Imprint of Inhomogeneous Reionization on the Power Spectrum of Galaxy Surveys at High Redshifts

We consider the effects of inhomogeneous reionization on the distribution of galaxies at high redshifts. Modulation of the formation process of the ionizing sources by large scale density modes makes reionization inhomogeneous and introduces a spread to the reionization times of different regions with the same size. After sources photo-ionize and heat these regions to a temperature \ga 10^4K at different times, their temperatures evolve as the ionized intergalactic medium (IGM) expands. The varying IGM temperature makes the minimum mass of galaxies spatially non-uniform with a fluctuation amplitude that increases towards small scales. These scale-dependent fluctuations modify the shape of the power spectrum of low-mass galaxies at high redshifts in a way that depends on the history of reionization. The resulting distortion of the primordial power spectrum is significantly larger than changes associated with uncertainties in the inflationary parameters, such as the spectral index of the scalar power spectrum or the running of the spectral index. Future surveys of high-redshift galaxies will offer a new probe of the thermal history of the IGM but might have a more limited scope in constraining inflation.Comment: 8 pages, 5 figures, replaced to match version accepted by Ap

Does Stellar Feedback Create HI Holes? An HST/VLA Study of Holmberg II

We use deep HST/ACS F555W and F814W photometry of resolved stars in the M81 Group dwarf irregular galaxy Ho II to study the hypothesis that the holes identified in the neutral ISM (HI) are created by stellar feedback. From the deep photometry, we construct color-magnitude diagrams (CMDs) and measure the star formation histories (SFHs) for stars contained in HI holes from two independent holes catalogs, as well as select control fields, i.e., similar sized regions that span a range of HI column densities. Converting the recent SFHs into stellar feedback energies, we find that enough energy has been generated to have created all holes. However, the required energy is not always produced over a time scale that is less than the estimated kinematic age of the hole. The combination of the CMDs, recent SFHs, and locations of young stars shows that the stellar populations inside HI holes are not coherent, single-aged, stellar clusters, as previously suggested, but rather multi-age populations distributed across each hole. From a comparison of the modeled and observed integrated magnitudes, and the locations and energetics of stars inside of HI holes, we propose a potential new model: a viable mechanism for creating the observed HI holes in Ho II is stellar feedback from multiple generations of SF spread out over tens or hundreds of Myr, and thus, the concept of an age for an HI hole is intrinsically ambiguous. We further find that \halpha and 24 micron emission, tracers of the most recent star formation, do not correlate well with the positions of the HI holes. However, UV emission, which traces star formation over roughly the last 100 Myr, shows a much better correlation with the locations of the HI holes.Comment: Accepted for Publication in The Astrophysical Journal; 28 Pages, 31 Figures, a version of this paper with full resolution figures is available at http://homepages.spa.umn.edu/~dweisz/ho_ii_weisz.pd

Early star-forming galaxies and the reionization of the Universe

Star forming galaxies represent a valuable tracer of cosmic history. Recent observational progress with Hubble Space Telescope has led to the discovery and study of the earliest-known galaxies corresponding to a period when the Universe was only ~800 million years old. Intense ultraviolet radiation from these early galaxies probably induced a major event in cosmic history: the reionization of intergalactic hydrogen. New techniques are being developed to understand the properties of these most distant galaxies and determine their influence on the evolution of the universe.Comment: Review article appearing in Nature. This posting reflects a submitted version of the review formatted by the authors, in accordance with Nature publication policies. For the official, published version of the review, please see http://www.nature.com/nature/archive/index.htm

A comparative analysis of algorithms for somatic SNV detection in cancer

Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.Nicola D. Roberts, R. Daniel Kortschak, Wendy T. Parker, Andreas W. Schreiber, Susan Branford, Hamish S. Scott, Garique Glonek and David L. Adelso

Persistent Asymmetric Structure of Sagittarius A* on Event Horizon Scales

The Galactic Center black hole Sagittarius A* (Sgr A*) is a prime observing target for the Event Horizon Telescope (EHT), which can resolve the 1.3 mm emission from this source on angular scales comparable to that of the general relativistic shadow. Previous EHT observations have used visibility amplitudes to infer the morphology of the millimeter-wavelength emission. Potentially much richer source information is contained in the phases. We report on 1.3 mm phase information on Sgr A* obtained with the EHT on a total of 13 observing nights over 4 years. Closure phases, the sum of visibility phases along a closed triangle of interferometer baselines, are used because they are robust against phase corruptions introduced by instrumentation and the rapidly variable atmosphere. The median closure phase on a triangle including telescopes in California, Hawaii, and Arizona is nonzero. This result conclusively demonstrates that the millimeter emission is asymmetric on scales of a few Schwarzschild radii and can be used to break 180-degree rotational ambiguities inherent from amplitude data alone. The stability of the sign of the closure phase over most observing nights indicates persistent asymmetry in the image of Sgr A* that is not obscured by refraction due to interstellar electrons along the line of sight.Comment: 11 pages, accepted to Ap

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Mutational analysis of human immunodeficiency virus type 1 protease suggests functional homology with aspartic proteinases.

Processing of the retroviral gag and pol gene products is mediated by a viral protease. Bacterial expression systems have been developed which permit genetic analysis of the human immunodeficiency virus type 1 protease as measured by cleavage of the pol protein precursor. Deletion analysis of the pol reading frame locates the sequences required to encode a protein with appropriate proteolytic activity near the left end of the pol reading frame but largely outside the gag-pol overlap region, which is at the extreme left end of pol. Most missense mutations within an 11-amino-acid domain highly conserved among retroviral proteases and with sequence similarity to the active site of aspartic proteinases abolish appropriate processing, suggesting that the retrovirus proteases share a catalytic mechanism with aspartic proteinases. Substitution of the amino acids flanking the scissile bond at three of the processing sites encoded by pol demonstrates distinct sequence requirements for cleavage at these different sites. The inclusion of a charged amino acid at the processing site blocks cleavage. A subset of these substitutions also inhibits processing at the nonmutated sites

Plasmid origin of replication of herpesvirus papio: DNA sequence and enhancer function.

Herpesvirus papio (HVP) is a lymphotropic virus of baboons which is related to Epstein-Barr virus (EBV) and produces latent infection. The nucleotide sequence of the 5,775-base-pair (bp) EcoRI K fragment of HVP, which has previously been shown to confer the ability to replicate autonomously, has been determined. Within this DNA fragment is a region which bears structural and sequence similarity to the ori-P region of EBV. The HVP ori-P region has a 10- by 26-bp tandem array which is related to the 20- by 30-bp tandem array from the EBV ori-P region. In HVP there is an intervening region of 764 bp followed by five partial copies of the 26-bp monomer. Both the EBV and HVP 3' regions have the potential to form dyad structures which, however, differ in arrangement. We also demonstrate that a transcriptional enhancer which requires transactivation by a virus-encoded factor is present in the HVP ori-P