Archeological Of The Proposed FM 1626 Pass-Through Toll Project From Ranch-To-Market 967 To Farm-To-Market 2770 In Hays County, Texas

Hicks & Company archeologists conducted an intensive, 100-percent linear archeological survey of approximately 3.3 miles of proposed expansions to Farm-to-Market (FM) 1626 west of the city of Buda, Hays County, Texas. The survey was conducted between July 2008 and October 2016 for compliance with the Antiquities Code of Texas and Section 106 of the National Historic Preservation Act on behalf of Hays County, the project engineer Klotz Associates, and the Texas Department of Transportation (TxDOT). The Area of Potential Effects (APE) for the proposed project is composed of 54.3 acres of existing right of way and 8.08 acres of proposed expanded right of way (measuring 62.38 acres of existing plus proposed expanded right of way), and approximately 1.07 acres of temporary construction easements located outside of the existing or proposed right of way. While the proposed expanded right of way corridor has been determined, the project engineer requested that a 200-foot-wide corridor be investigated (extending 100 feet in either direction from the existing centerline) to allow for flexibility in road design, potential utility relocation, and other possible areas of concern, resulting in a total of approximately 81 acres of land surveyed. Investigations were coordinated with the Texas Historical Commission through TxDOT under Texas Antiquities Committee Permit Number 4981. On three occasions between July 28, 2008, and August 10, 2009 Hicks & Company archeologists conducted an intensive linear archeological survey of the proposed FM 1626 improvements project west of the city of Buda, Texas, on behalf of Hays County and TxDOT, returning to the field on January 21, 2016 to survey for proposed temporary construction easements located outside of the existing right of way or proposed new right of way, and again on October 26, 2016 to survey proposed new right of way in previously inaccessible parcels, completing the survey. The survey consisted of pedestrian inspection supplemented by shovel testing (N=102) and mechanical backhoe trench excavations (N=7) in the area north of Onion Creek. One backhoe trench excavated on the north bank of Onion Creek was positive for two pieces of lithic debitage, along with 32 shovel tests throughout the APE that were positive for cultural materials. One previously unrecorded site (Site 41HY449) was documented during the survey. This prehistoric surficial scatter does not meet the significance criteria for listing on the National Register of Historic Places (NRHP) or as a State Antiquities Landmark (SAL). In addition to this newly recorded site, archeologists visited elements of seven previously recorded sites (Sites 41HY199-202, 41HY209-210, and 41HY219) within the APE. Elements of one of these, Site 41HY200, could not be found within the archeological APE. Of these, only elements of Site 41HY201 are considered to have potential to deem the site eligible for inclusion on the NRHP or for designation as an SAL. The project engineer has altered plans in the vicinity of the site to avoid impacts to those resources. All other sites were found to be heavily disturbed, no longer extant, or within shallow surficial contexts atop bedrock with limited research value. Archeologists also visited the expansion areas adjacent to historic Barton Cemetery. Although the cemetery lies in close proximity to the APE, the County proposes no expansions in the immediate vicinity of the cemetery beyond a proposed retaining wall with riprap slope within the existing right of way outside the cemetery. This retaining wall is to be constructed approximately ten feet within current existing right of way. By design, retaining walls planned for this project will be fixed in place to concrete leveling pads set in place on top of the current grade and supported by earth reinforcement buildup of imported fill material. During survey, an overgrown road or trail that follows the current cemetery fenceline reinforces the assumption that the existing cemetery boundary served as the historic boundary as well, significantly reducing the potential for unmarked burials to be located within the current archeological APE. Construction within the APE is recommended to proceed with no further cultural resources investigation. The current investigations followed a no-collection policy. All projectrelated records, forms, and photographs will be permanently housed at the Texas Archeological Research Laboratory in Austin, Texas

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

Origins Space Telescope: Baseline mission concept

The Origins Space Telescope will trace the history of our origins from the time dust and heavy elements permanently altered the cosmic landscape to present-day life. How did galaxies evolve from the earliest galactic systems to those found in the Universe today? How do habitable planets form? How common are life-bearing worlds? To answer these alluring questions, Origins will operate at mid-and far-infrared (IR) wavelengths and offer powerful spectroscopic instruments and sensitivity three orders of magnitude better than that of the Herschel Space Observatory, the largest telescope flown in space to date. We describe the baseline concept for Origins recommended to the 2020 US Decadal Survey in Astronomy and Astrophysics. The baseline design includes a 5.9-m diameter telescope cryocooled to 4.5 K and equipped with three scientific instruments. A mid-infrared instrument (Mid-Infrared Spectrometer and Camera Transit spectrometer) will measure the spectra of transiting exoplanets in the 2.8 to 20 μm wavelength range and offer unprecedented spectrophotometric precision, enabling definitive exoplanet biosignature detections. The far-IR imager polarimeter will be able to survey thousands of square degrees with broadband imaging at 50 and 250 μm. The Origins Survey Spectrometer will cover wavelengths from 25 to 588 μm, making wide-area and deep spectroscopic surveys with spectral resolving power R ∼ 300, and pointed observations at R ∼ 40,000 and 300,000 with selectable instrument modes. Origins was designed to minimize complexity. The architecture is similar to that of the Spitzer Space Telescope and requires very few deployments after launch, while the cryothermal system design leverages James Webb Space Telescope technology and experience. A combination of current-state-of-the-art cryocoolers and next-generation detector technology will enable Origins\u27 natural background-limited sensitivity

Global Spatial Risk Assessment of Sharks Under the Footprint of Fisheries

Effective ocean management and conservation of highly migratory species depends on resolving overlap between animal movements and distributions and fishing effort. Yet, this information is lacking at a global scale. Here we show, using a big-data approach combining satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively) and were also associated with significant increases in fishing effort. We conclude that pelagic sharks have limited spatial refuge from current levels of high-seas fishing effort. Results demonstrate an urgent need for conservation and management measures at high-seas shark hotspots and highlight the potential of simultaneous satellite surveillance of megafauna and fishers as a tool for near-real time, dynamic management

Justify your alpha

Benjamin et al. proposed changing the conventional “statistical significance” threshold (i.e.,the alpha level) from p ≤ .05 to p ≤ .005 for all novel claims with relatively low prior odds. They provided two arguments for why lowering the significance threshold would “immediately improve the reproducibility of scientific research.” First, a p-value near .05provides weak evidence for the alternative hypothesis. Second, under certain assumptions, an alpha of .05 leads to high false positive report probabilities (FPRP2 ; the probability that a significant finding is a false positive