery in (Pre-) Clinical Studies

Both preclinical in vivo experiments and clinical trials are indispensable for analysis of tissue reactions in evaluating the compatibility of biomaterials or medical devices, i.e. the cell types interacting with the material, integration or degradation behavior, implant bed vascularization and immunological response. In particular, both the histological workup (including the processes such as embedding, cutting, histochemical and immunohistochemical staining methods), as well as qualitative and quantitative analysis are crucial steps enabling the final evaluation of biocompatibility. We present a short overview of the most important steps of the different workup and analytical methods used in preclinical and clinical biopsies for both novice and experienced researchers in the field of biomaterial science.

Over high or low dietary protein levels depressed the growth, TOR signaling, apoptosis, immune and anti-stress of abalone Haliotis discus hannai

A 120-day feeding trial was conducted to investigate the effects of relative higher and lower dietary protein levels on the growth, immunity and anti-stress of abalone Haliotis discus hannai fed diets with 17.64% (low), 30.49% (normal) and 43.27% (high) of proteins, respectively. The results showed that compared with 30.49% of dietary protein, 17.64% and 43.27% of dietary protein levels significantly decreased the weight gain rate and the activities of α-amylase, trypsin, alanine aminotransferase and aspartate aminotransferase in the hepatopancreas and serum of abalone (P < 0.05). Abalone fed 30.49% of dietary protein had the highest activity of superoxidase, acid phosphatase, alkaline phosphatase, lysozyme and the total anti-oxidative capacity, and the lowest content of malondialdehyde in the serum and hepatopancreas (P < 0.05). The gene expressions of TOR, S6k, Bcl-2, IκB, NfκB, TNF-α and Nrf₂ were significantly up-regulated in the group with 30.49% of dietary protein (P < 0.05). Pathological abnormalities in hepatocyte cells of abalone were found in the groups with 17.64% and 43.27% of dietary protein. Meanwhile, accumulative mortalities of abalone after the Vibrio parahaemolyticus challenge test and heat stress test were significantly increased within these two groups (P < 0.05). In conclusion, the excessive (43.27) or deficient (17.64) dietary protein levels depressed the growth and immunity of abalone. Combined with the stress tests results, 17.63% or 43.27% of dietary protein contents are not recommended to the abalone facing the stress of vibriosis or high-water temperature (≥28 °C).

Employment of cytology for in vitro skin irritation test using a reconstructed human epidermis model, Keraskin™

Skin irritation tests using reconstructed human epidermis (RhE) employ viability as an endpoint, but color interference or borderline results are often problematic. We examined whether the cytology of cells from treated RhE could determine skin irritancy. Six chemicals (three irritants; DnP, 1-B, PH, three non-irritants; DP, APA, HS) were evaluated in a RhE, Keraskin™. DP, HS, and PH were clearly classified with viability, but DnP, 1-B, and APA were often falsely determined, due to borderline values falling near the cutoff, 50%. In histology, the tissues treated with DnP, 1-B, and PH showed erosion of the stratum corneum, vacuolization, and necrosis in the basal layer. DP- and HS-treated tissues showed relatively normal morphology but APA induced necrosis similar to irritants. Cytology revealed that DnP, 1-B or PH depleted cells and induced irregular and abnormal cell shapes. In contrast, relatively regular and normal shapes and clear distinction between the nucleus and cytoplasm was observed for DP, APA and HS. To further confirm it, additional 10 substances, including false positives from OECD TG 439, were tested. Overall (16 substances in total), cytology: total area predicted the skin irritancy of test chemicals with the highest accuracy (87.5%) followed by cytology: cell count (81.3%), histology (75%) and viability (68.8%), confirming the utility of cytology as an alternative endpoint in the skin irritation test using RhE.

Predict Ki-67 Positive Cells in H&E-Stained Images Using Deep Learning Independently From IHC-Stained Images

OBJECTIVE

To obtain molecular information in slides directly from H&E staining slides, which apparently display morphological information, to show that some differences in molecular level have already encoded in morphology.

METHODS

In this paper, we selected Ki-67-expression as the representative of molecular information. We proposed a method that can predict Ki-67 positive cells directly from H&E stained slides by a deep convolutional network model. To train this model, we constructed a dataset containing Ki-67 negative or positive cell images and background images. These images were all extracted from H&E stained WSIs and the Ki-67 expression was acquired from the corresponding IHC stained WSIs. The trained model was evaluated both on classification performance and the ability to quantify Ki-67 expression in H&E stained images.

RESULTS

The model achieved an average accuracy of 0.9371 in discrimination of Ki-67 negative cell images, positive cell images and background images. As for evaluation of quantification performance, the correlation coefficient between the quantification results of H&E stained images predicted by our model and that of IHC stained images obtained by color channel filtering is 0.80.

CONCLUSION AND SIGNIFICANCE

Our study indicates that the deep learning model has a good performance both on prediction of Ki-67 positive cells and quantification of Ki-67 expression in cancer samples stained by H&E. More generally, this study shows that deep learning is a powerful tool in exploring the relationship between morphological information and molecular information.

AVAILABILITY AND IMPLEMENTATION

The main program is available at https://github.com/liuyiqing2018/predict_Ki-67_from_HE.

Colon cancer detection by using Poincaré sphere and 2D polarimetric mapping of ex vivo colon samples

This work is dedicated to the diagnosis and grading of colon cancer by a combined use of Poincaré sphere and 2D Stokes vector polarimetry mapping approaches. The major challenge consists in exploring the applicability of polarized light for noninvasive screening of the histological abnormalities within the samples of biological tissues. Experimental studies were conducted in ex vivo colon sample, excised after surgical procedure for colon tumor removal of G2-adenocarcinoma lesion. Polarimetric measurements in linear and circular regime were carried via personally developed polarimetric, optical set-up, using supercontinuous fiber laser with irradiation fixed at 635 nm. We apply the Poincaré sphere and two-dimensional Stokes vector scanning approach for screening the corresponding tissue samples. A comparison between linear and circular polarization states is made both for quantitative and qualitative evaluations. It is shown that circular polarization has better diagnostic capabilities than linear polarization, with higher dynamic ranges of the polarimetric parameters and better values of the diagnostic quantities. In addition to the standard polarimetry parameters, utilized as essential diagnostic markers, we apply statistical analysis to obtain more detailed information in frame of the applied diagnostic approach.

Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis

The importance of fibrillar collagen topology and organization in disease progression and prognostication in different types of cancer has been characterized extensively in many research studies. These explorations have either used specialized imaging approaches, such as specific stains (e.g., picrosirius red), or advanced and costly imaging modalities (e.g., second harmonic generation imaging (SHG)) that are not currently in the clinical workflow. To facilitate the analysis of stromal biomarkers in clinical workflows, it would be ideal to have technical approaches that can characterize fibrillar collagen on standard H&E stained slides produced during routine diagnostic work. Here, we present a machine learning-based stromal collagen image synthesis algorithm that can be incorporated into existing H&E-based histopathology workflow. Specifically, this solution applies a convolutional neural network (CNN) directly onto clinically standard H&E bright field images to extract information about collagen fiber arrangement and alignment, without requiring additional specialized imaging stains, systems or equipment.

Short-term tissue permeability actions of dextran sulfate sodium studied in a colon organ culture system

Dextran sulfate sodium (DSS)-induced colitis is the most commonly used animal model for inflammatory bowel diseases. However, the precise molecular action of DSS, in particular its initial effect on the epithelial tissue permeability, is still poorly understood. In the present work, organ culture of mouse – and pig colon explants were performed for 1–2 h in the presence/absence of 2% DSS together with polar- and lipophilic fluorescent probes. Probe permeability was subsequently assessed by fluorescence microscopy. DSS rapidly increased paracellular permeability of 70-kDa dextran without otherwise affecting the overall epithelial integrity. FITC-conjugated DSS likewise permeated the epithelial barrier and strongly accumulated in nuclei of cells scattered in the lamina propria. By immunolabeling, plasma cells, T cells, macrophages, mast cells, and fibroblasts were identified as possible targets for DSS, indicating that accumulation of the polyanion in nuclei was not confined to a particular type of cell in the lamina propria. In contrast, colonocytes were rarely targeted by DSS, but as visualized by transmission electron microscopy, it induced the formation of vacuole-like structures in the intercellular space between adjacent epithelial cells. Nuclei of various cell types in the lamina propria, including both cells of the innate and adaptive immune system, are novel targets for a rapid action of DSS, and from previous in vitro studies, polyanions like DSS are known to disrupt nucleosomes by binding to the histones. We therefore propose that nuclear targeting is one way whereby DSS exerts its inflammatory action as a colitogen in animal models of inflammatory bowel diseases.

Understanding How Infrared Beak Treatment Affects the Beak Tissue and the Healing Response of Brown and White Feathered Layer Pullets

Simple Summary

Beak treatment of commercial laying hens remains an important management practice as it is one of the most effective methods of controlling and preventing cannibalism. Infrared beak treatment is the most recent beak treatment method to be utilized and the available literature shows that it has less of a negative impact on birds compared to older methods of beak treatment. Although there is considerable research evaluating the impact of infrared beak treatment on the production and welfare of laying hens, it is still not fully understood how it affects the beak tissue during the first few days post treatment. This is important to understand as it can provide insight into whether or not treated birds are experiencing pain, which has consequences for both welfare and productivity. This study examined the effect of infrared beak treatment on the histology of the beak during early life (first 21 days). Epithelial regeneration started as soon as five days post treatment. There was no evidence that infrared beak treatment resulted in the formation of neuromas or any other indication of chronic pain.

Abstract

Infrared beak treatment has less of a negative impact on laying hen welfare compared to other methods of beak treatment; however, it is still not fully understood how infrared beak treatment affects the beak tissue during the first few days post treatment. The objective of this study was to examine the histology of infrared beak treated vs. untreated beaks of 2 strains of layer chicks during early life. One-hundred Lohmann Brown-Lite (LB) and 100 Lohmann LSL-Lite (LW) chicks were obtained; 50 chicks per strain were infrared beak treated post hatch (IR) with the remainder being sham untreated controls (C). Data collected included presence of beak sloughing, length, and histology. Histology slides were analyzed and scored on a scale of 0 to 4, with 0 indicating no lesions and 4 indicating severe inflammation. Sloughing of the treated beak tissue began at 10 days and was complete by 20 days. IR pullets had shorter beak lengths once sloughing was initiated and less overall beak growth. No differences in healing scores were found between treated LB and LW beaks; all treated LB beaks were healed by 21 days while some LW beaks still showed inflammation. Overall, infrared beak treatment was effective at reducing beak growth post treatment. Healing occurred post treatment in both strains as evident by complete regeneration of the epithelium and a reduction in inflammation.

A dense multi-path decoder for tissue segmentation in histopathology images

BACKGROUND AND OBJECTIVE

Segmenting different tissue components in histopathological images is of great importance for analyzing tissues and tumor environments. In recent years, an encoder-decoder family of convolutional neural networks has increasingly adopted to develop automated segmentation tools. While an encoder has been the main focus of most investigations, the role of a decoder so far has not been well studied and understood. Herein, we proposed an improved design of a decoder for the segmentation of epithelium and stroma components in histopathology images.

METHODS

The proposed decoder is built upon a multi-path layout and dense shortcut connections between layers to maximize the learning and inference capability. Equipped with the proposed decoder, neural networks are built using three types of encoders (VGG, ResNet and preactived ResNet). To assess the proposed method, breast and prostate tissue datasets are utilized, including 108 and 52 hematoxylin and eosin (H&E) breast tissues images and 224 H&E prostate tissue images.

RESULTS

Combining the pre-activated ResNet encoder and the proposed decoder, we achieved a pixel wise accuracy (ACC) of 0.9122, a rand index (RAND) score of 0.8398, an area under receiver operating characteristic curve (AUC) of 0.9716, Dice coefficient for stroma (DICE_STR) of 0.9092 and Dice coefficient for epithelium (DICE_EPI) of 0.9150 on the breast tissue dataset. The same network obtained 0.9074 ACC, 0.8320 Rand index, 0.9719 AUC, 0.9021 DICE_EPI and 0.9121 DICE_STR on the prostate dataset.

CONCLUSIONS

In general, the experimental results confirmed that the proposed network is superior to the networks combined with the conventional decoder. Therefore, the proposed decoder could aid in improving tissue analysis in histopathology images.

Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association

The advent of whole-slide imaging in digital pathology has brought about the advancement of computer-aided examination of tissue via digital image analysis. Digitized slides can now be easily annotated and analyzed via a variety of algorithms. This study reviews the fundamentals of tissue image analysis and aims to provide pathologists with basic information regarding the features, applications, and general workflow of these new tools. The review gives an overview of the basic categories of software solutions available, potential analysis strategies, technical considerations, and general algorithm readouts. Advantages and limitations of tissue image analysis are discussed, and emerging concepts, such as artificial intelligence and machine learning, are introduced. Finally, examples of how digital image analysis tools are currently being used in diagnostic laboratories, translational research, and drug development are discussed.

Histological Analyses of Acute Alcoholic Liver Injury in Zebrafish

Alcoholic Liver Disease (ALD) refers to damage to the liver due to acute or chronic alcohol abuse. It is among the leading causes of alcohol-related morbidity and mortality and affects more than 2 million people in the United States. A better understanding of the cellular and molecular mechanisms underlying alcohol-induced liver injury is crucial for developing effective treatment for ALD. Zebrafish larvae exhibit hepatic steatosis and fibrogenesis after just 24 h of exposure to 2% ethanol, making them useful for the study of acute alcoholic liver injury. This work describes the procedure for acute ethanol treatment in zebrafish larvae and shows that it causes steatosis and swelling of the hepatic blood vessels. A detailed protocol for Hematoxylin and Eosin (H&E) staining that is optimized for the histological analysis of the zebrafish larval liver, is also described. H&E staining has several unique advantages over immunofluorescence, as it marks all liver cells and extracellular components simultaneously and can readily detect hepatic injury, such as steatosis and fibrosis. Given the increasing usage of zebrafish in modeling toxin and virus-induced liver injury, as well as inherited liver diseases, this protocol serves as a reference for the histological analyses performed in all these studies.

An alternative reference space for H&E color normalization

Digital imaging of H&E stained slides has enabled the application of image processing to support pathology workflows. Potential applications include computer-aided diagnostics, advanced quantification tools, and innovative visualization platforms. However, the intrinsic variability of biological tissue and the vast differences in tissue preparation protocols often lead to significant image variability that can hamper the effectiveness of these computational tools. We developed an alternative representation for H&E images that operates within a space that is more amenable to many of these image processing tools. The algorithm to derive this representation operates by exploiting the correlation between color and the spatial properties of the biological structures present in most H&E images. In this way, images are transformed into a structure-centric space in which images are segregated into tissue structure channels. We demonstrate that this framework can be extended to achieve color normalization, effectively reducing inter-slide variability.

The differentiation potential of gingival mesenchymal stem cells induced by apical tooth germ cell‑conditioned medium

Gingival-derived mesenchymal stem cells (GMSCs) have recently been harvested; however, the use of GMSCs in periodontal tissue engineering requires further study. The present study established an indirect co‑culture system between rat apical tooth germ‑conditioned medium (APTG‑CM) and GMSCs, in order to determine the effects on periodontal tissue differentiation in vitro and in vivo. Using the limiting dilution technique, single‑colony derived human GMSCs and periodontal ligament stem cells (PDLSCs) were isolated and expanded to obtain homogeneous populations. PDLSCs were used as a positive control group. Cell cycle distribution, alkaline phosphatase (ALP) activity, mineralization behavior, expression of genes associated with a cementoblast phenotype (osteocalcin, bone sialoprotein, ALP, type I collagen, cementum‑derived protein 23), and in vivo differentiation capacities of GMSCs/PDLSCs co‑cultured with APTG‑CM were evaluated. Flow cytometry indicated that GMSCs and PDLSCs were positive for STRO‑1 and CD105, whereas CD45 expression was negative. The cell types were capable of forming colonies, and of osteogenic and adipogenic differentiation in response to appropriate stimuli. The induced GMSCs and PDLSCs exhibited numerous characteristics associated with cementoblast lineages, as indicated by increased proliferation and ALP activity, and upregulated expression of cementum‑associated genes in vitro. In vivo, cementum/periodontal ligament‑like structures were shown to form along the dentin surface and ceramic bovine bone in GMSCs and PDLSCs induced by APTG‑CM group. Conversely, vertical fibers could not insert in the control group, which was not co‑cultured with APTG‑CM. In conclusion, GMSCs are likely to have a role in periodontal tissue regeneration. In addition, APTG‑CM was able to provide a cementogenic microenvironment and promote differentiation of GMSCs along the cementoblastic lineage.

An optimized color transformation for the analysis of digital images of hematoxylin & eosin stained slides

Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.

Accomplishments of the Trustees and laboratory staff of the Biological Stain Commission, 2002-2013

During the 12 years from 2002 to 2013, the Trustees and laboratory personnel of the Biological Stain Commission (BSC) can claim many accomplishments. These accomplishments are itemized under 11 categories: continuous publication of the official journal, Biotechnic & Histochemistry; production of four special issues of Biotechnic & Histochemistry devoted to specific dyes or stains; standardization of staining and dye purity; mechanisms of staining and prediction of dye behavior; publication of books or book chapters; effects of fixation and processing on staining; cancer research; immunohistochemistry; BSC Laboratory activities; miscellaneous publications; and administrative accomplishments.