Daily Heart Rate Variability before and after Concussion in an American College Football Player

This case report demonstrates the effects of sport-related concussion (SRC) on heart rate variability (HRV) in an American college football player. Daily measures of resting, ultra-short natural logarithm of the root mean square of successive differences (LnRMSSD), subjective wellbeing, and Player Load were obtained each training day throughout a 4-week spring camp and 4 weeks of preseason training. SRC occurred within the first 2 weeks of the preseason. During spring camp and preseason pre-SRC, the athlete demonstrated minimal day-to-day fluctuations in LnRMSSD, which increased post-SRC (LnRMSSD coefficient of variation pre-SRC ≤ 3.1%, post-SRC = 5.8%). Moderate decrements in daily-averaged LnRMSSD were observed post-SRC relative to pre-SRC (Effect Size ± 90% Confidence Interval = −1.12 ± 0.80), and the 7-day rolling average fell below the smallest worthwhile change for the remainder of the preseason. LnRMSSD responses to SRC appeared similar to trends associated with stress and training fatigue. Therefore, performance and sports medicine staff should maintain regular communication regarding player injury and fatigue status so that HRV can be interpreted in the appropriate context. Detection and monitoring of autonomic dysregulation post-SRC may require near-daily assessment, as LnRMSSD showed greater daily fluctuations rather than chronic suppression following the head injury

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

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

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

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

Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias

We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer's dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia

Energy-Degeneracy-Driven Covalency in Actinide Bonding

Evaluating the nature of chemical bonding for actinide elements represents one of the most important and long-standing problems in actinide science. We directly address this challenge and contribute a Cl K-edge X-ray absorption spectroscopy and relativistic density functional theory study that quantitatively evaluates An–Cl covalency in AnCl62– (AnIV = Th, U, Np, Pu). The results showed significant mixing between Cl 3p- and AnIV 5f- and 6d-orbitals (t1u*/t2u* and t2g*/eg*), with the 6d-orbitals showing more pronounced covalent bonding than the 5f-orbitals. Moving from Th to U, Np, and Pu markedly changed the amount of M–Cl orbital mixing, such that AnIV 6d- and Cl 3p-mixing decreased and metal 5f- and Cl 3p-orbital mixing increased across this series