Colloquium: Comparison of Astrophysical and Terrestrial Frequency Standards

We have re-analyzed the stability of pulse arrival times from pulsars and white dwarfs using several analysis tools for measuring the noise characteristics of sampled time and frequency data. We show that the best terrestrial artificial clocks substantially exceed the performance of astronomical sources as time-keepers in terms of accuracy (as defined by cesium primary frequency standards) and stability. This superiority in stability can be directly demonstrated over time periods up to two years, where there is high quality data for both. Beyond 2 years there is a deficiency of data for clock/clock comparisons and both terrestrial and astronomical clocks show equal performance being equally limited by the quality of the reference timescales used to make the comparisons. Nonetheless, we show that detailed accuracy evaluations of modern terrestrial clocks imply that these new clocks are likely to have a stability better than any astronomical source up to comparison times of at least hundreds of years. This article is intended to provide a correct appreciation of the relative merits of natural and artificial clocks. The use of natural clocks as tests of physics under the most extreme conditions is entirely appropriate; however, the contention that these natural clocks, particularly white dwarfs, can compete as timekeepers against devices constructed by mankind is shown to be doubtful.Comment: 9 pages, 2 figures; presented at the International Frequency Control Symposium, Newport Beach, Calif., June, 2010; presented at Pulsar Conference 2010, October 12th, Sardinia; accepted 13th September 2010 for publication in Reviews of Modern Physic

Oxygen Gas Phase Abundance Revisited

We present new measurements of the interstellar gas-phase oxygen abundance along the sight lines towards 19 early-type galactic stars at an average distance of 2.6 kpc. We derive O {\small I} column densities from {\it HST}/STIS observations of the weak 1355 \AA intersystem transition. We derive total hydrogen column densities [N(H {\small I})+2N(H$_2$)] using {\it HST}/STIS observations of \lya and {\it FUSE} observations of molecular hydrogen. The molecular hydrogen content of these sight lines ranges from f(H$_2$) = 2N(H$_2$)/[N(H {\small I})+2N(H$_2$)] = 0.03 to 0.47. The average $$ of 6.3$\times10^{21}$ cm$^{-2}$ mag$^{-1}$ with a standard deviation of 15% is consistent with previous surveys. The mean oxygen abundance along these sight lines, which probe a wide range of galactic environments in the distant ISM, is 10$^6$ \oh = $408 \pm 13$ (1 $\sigma$ in the mean). %$({\rm O/H})_{gas} = 408 \pm 14$(1 $\sigma$). We see no evidence for decreasing gas-phase oxygen abundance with increasing molecular hydrogen fraction and the relative constancy of \oh suggests that the component of dust containing the oxygen is not readily destroyed. We estimate that, if 60% of the dust grains are resilient against destruction by shocks, the distant interstellar total oxygen abundance can be reconciliated with the solar value derived from the most recent measurements %by Holweger and by Allende Prieto, Lambert & Asplund: of 10$^6$ \oh$_\odot$ = 517 $\pm$ 58 (1 $\sigma$). We note that the smaller oxygen abundances derived for the interstellar gas within 500 pc %by Meyer, Cardelli & Jura or from nearby B star surveys are consistent with a local elemental deficit.Comment: 9 figures, 37 page

Two mass distributions in the L1641 molecular clouds: the Herschel connection of dense cores and filaments in Orion A

We present the Herschel Gould Belt survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 Solar Masses and drives the shape of the CMF at higher masses, which we fit with a power law of the form dN /dlogM ∝ M -1.4±0.4 . The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8⊙ and leads to a flattening of the CMF at masses lower than ˜4⊙. We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years

Great Lakes Runoff Intercomparison Project Phase 3: Lake Erie (GRIP-E)

Hydrologic model intercomparison studies help to evaluate the agility of models to simulate variables such as streamflow, evaporation, and soil moisture. This study is the third in a sequence of the Great Lakes Runoff Intercomparison Projects. The densely populated Lake Erie watershed studied here is an important international lake that has experienced recent flooding and shoreline erosion alongside excessive nutrient loads that have contributed to lake eutrophication. Understanding the sources and pathways of flows is critical to solve the complex issues facing this watershed. Seventeen hydrologic and land-surface models of different complexity are set up over this domain using the same meteorological forcings, and their simulated streamflows at 46 calibration and seven independent validation stations are compared. Results show that: (1) the good performance of Machine Learning models during calibration decreases significantly in validation due to the limited amount of training data; (2) models calibrated at individual stations perform equally well in validation; and (3) most distributed models calibrated over the entire domain have problems in simulating urban areas but outperform the other models in validation

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

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London