A deep learning algorithm to detect cutaneous squamous cell carcinoma on frozen sections in Mohs micrographic surgery: A retrospective assessment.

Intraoperative margin analysis is crucial for the successful removal of cutaneous squamous cell carcinomas (cSCC). Artificial intelligence technologies (AI) have previously demonstrated potential for facilitating rapid and complete tumour removal using intraoperative margin assessment for basal cell carcinoma. However, the varied morphologies of cSCC present challenges for AI margin assessment. The aim of this study was to develop and evaluate the accuracy of an AI algorithm for real-time histologic margin analysis of cSCC. To do this, a retrospective cohort study was conducted using frozen cSCC section slides. These slides were scanned and annotated, delineating benign tissue structures, inflammation and tumour to develop an AI algorithm for real-time margin analysis. A convolutional neural network workflow was used to extract histomorphological features predictive of cSCC. This algorithm demonstrated proof of concept for identifying cSCC with high accuracy, highlighting the potential for integration of AI into the surgical workflow. Incorporation of AI algorithms may improve efficiency and completeness of real-time margin assessment for cSCC removal, particularly in cases of moderately and poorly differentiated tumours/neoplasms. Further algorithmic improvement incorporating surrounding tissue context is necessary to remain sensitive to the unique epidermal landscape of well-differentiated tumours, and to map tumours to their original anatomical position/orientation.

Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining.

The advent of spatial transcriptomics technologies has heralded a renaissance in research to advance our understanding of the spatial cellular and transcriptional heterogeneity within tissues. Spatial transcriptomics allows investigation of the interplay between cells, molecular pathways, and the surrounding tissue architecture and can help elucidate developmental trajectories, disease pathogenesis, and various niches in the tumor microenvironment. Photoaging is the histological and molecular skin damage resulting from chronic/acute sun exposure and is a major risk factor for skin cancer. Spatial transcriptomics technologies hold promise for improving the reliability of evaluating photoaging and developing new therapeutics. Challenges to current methods include limited focus on dermal elastosis variations and reliance on self-reported measures, which can introduce subjectivity and inconsistency. Spatial transcriptomics offers an opportunity to assess photoaging objectively and reproducibly in studies of carcinogenesis and discern the effectiveness of therapies that intervene in photoaging and preventing cancer. Evaluation of distinct histological architectures using highly-multiplexed spatial technologies can identify specific cell lineages that have been understudied due to their location beyond the depth of UV penetration. However, the cost and interpatient variability using state-of-the-art assays such as the 10x Genomics Spatial Transcriptomics assays limits the scope and scale of large-scale molecular epidemiologic studies. Here, we investigate the inference of spatial transcriptomics information from routine hematoxylin and eosin-stained (H&E) tissue slides. We employed the Visium CytAssist spatial transcriptomics assay to analyze over 18,000 genes at a 50-micron resolution for four patients from a cohort of 261 skin specimens collected adjacent to surgical resection sites for basal cell and squamous cell keratinocyte tumors. The spatial transcriptomics data was co-registered with 40x resolution whole slide imaging (WSI) information. We developed machine learning models that achieved a macro-averaged median AUC and F1 score of 0.80 and 0.61 and Spearman coefficient of 0.60 in inferring transcriptomic profiles across the slides, and accurately captured biological pathways across various tissue architectures.

Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis.

Graph-based deep learning has shown great promise in cancer histopathology image analysis by contextualizing complex morphology and structure across whole slide images to make high quality downstream outcome predictions (ex: prognostication). These methods rely on informative representations (i.e., embeddings) of image patches comprising larger slides, which are used as node attributes in slide graphs. Spatial omics data, including spatial transcriptomics, is a novel paradigm offering a wealth of detailed information. Pairing this data with corresponding histological imaging localized at 50-micron resolution, may facilitate the development of algorithms which better appreciate the morphological and molecular underpinnings of carcinogenesis. Here, we explore the utility of leveraging spatial transcriptomics data with a contrastive crossmodal pretraining mechanism to generate deep learning models that can extract molecular and histological information for graph-based learning tasks. Performance on cancer staging, lymph node metastasis prediction, survival prediction, and tissue clustering analyses indicate that the proposed methods bring improvement to graph based deep learning models for histopathological slides compared to leveraging histological information from existing schemes, demonstrating the promise of mining spatial omics data to enhance deep learning for pathology workflows.

Feasibility of Inferring Spatial Transcriptomics from Single-Cell Histological Patterns for Studying Colon Cancer Tumor Heterogeneity.

Background: Spatial transcriptomics involves studying the spatial organization of gene expression within tissues, offering insights into the molecular diversity of tumors. While spatial gene expression is commonly amalgamated from 1-10 cells across 50-micron spots, recent methods have demonstrated the capability to disaggregate this information at subspot resolution by leveraging both expression and histological patterns. However, elucidating such information from histology alone presents a significant challenge but if solved can better permit spatial molecular analysis at cellular resolution for instances where Visium data is not available, reducing study costs. This study explores integrating single-cell histological and transcriptomic data to infer spatial mRNA expression patterns in whole slide images collected from a cohort of stage pT3 colorectal cancer patients. A cell graph neural network algorithm was developed to align histological information extracted from detected cells with single cell RNA patterns through optimal transport methods, facilitating the analysis of cellular groupings and gene relationships. This approach leveraged spot-level expression as an intermediary to co-map histological and transcriptomic information at the single-cell level. Results: Our study demonstrated that single-cell transcriptional heterogeneity within a spot could be predicted from histological markers extracted from cells detected within a spot. Furthermore, our model exhibited proficiency in delineating overarching gene expression patterns across whole-slide images. This approach compared favorably to traditional patch-based computer vision methods as well as other methods which did not incorporate single cell expression during the model fitting procedures. Topological nuances of single-cell expression within a Visium spot were preserved using the developed methodology. Conclusion: This innovative approach augments the resolution of spatial molecular assays utilizing histology as a sole input through synergistic co-mapping of histological and transcriptomic datasets at the single-cell level, anchored by spatial transcriptomics. While initial results are promising, they warrant rigorous validation. This includes collaborating with pathologists for precise spatial identification of distinct cell types and utilizing sophisticated assays, such as Xenium, to attain deeper subcellular insights.

The Overlooked Role of Specimen Preparation in Bolstering Deep Learning-Enhanced Spatial Transcriptomics Workflows.

The application of deep learning methods to spatial transcriptomics has shown promise in unraveling the complex relationships between gene expression patterns and tissue architecture as they pertain to various pathological conditions. Deep learning methods that can infer gene expression patterns directly from tissue histomorphology can expand the capability to discern spatial molecular markers within tissue slides. However, current methods utilizing these techniques are plagued by substantial variability in tissue preparation and characteristics, which can hinder the broader adoption of these tools. Furthermore, training deep learning models using spatial transcriptomics on small study cohorts remains a costly endeavor. Necessitating novel tissue preparation processes enhance assay reliability, resolution, and scalability. This study investigated the impact of an enhanced specimen processing workflow for facilitating a deep learning-based spatial transcriptomics assessment. The enhanced workflow leveraged the flexibility of the Visium CytAssist assay to permit automated H&E staining (e.g., Leica Bond) of tissue slides, whole-slide imaging at 40x-resolution, and multiplexing of tissue sections from multiple patients within individual capture areas for spatial transcriptomics profiling. Using a cohort of thirteen pT3 stage colorectal cancer (CRC) patients, we compared the efficacy of deep learning models trained on slide prepared using an enhanced workflow as compared to the traditional workflow which leverages manual tissue staining and standard imaging of tissue slides. Leveraging Inceptionv3 neural networks, we aimed to predict gene expression patterns across matched serial tissue sections, each stemming from a distinct workflow but aligned based on persistent histological structures. Findings indicate that the enhanced workflow considerably outperformed the traditional spatial transcriptomics workflow. Gene expression profiles predicted from enhanced tissue slides also yielded expression patterns more topologically consistent with the ground truth. This led to enhanced statistical precision in pinpointing biomarkers associated with distinct spatial structures. These insights can potentially elevate diagnostic and prognostic biomarker detection by broadening the range of spatial molecular markers linked to metastasis and recurrence. Future endeavors will further explore these findings to enrich our comprehension of various diseases and uncover molecular pathways with greater nuance. Combining deep learning with spatial transcriptomics provides a compelling avenue to enrich our understanding of tumor biology and improve clinical outcomes. For results of the highest fidelity, however, effective specimen processing is crucial, and fostering collaboration between histotechnicians, pathologists, and genomics specialists is essential to herald this new era in spatial transcriptomics-driven cancer research.

Potential to Enhance Large Scale Molecular Assessments of Skin Photoaging through Virtual Inference of Spatial Transcriptomics from Routine Staining.

The advent of spatial transcriptomics technologies has heralded a renaissance in research to advance our understanding of the spatial cellular and transcriptional heterogeneity within tissues. Spatial transcriptomics allows investigation of the interplay between cells, molecular pathways and the surrounding tissue architecture and can help elucidate developmental trajectories, disease pathogenesis, and various niches in the tumor microenvironment. Photoaging is the histological and molecular skin damage resulting from chronic/acute sun exposure and is a major risk factor for skin cancer. Spatial transcriptomics technologies hold promise for improving the reliability of evaluating photoaging and developing new therapeutics. Current challenges, including limited focus on dermal elastosis variations and reliance on self-reported measures, can introduce subjectivity and inconsistency. Spatial transcriptomics offer an opportunity to assess photoaging objectively and reproducibly in studies of carcinogenesis and discern the effectiveness of therapies that intervene on photoaging and prevent cancer. Evaluation of distinct histological architectures using highly-multiplexed spatial technologies can identify specific cell lineages that have been understudied due to their location beyond the depth of UV penetration. However, the cost and inter-patient variability using state-of-the-art assays such as the 10x Genomics Spatial Transcriptomics assays limits the scope and scale of large-scale molecular epidemiologic studies. Here, we investigate the inference of spatial transcriptomics information from routine hematoxylin and eosin-stained (H&E) tissue slides. We employed the Visium CytAssist spatial transcriptomics assay to analyze over 18,000 genes at a 50-micron resolution for four patients from a cohort of 261 skin specimens collected adjacent to surgical resection sites for basal and squamous keratinocyte tumors. The spatial transcriptomics data was co-registered with 40x resolution whole slide imaging (WSI) information. We developed machine learning models that achieved a macro-averaged median AUC and F1 score of 0.80 and 0.61 and Spearman coefficient of 0.60 in inferring transcriptomic profiles across the slides, and accurately captured biological pathways across various tissue architectures.

Spatial Omics Driven Crossmodal Pretraining Applied to Graph-based Deep Learning for Cancer Pathology Analysis.

Graph-based deep learning has shown great promise in cancer histopathology image analysis by contextualizing complex morphology and structure across whole slide images to make high quality downstream outcome predictions (ex: prognostication). These methods rely on informative representations (i.e., embeddings) of image patches comprising larger slides, which are used as node attributes in slide graphs. Spatial omics data, including spatial transcriptomics, is a novel paradigm offering a wealth of detailed information. Pairing this data with corresponding histological imaging localized at 50-micron resolution, may facilitate the development of algorithms which better appreciate the morphological and molecular underpinnings of carcinogenesis. Here, we explore the utility of leveraging spatial transcriptomics data with a contrastive crossmodal pretraining mechanism to generate deep learning models that can extract molecular and histological information for graph-based learning tasks. Performance on cancer staging, lymph node metastasis prediction, survival prediction, and tissue clustering analyses indicate that the proposed methods bring improvement to graph based deep learning models for histopathological slides compared to leveraging histological information from existing schemes, demonstrating the promise of mining spatial omics data to enhance deep learning for pathology workflows.

A deep learning algorithm to detect cutaneous squamous cell carcinoma on frozen sections in Mohs micrographic surgery: a retrospective assessment.

Importance: Intraoperative margin analysis is crucial for the successful removal of cutaneous squamous cell carcinomas (cSCC). Artificial intelligence technologies (AI) have previously demonstrated potential for facilitating rapid and complete tumor removal using intraoperative margin assessment for basal cell carcinoma. However, the varied morphologies of cSCC present challenges for AI margin assessment. Objective: To develop and evaluate the accuracy of an AI algorithm for real-time histologic margin analysis of cSCC. Design: A retrospective cohort study was conducted using frozen cSCC section slides and adjacent tissues. Setting: This study was conducted in a tertiary care academic center. Participants: Patients undergoing Mohs micrographic surgery for cSCC between January and March 2020. Exposures: Frozen section slides were scanned and annotated, delineating benign tissue structures, inflammation, and tumor to develop an AI algorithm for real-time margin analysis. Patients were stratified by tumor differentiation status. Epithelial tissues including epidermis and hair follicles were annotated for moderate-well to well differentiated cSCC tumors. A convolutional neural network workflow was used to extract histomorphological features predictive of cSCC at 50-micron resolution. Main Outcomes and Measures: The performance of the AI algorithm in identifying cSCC at 50-micron resolution was reported using the area under the receiver operating characteristic curve. Accuracy was also reported by tumor differentiation status and by delineation of cSCC from epidermis. Model performance using histomorphological features alone was compared to architectural features (i.e., tissue context) for well-differentiated tumors. Results: The AI algorithm demonstrated proof of concept for identifying cSCC with high accuracy. Accuracy differed by differentiation status, driven by challenges in separating cSCC from epidermis using histomorphological features alone for well-differentiated tumors. Consideration of broader tissue context through architectural features improved the ability to delineate tumor from epidermis. Conclusions and Relevance: Incorporating AI into the surgical workflow may improve efficiency and completeness of real-time margin assessment for cSCC removal, particularly in cases of moderately and poorly differentiated tumors/neoplasms. Further algorithmic improvement is necessary to remain sensitive to the unique epidermal landscape of well-differentiated tumors, and to map tumors to their original anatomical position/orientation. Future studies should assess the efficiency improvements and cost benefits and address other confounding pathologies such as inflammation and nuclei. Funding sources: JL is supported by NIH grants R24GM141194, P20GM104416 and P20GM130454. Support for this work was also provided by the Prouty Dartmouth Cancer Center development funds. Key Points: Question: How can the efficiency and accuracy of real-time intraoperative margin analysis for the removal of cutaneous squamous cell carcinoma (cSCC) be improved, and how can tumor differentiation be incorporated into this approach?Findings: A proof-of-concept deep learning algorithm was trained, validated, and tested on frozen section whole slide images (WSI) for a retrospective cohort of cSCC cases, demonstrating high accuracy in identifying cSCC and related pathologies. Histomorphology alone was found to be insufficient to delineate tumor from epidermis in histologic identification of well-differentiated cSCC. Incorporation of surrounding tissue architecture and shape improved the ability to delineate tumor from normal tissue.Meaning: Integrating artificial intelligence into surgical procedures has the potential to enhance the thoroughness and efficiency of intraoperative margin analysis for cSCC removal. However, accurately accounting for the epidermal tissue based on the tumor's differentiation status requires specialized algorithms that consider the surrounding tissue context. To meaningfully integrate AI algorithms into clinical practice, further algorithmic refinement is needed, as well as the mapping of tumors to their original surgical site, and evaluation of the cost and efficacy of these approaches to address existing bottlenecks.

Effect of Fuel Preheating on Engine Characteristics of Waste Animal Fat-Oil Biodiesel in Compression Ignition Engine.

The present study aims at understanding the effects of fuel preheating on engine characteristics of waste animal fat-oil (WAF-O) biodiesel in a single-cylinder CI engine, with the preheating technique proposed as an effective means for enhancing the fuel properties. To understand the effects of the preheated fuel, the WAF-O biodiesel was preheated at 60, 80, 100 and 120 °C and tested along with neat diesel and unheated WAF-O biodiesel. For this purpose, biodiesel was produced from different animal wastes by means of KOH-assisted ethanol-based transesterification, reporting its maximum yield as 96.37 ± 1.8%, with significant distribution of unsaturated oleic acid, saturated palmitic acid and stearic acid. Upon evaluating its fuel characteristics as per ASTM D6751 standards, a rise in preheating temperature by 1 °C reduced the density and kinematic viscosity of WAF-O biodiesel by 0.383 kg/m3 and 0.025 mm2/s, respectively, and was explained by the weakening of intermolecular forces between its fatty acid ester molecules. Preheated samples reported superior combustion characteristics by exhibiting increased in-cylinder pressure (2.24%, on average) and heat release rates in addition to their shortened ignition delay (1−4 °CA). Furthermore, preheating of WAF-O biodiesel reduced its specific fuel consumption and increased its brake thermal efficiency by 7.86% (on average) and 9.23% (on average), respectively. However, higher preheating temperatures (>120 °C) resulted in increased fuel consumption owing to its varied flow characteristics. In addition to the changes in combustion characteristics, preheating WAF-O bio-diesel also resulted in reduced carbon monoxide, nitrous oxide and hydrocarbon emission by 13.88%, 7.21% and 26.94%, respectively, and increased carbon dioxide emission by 7.58%. Summing up, the enhancements in overall engine characteristics of preheated samples were accounted for by their improvised fuel injection characteristics due to their reduced density and viscosity, which ensured for their effective combustion.

Investigations on the enhanced dye degradation activity of heterogeneous BiFeO3-GdFeO3 nanocomposite photocatalyst.

Perovskite types of nanocomposites of BiFeO3-GdFeO3 (BFO-GFO) has been synthesized using sol-gel route for the first time. The nanocomposite powders were characterized by powder X-Ray diffraction (PXRD) to confirm the existence of mixed crystallographic phases. EDX analysis on nanocomposites estimates the composition of individual element present in BFO-GFO matrix. The induced strain upon loading GdFeO3(GFO) in BiFeO3 (BFO) matrix has been computed with the aid of Williamson -Hall (W-H) plot. Surface morphologies of nanocomposite powders has been studied using Field Emission Scanning Electron Microscope (FESEM) images. The observed changes in the band gap energies of nanocomposite powders due to the inclusion of GFO has been ascertained from the tauc plots. PL emission of BFO upon loading GFO found to have detected in the IR region due to defect level transition. Finally, the methylene blue dye (MB) degradation characteristics of BFO, GFO and the nanocomposite powders of BFO-GFO have also been studied. The overall results obtained has been discussed in detail.

Synthesis, Optical and Electrochemical Properties of Y2O3 Nanoparticles Prepared by Co-Precipitation Method.

Y2O3 nanoparticles were synthesized by co-precipitation route using yttrium nitrate hexahydrate and ammonium hydroxide as precursors. The prepared sample was calcined at 500 degrees C and subjected to various characterization studies like thermal analysis (TG/DTA), X-ray diffraction (XRD), transmission electron microscope (TEM), UV-visible (UV-Vis) and photoluminescence (PL) spectroscopy. The XRD pattern showed the cubic fluorite structure of Y2O3 without any impurity peaks, revealing high purity of the prepared sample. TEM images revealed that the calcined Y2O3 nanoparticles consist of spherical-like morphology with an average particle size of 12 nm. The absorption spectrum of calcined samples shows blue-shift compared to the as-prepared sample, which was further confirmed by PL studies. The possible formation mechanism of Y2O3 nanoparticles has been discussed based on the experimental results. Electrochemical behavior of Y2O3 nanoparticles was studied by cyclic voltammetry to assess their suitability for supercapacitor applications.