Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These ligand-based protein networks, which implicitly predict the ability of neighboring proteins to bind related ligands, may complement biologically-oriented gene networks, which are used to predict functional or disease relevance. To quantify the degree to which such ligand-based protein associations might complement functional genomic associations, including sequence similarity, physical protein-protein interactions, co-expression, and disease gene annotations, we calculated a network based on the Similarity Ensemble Approach (SEA: sea.docking.org), where protein neighbors reflect the similarity of their ligands. We also measured the similarity with functional genomic networks over a common set of 1,131 genes, and found that the networks had only small overlaps, which were significant only due to the large scale of the data. Consistent with the view that the networks contain different information, combining them substantially improved Molecular Function prediction within GO (from AUROC~0.63-0.75 for the individual data modalities to AUROC~0.8 in the aggregate). We investigated the boost in guilt-by-association gene function prediction when the networks are combined and describe underlying properties that can be further exploited

The Large, Oxygen-Rich Halos of Star-Forming Galaxies Are A Major Reservoir of Galactic Metals

The circumgalactic medium (CGM) is fed by galaxy outflows and accretion of intergalactic gas, but its mass, heavy element enrichment, and relation to galaxy properties are poorly constrained by observations. In a survey of the outskirts of 42 galaxies with the Cosmic Origins Spectrograph onboard the Hubble Space Telescope, we detected ubiquitous, large (150 kiloparsec) halos of ionized oxygen surrounding star-forming galaxies, but we find much less ionized oxygen around galaxies with little or no star formation. This ionized CGM contains a substantial mass of heavy elements and gas, perhaps far exceeding the reservoirs of gas in the galaxies themselves. It is a basic component of nearly all star-forming galaxies that is removed or transformed during the quenching of star formation and the transition to passive evolution.Comment: This paper is part of a set of three papers on circumgalactic gas observed with the Cosmic Origins Spectrograph on HST, to be published in Science, together with related papers by Tripp et al. and Lehner & Howk, in the November 18, 2011 edition. This version has not undergone final copyediting. Please see Science online for the final printed versio

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.

Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival

MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over-or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics

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

The COS Absorption Survey of Baryon Harbors (CASBaH): Warm-hot Circumgalactic Gas Reservoirs Traced by Ne VIII Absorption

We survey the highly ionized circumgalactic media (CGM) of 29 blindly selected galaxies at 0.49 < z_(gal) < 1.44 based on high-S/N ultraviolet spectra of z > 1 QSOs and the galaxy database from the COS Absorption Survey of Baryon Harbors (CASBaH). We detect the Ne VIII doublet in nine of the galaxies, and for gas with N(Ne VIII) > 10^13.3 cm^-2 (> 10^13.5 cm^-2), we derive a Ne VIII covering fraction f_c = 75 +15/-25% (44 +22/-20%) within impact parameter (rho) < 200 kpc of M_* = 10^(9.5-11.5) Msol galaxies and f_c = 70 +16/-22% (f_c = 42 +20/-17%) within rho < 1.5 virial radii. We estimate the mass in Ne VIII-traced gas to be M_gas(Ne VIII) > 10^9.5 Msol (Z/Zsol)^-1, or 6-20% of the expected baryonic mass if the Ne VIII absorbers have solar metallicity. Ionizing Ne VII to Ne VIII requires 207 eV, and photons with this energy are scarce in the CGM. However, for the median halo mass and redshift of our sample, the virial temperature is close to the peak temperature for the Ne VIII ion, and the Ne VIII-bearing gas is plausibly collisionally ionized near this temperature. Moreover, we find that photoionized Ne VIII requires cool and low-density clouds that would be highly underpressured (by approximately two orders of magnitude) relative to the putative, ambient virialized medium, complicating scenarios where such clouds could survive. Thus, more complex (e.g., non-equilibrium) models may be required; this first statistical sample of Ne VIII absorber/galaxy systems will provide stringent constraints for future CGM studies.Comment: Published in ApJL, Volume 877, Issue 2, Article L2

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

Semiconductor Surface Studies

Contains an introduction, reports on two research projects, and a list of publications.Joint Services Electronics Program Grant DAAH04-95-1-003

Prevalence and Predictors of Urinary Tract Infection and Severe Malaria Among Febrile Children Attending Makongoro Health Centre in Mwanza City, North-Western Tanzania.

In malaria endemic areas, fever has been used as an entry point for presumptive treatment of malaria. At present, the decrease in malaria transmission in Africa implies an increase in febrile illnesses related to other causes among underfives. Moreover, it is estimated that more than half of the children presenting with fever to public clinics in Africa do not have a malaria infection. Thus, for a better management of all febrile illnesses among under-fives, it becomes relevant to understand the underlying aetiology of the illness. The present study was conducted to determine the relative prevalence and predictors of P. falciparum malaria, urinary tract infections and bacteremia among under-fives presenting with a febrile illness at the Makongoro Primary Health Centre, North-Western Tanzania. From February to June 2011, a cross-sectional analytical survey was conducted among febrile children less than five years of age. Demographic and clinical data were collected using a standardized pre-tested questionnaire. Blood and urine culture was done, followed by the identification of isolates using in-house biochemical methods. Susceptibility patterns to commonly used antibiotics were investigated using the disc diffusion method. Giemsa stained thin and thick blood smears were examined for any malaria parasites stages. A total of 231 febrile under-fives were enrolled in the study. Of all the children, 20.3% (47/231, 95%CI, 15.10-25.48), 9.5% (22/231, 95%CI, 5.72-13.28) and 7.4% (17/231, 95%CI, 4.00-10.8) had urinary tract infections, P. falciparum malaria and bacteremia respectively. In general, 11.5% (10/87, 95%CI, 8.10-14.90) of the children had two infections and only one child had all three infections. Predictors of urinary tract infections (UTI) were dysuria (OR = 12.51, 95% CI, 4.28-36.57, P < 0.001) and body temperature (40-41 C) (OR = 12.54, 95% CI, 4.28-36.73, P < 0.001). Predictors of P. falciparum severe malaria were pallor (OR = 4.66 95%CI, 1.21-17.8, P = 0.025) and convulsion (OR = 102, 95% CI, 10-996, P = 0.001). Escherichia coli were the common gram negative isolates from urine (72.3%, 95% CI, 66.50-78.10) and blood (40%, 95%CI, and 33.70-46.30). Escherichia coli from urine were 100% resistant to ampicillin, 97% resistant to co-trimoxazole, 85% resistant to augmentin and 32.4% resistant to gentamicin; and they were 100%, 91.2% and 73.5% sensitive to meropenem, ciprofloxacin and ceftriaxone respectively. Urinary tract infection caused by multi drug resistant Escherichia coli was the common cause of febrile illness in our setting. Improvement of malaria diagnosis and its differential diagnosis from other causes of febrile illnesses may provide effective management of febrile illnesses among children in Tanzania