Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet typically deficient in magnesium (Mg), there some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of supplementation or T cell subsets has not been explored.

Non-alcoholic steatohepatitis (NASH) is a fatty liver disease characterized by accumulation of fat in hepatocytes with concurrent inflammation and associated morbidity, cirrhosis failure. After extraction core biopsy, tissue sections are stained hematoxylin eosin (H&E) to grade NASH activity, trichrome stage fibrosis. Methods computationally transform one stain into another on digital whole slide images (WSI) can lessen the need for additional physical staining besides H&E, reducing...

Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to low prevalence CNS tumors, major advances in targeted therapies been lagging compared other adult tumors. We collect single nuclei RNA-seq data from 84,700 35 three non-tumoral brain tissues characterize tumor heterogeneity transcriptomic alterations. distinguish cell subpopulations associated with specific types including...

Abstract DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, disease progression, but lack incorporation prior biological knowledge. Here, we present modular, user-friendly methodology software, MethylCapsNet MethylSPWNet , that group CpGs into biologically relevant capsules—such as promoter...

Abstract Background Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system (CNS) tumors. 5hmC is abundant the brain, and alterations to adult CNS tumors have been reported. However, traditional approaches measure DNA methylation do not distinguish between 5-methylcytosine (5mC) its oxidized counterpart 5hmC, including those used build tumor classification systems. We measured 5mC epigenome-wide at nucleotide resolution glioma, ependymoma,...

Abstract Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify type-specific to cytosine modifications we utilize a multi-omic approach that integrated bulk DNA modification data (methylation and hydroxymethylation) with both single-cell RNA-sequencing data. We demonstrate large reduction scope of significantly differentially modified cytosines tumors...

Abstract Non-alcoholic steatohepatitis (NASH) is a fatty liver disease characterized by accumulation of fat in hepatocytes with concurrent inflammation and associated morbidity, cirrhosis failure. After extraction core biopsy, tissue sections are stained hematoxylin eosin (H&E) to grade NASH activity, trichrome stage fibrosis. Methods computationally transform one stain into another on digital whole slide images (WSI) can lessen the need for additional physical staining besides H&E,...

Disease grading and staging is accomplished through the assignment of an ordinal rating. Bridge ratings occur when a rater assigns two adjacent categories. Most statistical methodology necessitates use single category. Consequently, bridge often go unreported in clinical research studies. We propose three methodologies ( Expanded, Mixture , Collapsed ) Category Models to account for ratings. perform simulations examine impact our approaches on detecting treatment effects, comment real-world...

<title>Abstract</title> Central nervous system (CNS) tumors are the leading cause of pediatric cancer death, and these patients have an increased risk for developing secondary neoplasms. Due to low prevalence CNS tumors, major advances in targeted therapies been lagging compared other adult tumors. We collected single nuclei RNA-seq data from 35 three non-tumoral brain tissues (84,700 nuclei) characterized tumor heterogeneity transcriptomic alterations. distinguished cell subpopulations...

<title>Abstract</title> Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify type-specific to cytosine modifications tumors we utilized a multi-omic approach that integrated bulk DNA modification data (methylation and hydroxymethylation) with both single-cell RNA-sequencing data. We demonstrate large reduction scope of significantly differentially...

Abstract DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, disease progression, but lack incorporation prior biological knowledge. Here, we present modular, user-friendly deep learning methodology software, MethylCapsNet MethylSPWNet , that group CpGs into biologically relevant capsules –...

Abstract The public health burden of non-alcoholic steatohepatitis (NASH), a liver condition characterized by excessive lipid accumulation and subsequent tissue inflammation fibrosis, has burgeoned with the spread western lifestyle habits. Progression fibrosis into cirrhosis is assessed using histological staging scales (e.g., NASH Clinical Research Network (NASH CRN)). These are used to monitor disease progression as well evaluate effectiveness therapies. However, clinical drug trials for...

Abstract Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system tumors. We measured genome-scale 5hmC glioma, ependymoma, and embryonal tumors from children, as well control brain tissues using oxidative bisulfite treatments. Tumor localized to regulatory elements crucial cell identity, including transcription factor binding sites super-enhancers. A linear model tested the CpG-specific differences between tumor non-tumor samples, subtypes....

Abstract Non-alcoholic steatohepatitis (NASH) is a liver disease characterized by excessive lipid accumulation and progression typically assessed through inspection of Trichrome stain for Fibrosis staging. As the public health burden NASH worsens due to evolving lifestyle habits, pathology laboratory resources will become increasingly strained rising demand specialized stains. Virtual staining processes, computational methods which can synthesize application chemical reagents, potentially...

Breast magnetic resonance imaging (MRI) is an important tool for the management of breast cancer patients and screening women at high risk cancer.To examine long-term trends in distribution histologic diagnoses obtained from MRI-guided biopsies.Retrospective analysis.We retrospectively reviewed biopsies 2004 to 2019. All cases underwent central pathology review lesions were classified based on most prominent finding present. Magnetic features extracted radiology reports when available...

Abstract Though aberrant cytosine modifications are prevalent in cancer, nucleotide-specific 5-hydroxymethylcytosine (5hmC) remain understudied, including pediatric CNS tumors. Brain 5-hydroxymethylation is linked with development and differentiation. We measured genome-scale 5hmC patients diagnoses of glioma, ependymoma, embryonal tumors under age 18 (n=36), non-tumor brain tissues (n=3). DNA was processed tandem oxidative (OxBS) bisulfite (BS) treatments followed by hybridization to the...

Abstract Identifying transcriptomic alterations in pediatric central nervous system (pCNS) tumors often relies on profiles from bulk tissue RNA-sequencing that can be confounded by varying cell type proportions across tumor and normal brain tissues. We utilized single nuclei (snRNA-seq) RNA-seq 33 pCNS 3 non-diseased samples collected the Norris Cotton Cancer Center to identify variation gene expression attributed overrepresentation of specific cell-type populations when determining...