Endogenous versus exogenous carbohydrate oxidation measured by stable isotopes in pre-pubescent children plus 13C abundances in foods consumed three days prior

Purpose: The purposes of the present study were to (a) examine resting metabolism, substrate utilization, and endogenous versus exogenous carbohydrate (CHO) oxidation before and after 30-g rapidly-digesting carbohydrate (RDC) ingestion using indirect calorimetry and breath test analysis of stable isotope concentrations in pre-pubescent children and (b) report the 13C abundances in foods consumed for three days prior. Methods: Nineteen children (n 1⁄4 10 boys, n 1⁄4 9 girls) at Tanner stage I or II participated (mean age ± 95% CI 1⁄4 9.84 ± 0.77 y) in this study. Food was administered to the children for three days preceding their scheduled breath tests. Breath tests and indirect calorimetry were performed after an 8-h fast before and 60 min following consumption of a 30-g simple RDC drink consisting of maltodextrin and sucrose. Open circuit spirometry and indirect calorimetry monitored resting metabolism and CHO oxidation. Separate breath samples were taken every 15 min. Samples of all foods and breath samples were analyzed for 13C and 12C abundances with a stable-isotope mass spectrometer. Results: 13C in expired breath samples were 23.81 + 1.64‰ at baseline and increased every 15 min after consumption of the CHO drink (p \u3c 0.001e0.009). Cumulative total, endogenous, and exogenous CHO utilization increased during the post-prandial period (p \u3c 0.001). Endogenous CHO oxidation was consistently greater than exogenous CHO oxidation (p \u3c 0.001e0.002). Blood glucose was elevated from baseline at 30- and 60-min post-prandial (p \u3c 0.001). Insulin did not change over time (p 1⁄4 0.184). Conclusions: The foods provided during the 3-day controlled diet effectively minimized 13C variation prior to metabolic testing. The 13C abundances of foods reported herein should serve as practical recommendations to reduce 13C intake before breath tests. While endogenous CHO oxidation remained greater in proportion to exogenous CHO oxidation, these findings suggest that even a relatively small amount of RDC can increase exogenous CHO oxidation and blood glucose in normal-weight children. To further examine shifts in endogenous versus exogenous CHO utilization, we recommend that future studies take steps to minimize 13C variation before breath tests and examine changes in substrate metabolism at rest and during exercise in normal weight and overweight pre-pubescent children. Clinical trial registration number: NCT03185884

Basic Understanding of Condensed Phases of Matter via Packing Models

Packing problems have been a source of fascination for millenia and their study has produced a rich literature that spans numerous disciplines. Investigations of hard-particle packing models have provided basic insights into the structure and bulk properties of condensed phases of matter, including low-temperature states (e.g., molecular and colloidal liquids, crystals and glasses), multiphase heterogeneous media, granular media, and biological systems. The densest packings are of great interest in pure mathematics, including discrete geometry and number theory. This perspective reviews pertinent theoretical and computational literature concerning the equilibrium, metastable and nonequilibrium packings of hard-particle packings in various Euclidean space dimensions. In the case of jammed packings, emphasis will be placed on the "geometric-structure" approach, which provides a powerful and unified means to quantitatively characterize individual packings via jamming categories and "order" maps. It incorporates extremal jammed states, including the densest packings, maximally random jammed states, and lowest-density jammed structures. Packings of identical spheres, spheres with a size distribution, and nonspherical particles are also surveyed. We close this review by identifying challenges and open questions for future research.Comment: 33 pages, 20 figures, Invited "Perspective" submitted to the Journal of Chemical Physics. arXiv admin note: text overlap with arXiv:1008.298

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment