Clubbie: Two Seasons with Baseball\u27s Broken Dreamers

The main theme of this manuscript is disillusionment. In order for this theme to hit home, I needed the character called Greg Larson, along with the reader, and (for the most part) the narrator, to discover this world of minor league baseball at the same time. This would allow me to tease the illusion—to set up baseball as this grand nostalgic enterprise in the beginning in a way that all three of us could believe it (with the exception of some expository asides from the narrator). I could describe my character’s boyish relationship with baseball so that it naturally lent itself to future heartache. That way, all of us together—Greg Larson, the reader, and the narrator—could hop in my beat-down gold Cadillac Deville and drive up to Maryland to lose our youth together, for better and for worse

Maximum likelihood analysis of systematic errors in interferometric observations of the cosmic microwave background

We investigate the impact of instrumental systematic errors in interferometric measurements of the cosmic microwave background (CMB) temperature and polarization power spectra. We simulate interferometric CMB observations to generate mock visibilities and estimate power spectra using the statistically optimal maximum likelihood technique. We define a quadratic error measure to determine allowable levels of systematic error that do not induce power spectrum errors beyond a given tolerance. As an example, in this study we focus on differential pointing errors. The effects of other systematics can be simulated by this pipeline in a straightforward manner. We find that, in order to accurately recover the underlying B-modes for r=0.01 at 28<l<384, Gaussian-distributed pointing errors must be controlled to 0.7^\circ rms for an interferometer with an antenna configuration similar to QUBIC, in agreement with analytical estimates. Only the statistical uncertainty for 28<l<88 would be changed at ~10% level. With the same instrumental configuration, we find the pointing errors would slightly bias the 2-\sigma upper limit of the tensor-to-scalar ratio r by ~10%. We also show that the impact of pointing errors on the TB and EB measurements is negligibly small.Comment: 10 pages, 4 figures, accepted for publication in ApJS. Includes improvements in clarity of presentation and Fig.4 added, in response to refere

Planning for population viability on Northern Great Plains national grasslands

Broad-scale information in concert with conservation of individual species must be used to develop conservation priorities and a more integrated ecosystem protection strategy. In 1999 the United States Forest Service initiated an approach for the 1.2 x 106 ha of national grasslands in the Northern Great Plains to fulfill the requirement to maintain viable populations of all native and desirable introduced vertebrate and plant species. The challenge was threefold: 1) develop basic building blocks in the conservation planning approach, 2) apply the approach to national grasslands, and 3) overcome differences that may exist in agency-specific legal and policy requirements. Key assessment components in the approach included a bioregional assessment, coarse-filter analysis, and fine-filter analysis aimed at species considered at-risk. A science team of agency, conservation organization, and university personnel was established to develop the guidelines and standards and other formal procedures for implementation of conservation strategies. Conservation strategies included coarse-filter recommendations to restore the tallgrass, mixed, and shortgrass prairies to conditions that approximate historical ecological processes and landscape patterns, and fine-filter recommendations to address viability needs of individual and multiple species of native animals and plants. Results include a cost-effective approach to conservation planning and recommendations for addressing population viability and biodiversity concerns on national grasslands in the Northern Grea

Mechanical load stimulates expression of novel genesin vivoandin vitroin avian flexor tendon cells

OBJECTIVE: Our experiments were designed to test the hypothesis that tendon cells might respond differently to applied strain in vitro than in vivo. DESIGN: We tested cells in whole tendons from exercised chickens and from isolated surface (TSC) and internal tendon (TIF) in vitro that were subjected to mechanical strain. We hypothesized that tendon cells differentially express genes in response to mechanical loading in vivo and in vitro. METHODS: We utilized an in-vivo exercise model in which chickens were run on a treadmill in an acute loading regime for 1 h 45 min with the balance of time at rest to 6 h total time. Gene expression was analyzed by a differential display technique. In addition, isolated avian flexor digitorum profundus TSC and TIF cells were subjected to cyclic stretching at 1 Hz, 5% average elongation for 6 h, +/- PDGF-BB, IGF-I, TGF-beta 1, PTH, estrogen, PGE2, or no drug and/or no load. mRNA was then collected and samples were subjected to differential display analysis. CONCLUSIONS: Load with or without growth factor and hormone treatments induced expression of novel genes as well as some known genes that were novel to tendon cells. We conclude that the study of gene expression in mechanically loaded cells in vivo and in vitro will lead to the discovery of novel and important marker proteins that may yield clues to positive and negative cell strain responses that are protective under one set of conditions and destructive under another

Early-type galaxies in the SDSS. I. The sample

A sample of nearly 9000 early-type galaxies, in the redshift range 0.01 < z < 0.3, was selected from the Sloan Digital Sky Survey using morphological and spectral criteria. This paper describes how the sample was selected, presents examples of images and seeing corrected fits to the observed surface brightness profiles, describes our method for estimating K-corrections, and shows that the SDSS spectra are of sufficiently high quality to measure velocity dispersions accurately. It also provides catalogs of the measured photometric and spectroscopic parameters. In related papers, these data are used to study how early-type galaxy observables, including luminosity, effective radius, surface brightness, color, and velocity dispersion, are correlated with one another.Comment: 63 pages, 21 figures. Accepted by AJ (scheduled for April 2003). This paper is part I of a revised version of astro-ph/0110344. The full version of Tables 2 and 3, i.e. the tables listing the photometric and spectroscopic parameters of ~ 9000 galaxies, are available at http://astrophysics.phys.cmu.edu/~bernardi/SDSS/Etypes/TABLE

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

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