The First Data Release of the KODIAQ Survey

We present and make publicly available the first data release (DR1) of the Keck Observatory Database of Ionized Absorption toward Quasars (KODIAQ) survey. The KODIAQ survey is aimed at studying galactic and circumgalactic gas in absorption at high-redshift, with a focus on highly-ionized gas traced by OVI, using the HIRES spectrograph on the Keck-I telescope. KODIAQ DR1 consists of a fully-reduced sample of 170 quasars at 0.29 < z_em < 5.29 observed with HIRES at high resolution (36,000 <= R <= 103,000) between 2004 and 2012. DR1 contains 247 spectra available in continuum normalized form, representing a sum total exposure time of ~1.6 megaseconds. These co-added spectra arise from a total of 567 individual exposures of quasars taken from the Keck Observatory Archive (KOA) in raw form and uniformly processed using a HIRES data reduction package made available through the XIDL distribution. DR1 is publicly available to the community, housed as a higher level science product at the KOA. We will provide future data releases that make further QSOs, including those with pre-2004 observations taken with the previous-generation HIRES detectors.Comment: 14 pages, 9 figures, Submitted to AJ. All data products available at the Keck Observatory Archive beginning May 15, 2015. URL: https://koa.ipac.caltech.edu/applications/KODIA

A natural histone H2A variant lacking the Bub1 phosphorylation site and regulated depletion of centromeric histone CENP-A foster evolvability in Candida albicans.

Eukaryotes have evolved elaborate mechanisms to ensure that chromosomes segregate with high fidelity during mitosis and meiosis, and yet specific aneuploidies can be adaptive during environmental stress. Here, we identify a chromatin-based system required for inducible aneuploidy in a human pathogen. Candida albicans utilizes chromosome missegregation to acquire tolerance to antifungal drugs and for nonmeiotic ploidy reduction after mating. We discovered that the ancestor of C. albicans and 2 related pathogens evolved a variant of histone 2A (H2A) that lacks the conserved phosphorylation site for kinetochore-associated Bub1 kinase, a key regulator of chromosome segregation. Using engineered strains, we show that the relative gene dosage of this variant versus canonical H2A controls the fidelity of chromosome segregation and the rate of acquisition of tolerance to antifungal drugs via aneuploidy. Furthermore, whole-genome chromatin precipitation analysis reveals that Centromere Protein A/ Centromeric Histone H3-like Protein (CENP-A/Cse4), a centromeric histone H3 variant that forms the platform of the eukaryotic kinetochore, is depleted from tetraploid-mating products relative to diploid parents and is virtually eliminated from cells exposed to aneuploidy-promoting cues. We conclude that genetically programmed and environmentally induced changes in chromatin can confer the capacity for enhanced evolvability via chromosome missegregation

Body size measures, hemostatic and inflammatory markers and risk of venous thrombosis: The Longitudinal Investigation of Thromboembolism Etiology

Obesity is an important venous thrombosis (VT) risk factor but the reasons for this are unclear

The Cryptococcus neoformans Rim101 Transcription Factor Directly Regulates Genes Required for Adaptation to the Host

The Rim101 protein is a conserved pH-responsive transcription factor that mediates important interactions between several fungal pathogens and the infected host. In the human fungal pathogen Cryptococcus neoformans, the Rim101 protein retains conserved functions to allow the microorganism to respond to changes in pH and other host stresses. This coordinated cellular response enables this fungus to effectively evade the host immune response. Preliminary studies suggest that this conserved transcription factor is uniquely regulated in C. neoformans both by the canonical pH-sensing pathway and by the cyclic AMP (cAMP)/protein kinase A (PKA) pathway. Here we present comparative transcriptional data that demonstrate a strong concordance between the downstream effectors of PKA and Rim101. To define Rim101-dependent gene expression during a murine lung infection, we used nanoString profiling of lung tissue infected with a wild-type or rim101Δ mutant strain. In this setting, we demonstrated that Rim101 controls the expression of multiple cell wall-biosynthetic genes, likely explaining the enhanced immunogenicity of the rim101Δ mutant. Despite its divergent upstream regulation, the C. neoformans Rim101 protein recognizes a conserved DNA binding motif. Using these data, we identified direct targets of this transcription factor, including genes involved in cell wall regulation. Therefore, the Rim101 protein directly controls cell wall changes required for the adaptation of C. neoformans to its host environment. Moreover, we propose that integration of the cAMP/PKA and pH-sensing pathways allows C. neoformans to respond to a broad range of host-specific signals

HD molecules at high redshift: The absorption system at z=2.3377 towards Q 1232+082

We present a detailed analysis of the H_2 and HD absorption lines detected in the Damped Lyman-alpha (DLA) system at z_abs=2.3377 towards the quasar Q1232+082. We show that this intervening cloud has a covering factor smaller than unity and covers only part of the QSO broad emission line region. The zero flux level has to be corrected at the position of the saturated H_2 and optically thin HD lines by about 10%. We accurately determine the Doppler parameter for HD and CI lines (b = 1.86+/-0.20 km/s). We find a ratio N(HD)/N(H_2)=(7.1 +3.7 -2.2)x10^-5 that is significantly higher than what is observed in molecular clouds of the Galaxy. Chemical models suggest that in the physical conditions prevailing in the central part of molecular clouds, deuterium and hydrogen are mostly in their molecular forms. Assuming this is true, we derive D/H = (3.6 +1.9 -1.1)x10^-5. This implies that the corresponding baryon density of the Universe is \Omega_b h^2 = (0.0182 +0.0047 -0.0042). This value coincides within 1\sigma with that derived from observations of the CMBR as well as from observations of the D/H atomic ratio in low-metallicity QSO absorption line systems. The observation of HD at high redshift is therefore a promising independent method to constrain \Omega_b. This observation indicates as well a low astration factor of deuterium. This can be interpreted as the consequence of an intense infall of primordial gas onto the associated galaxy.Comment: 8 pages, 7 figures, 3 tables. Accepted for publication in MNRA

Improvement of stabilizer based entanglement distillation protocols by encoding operators

This paper presents a method for enumerating all encoding operators in the Clifford group for a given stabilizer. Furthermore, we classify encoding operators into the equivalence classes such that EDPs (Entanglement Distillation Protocol) constructed from encoding operators in the same equivalence class have the same performance. By this classification, for a given parameter, the number of candidates for good EDPs is significantly reduced. As a result, we find the best EDP among EDPs constructed from [[4,2]] stabilizer codes. This EDP has a better performance than previously known EDPs over wide range of fidelity.Comment: 22 pages, 2 figures, In version 2, we enumerate all encoding operators in the Clifford group, and fix the wrong classification of encoding operators in version

Prescribing for the management of venous leg ulceration

Venous leg ulceration affects a large proportion of the elderly population and can have a profound impact on quality of life. Most patients with leg ulcers receive care from community nurses who are principally responsible for prescribing decisions in the management of venous leg ulceration. There is evidence to support the use of potable tap water for cleansing. Evidence supports the use of compression bandaging or compression hosiery for all patients with adequate arterial supply to the lower leg. There is also good evidence to support the prescription of oral pentoxifylline, preferably as an adjunct to compression or, for patients unable to tolerate compression, as a stand-alone therapy. The evidence base for dressings is less robust, but simple low-cost, low-adherent dressings are a reasonable first-line choice for under-compression