Creating traveling waves from standing waves from the gyrotropic paramagnetic properties of Fe3+^{3+} ions in a high-Q whispering gallery mode sapphire resonator

We report observations of the gyrotropic change in magnetic susceptibility of the Fe$^{3+}$ electron paramagnetic resonance at 12.037GHz (between spin states $|1/2>$ and $|3/2>$) in sapphire with respect to applied magnetic field. Measurements were made by observing the response of the high-Q Whispering Gallery doublet (WGH$_{\pm17,0,0}$) in a Hemex sapphire resonator cooled to 5 K. The doublets initially existed as standing waves at zero field and were transformed to traveling waves due to the gyrotropic response.Comment: Accepted for publication in Phys. Rev.

Computation in Classical Mechanics

There is a growing consensus that physics majors need to learn computational skills, but many departments are still devoid of computation in their physics curriculum. Some departments may lack the resources or commitment to create a dedicated course or program in computational physics. One way around this difficulty is to include computation in a standard upper-level physics course. An intermediate classical mechanics course is particularly well suited for including computation. We discuss the ways we have used computation in our classical mechanics courses, focusing on how computational work can improve students' understanding of physics as well as their computational skills. We present examples of computational problems that serve these two purposes. In addition, we provide information about resources for instructors who would like to include computation in their courses.Comment: 6 pages, 3 figures, submitted to American Journal of Physic

Novel associations for hypothyroidism include known autoimmune risk loci

Hypothyroidism is the most common thyroid disorder, affecting about 5% of the general population. Here we present the first large genome-wide association study of hypothyroidism, in 2,564 cases and 24,448 controls from the customer base of 23andMe, Inc., a personal genetics company. We identify four genome-wide significant associations, two of which are well known to be involved with a large spectrum of autoimmune diseases: rs6679677 near _PTPN22_ and rs3184504 in _SH2B3_ (p-values 3.5e-13 and 3.0e-11, respectively). We also report associations with rs4915077 near _VAV3_ (p-value 8.3e-11), another gene involved in immune function, and rs965513 near _FOXE1_ (p-value 3.1e-14). Of these, the association with _PTPN22_ confirms a recent small candidate gene study, and _FOXE1_ was previously known to be associated with thyroid-stimulating hormone (TSH) levels. Although _SH2B3_ has been previously linked with a number of autoimmune diseases, this is the first report of its association with thyroid disease. The _VAV3_ association is novel. These results suggest heterogeneity in the genetic etiology of hypothyroidism, implicating genes involved in both autoimmune disorders and thyroid function. Using a genetic risk profile score based on the top association from each of the four genome-wide significant regions in our study, the relative risk between the highest and lowest deciles of genetic risk is 2.1

Mental defeat and suicidality in chronic pain : a prospective analysis

Living with chronic pain has been identified as a significant risk factor for suicide. Qualitative and cross-sectional studies have reported an association between mental defeat and suicidal thoughts and behavior in patients with chronic pain. In this prospective cohort study, we hypothesized that higher levels of mental defeat would be associated with increased suicide risk at a 6-month follow-up. A total of 524 patients with chronic pain completed online questionnaires measuring variables related to suicide risk, mental defeat, sociodemographic, psychological, pain, activity, and health variables. At 6 months, 70.8% (n=371) of respondents completed the questionnaires again. Weighted univariate and multivariable regression models were run to predict suicide risk at 6 months. The clinical suicide risk cutoff was met by 38.55% of participants at baseline and 36.66% at 6 months. Multivariable modeling revealed that mental defeat, depression, perceived stress, head pain, and active smoking status significantly increased the odds of reporting higher suicide risk, while older age reduced the odds. Receiver operating characteristic (ROC) analysis showed that assessment of mental defeat, perceived stress, and depression is effective in discriminating between ‘low’ and ‘high’ suicide risk. Awareness of the prospective links from mental defeat, depression, perceived stress, head pain, and active smoking status to increased suicide risk in patients with chronic pain may offer a novel avenue for assessment and preventative intervention

Improving the deterministic skill of air quality ensembles

<p><strong>Abstract.</strong> Forecasts from chemical weather models are subject to uncertainties in the input data (e.g. emission inventory, initial and boundary conditions) as well as the model itself (e.g. physical parameterization, chemical mechanism). Multi-model ensemble forecasts can improve the forecast skill provided that certain mathematical conditions are fulfilled. We demonstrate through an intercomparison of two dissimilar air quality ensembles that unconditional raw forecast averaging, although generally successful, is far from optimum. One way to achieve an optimum ensemble is also presented. The basic idea is to either add optimum weights to members or constrain the ensemble to those members that meet certain conditions in time or frequency domain. The methods are evaluated against ground level observations collected from the EMEP and Airbase databases.<br><br> The two ensembles were created for the first and second phase of the Air Quality Model Evaluation International Initiative (AQMEII). Verification statistics shows that the deterministic models simulate better O<sub>3</sub> than NO<sub>2</sub> and PM<sub>10</sub>, linked to different levels of complexity in the represented processes. The ensemble mean achieves higher skill compared to each station's best deterministic model at 39 %–63 % of the sites. The skill gained from the favourable ensemble averaging has at least double the forecast skill compared to using the full ensemble. The method proved robust for the 3-monthly examined time-series if the training phase comprises 60 days. Further development of the method is discussed in the conclusion.</p&gt

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

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 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