Large Scale Structure traced by Molecular Gas at High Redshift

We present observations of redshifted CO(1-0) and CO(2-1) in a field containing an overdensity of Lyman break galaxies (LBGs) at z=5.12. Our Australia Telescope Compact Array observations were centered between two spectroscopically-confirmed z=5.12 galaxies. We place upper limits on the molecular gas masses in these two galaxies of M(H_2) <1.7 x 10^10 M_sun and <2.9 x 10^9 M_sun (2 sigma), comparable to their stellar masses. We detect an optically-faint line emitter situated between the two LBGs which we identify as warm molecular gas at z=5.1245 +/- 0.0001. This source, detected in the CO(2-1) transition but undetected in CO(1-0), has an integrated line flux of 0.106 +/- 0.012 Jy km/s, yielding an inferred gas mass M(H_2)=(1.9 +/- 0.2) x 10^10 M_sun. Molecular line emitters without detectable counterparts at optical and infrared wavelengths may be crucial tracers of structure and mass at high redshift.Comment: 4 pages, accepted for publication in ApJ Letter

Advances and Limitations in Open Source Arabic-Script OCR: A Case Study

This work presents an accuracy study of the open source OCR engine, Kraken, on the leading Arabic scholarly journal, al-Abhath. In contrast with other commercially available OCR engines, Kraken is shown to be capable of producing highly accurate Arabic-script OCR. The study also assesses the relative accuracy of typeface-specific and generalized models on the al-Abhath data and provides a microanalysis of the “error instances” and the contextual features that may have contributed to OCR misrecognition. Building on this analysis, the paper argues that Arabic-script OCR can be significantly improved through (1) a more systematic approach to training data production, and (2) the development of key technological components, especially multi-language models and improved line segmentation and layout analysis. / Cet article présente une étude d’exactitude du moteur ROC open source, Krakan, sur la revue académique arabe de premier rang, al-Abhath. Contrairement à d’autres moteurs ROC disponibles sur le marché, Kraken se révèle être capable de produire de la ROC extrêmement exacte de l’écriture arabe. L’étude évalue aussi l’exactitude relative des modèles spécifiquement configurés à des polices et celle des modèles généralisés sur les données d’al-Abhath et fournit une microanalyse des « occurrences d’erreurs », ainsi qu’une microanalyse des éléments contextuels qui pourraient avoir contribué à la méreconnaissance ROC. S’appuyant sur cette analyse, cet article fait valoir que la ROC de l’écriture arabe peut être considérablement améliorée grâce à (1) une approche plus systématique d’entraînement de la production de données et (2) grâce au développement de composants technologiques fondamentaux, notammentl’amélioration des modèles multilingues, de la segmentation de ligne et de l’analyse de la mise en page. Kiessling, Benjamin, Gennady Kurin, Matthew Miller, and Kader Smail. 2021. “Advances and Limitations in Open Source Arabic-Script OCR: A Case Study.

Yes-Associated Protein Expression in Head and Neck Squamous Cell Carcinoma Nodal Metastasis

INTRODUCTION:Yes-associated protein (YAP) is considered an oncogene found amplified in multiple tumors, including head and neck squamous cell carcinoma (HNSCC). However, the role for YAP expression in HNSCC is not understood. Based on the central role of YAP in the hippo pathway, we tested if YAP was associated with the stage of HNSCC progression and metastatic potential. METHODS:To determine the expression of YAP in human benign and HNSCC tissue specimens, immunohistochemical analyses were performed in whole tissue samples and tissue microarrays. The expression of YAP in tissues of microarray was first associated with clinic-pathologic factors and results verified in samples from whole tissue sections. To investigate the role of YAP and p63 in regulating HNSCC epithelial to mesenchymal transition, epithelial and mesenchymal markers were assayed in Fadu and SCC-25 cells, HNSCC cells with endogenously elevated YAP expression and siRNA-mediated expression knockdown. RESULTS:Analysis of human HNSCC tissues suggested YAP expression was elevated in tumors compared to benign tissues and specifically localized at the tumor invasive front (p value < 0.05). But, indexed YAP expression was lower with greater tumor grade (p value  =  0.02). In contrast, p63 expression was primarily elevated in high-grade tumors. Interestingly, both YAP and p63 was strongly expressed at the tumor invasive front and in metastatic HNSCC. Strikingly, we demonstrated YAP expression in the primary HNSCC tumor was associated with nodal metastasis in univariate analysis (p value  =  0.02). However, the knockdown of YAP in Fadu and SCC-25 cell lines was not associated with changes in epithelial to mesenchymal transdifferentiation or p63 expression. CONCLUSION:Together, YAP expression, in combination with p63 can facilitate identification of HNSCC tumors from hyperplastic and benign tissues and the metastatic function of YAP in HNSCC may not be a result of epithelia to mesenchymal transdifferentiation

Numerical simulations on the relative importance of starbursts and AGN in ultra-luminous infrared galaxies

We investigate the relative importance of starbursts and AGN in nuclear activities of ultra-luminous infrared galaxies (ULIRGs) based on chemodynamical simulations combined with spectrophotometric synthesis codes. We numerically investigate both the gas accretion rates (m_acc) onto super massive black holes (SMBHs) and the star formation rates (m_sf) in ULIRGs formed by gas-rich galaxy mergers and thereby discuss what powers ULIRGs. Our principal results, which can be tested against observations, are as follows. (1) ULIRGs powered by AGN can be formed by major merging between luminous, gas-rich disk galaxies with prominent bulges containing SMBHs, owing to the efficient gas fuelling m_acc > 1 M_sun/yr of the SMBH. AGN in these ULIRGs can be surrounded by compact poststarburst stellar populations (e.g., A-type stars). (2) ULIRGs powered by starbursts with m_sf ~ 100 M_sun/yr can be formed by merging between gas-rich disk galaxies with small bulges having the bulge-to-disk-ratio (f_b) as small as 0.1. (3) The relative importance of starbursts and AGN can depend on physical properties of merger progenitor disks, such as f_b, gas mass fraction, and total masses. For example, more massive galaxy mergers are more likely to become AGN-dominated ULIRGs. (4) For most models, major mergers can become ULIRGs, powered either by starbursts or by AGN, only when the two bulges finally merge. Interacting disk galaxies can become ULIRGs with well separated two cores (> 20kpc) at their pericenter when they are very massive and have small bulges. (5) Irrespective of the choice of model, interacting/merging galaxies show the highest accretion rates onto the central SMBHs, and the resultant rapid growth of the SMBHs occur when their star formation rates are very high.Comment: 18 pages, 15 figures (f1.jpg for color figure of figure 1), accepted in MNRA

Broadband Photometry of 105 Giant Arcs: Redshift Constraints and Implications for Giant Arc Statistics

We measure the photometric properties of 105 giant arcs that were identified in systematic searches for galaxy-cluster-scale strong lenses in the Second Red-Sequence Cluster Survey (RCS-2) and the Sloan Digital Sky Survey (SDSS). The cluster lenses span 0.2 < z_lens < 1.2 in redshift, with a median z_lens = 0.58. Using broadband color criteria we sort the entire arc sample into redshift bins based on u-g and g-r colors, and also r-z colors for the ~90% of arcs that have z-band data. This analysis yields broad redshift constraints with 71 +5 -4 % of the arcs at z > 1.0, 64 +6 -4 % at z > 1.4, 56 +5 -4 % at z > 1.9, and 21 +4 -2 % at z > 2.7. The remaining 29 +3 -5 % have z < 1. The inferred median redshift is z_s = 2.0 +/- 0.1, in good agreement with a previous determination from a smaller sample of brighter arcs (g < 22.5). This agreement confirms that z_s = 2.0 +/- 0.1 is the typical redshift for giant arcs with g < 24 that are produced by cluster-scale strong lenses, and that there is no evidence for strong evolution in the redshift distribution of arcs over a wide range of g-band magnitudes (20 < g < 24). Establishing that half of all giant arcs are at z > 2 contributes significantly toward relieving the tension between the number of arcs observed and the number expected in a Lambda-CDM cosmology, but there is considerable evidence to suggest that a discrepancy persists. Additionally, this work confirms that forthcoming large samples of giant arcs will supply the observational community with many magnified galaxies at z > 2.Comment: 16 pages, 8 figures, 3 tables, Accepted to ApJ; University of Chicago Department of Astronomy & Astrophysics PhD Thesi

A bright, spatially extended lensed galaxy at z = 1.7 behind the cluster RCS2 032727-132623

We present the discovery of an extremely bright and extended lensed source from the second Red Sequence Cluster Survey (RCS2). RCSGA 032727-132609 is spectroscopically confirmed as a giant arc and counter-image of a background galaxy at $z=1.701$, strongly-lensed by the foreground galaxy cluster RCS2 032727-132623 at $z=0.564$. The giant arc extends over $\sim 38$\,\arcsec and has an integrated $g$-band magnitude of 19.15, making it $\sim 20$ times larger and $\sim 4$ times brighter than the prototypical lensed galaxy MS1512-cB58. This is the brightest distant lensed galaxy in the Universe known to date. Its location in the `redshift desert' provides unique opportunities to connect between the large samples of galaxies known at $z\sim3$ and $z\sim1$. We have collected photometry in 9 bands, ranging from $u$ to $K_s$, which densely sample the rest-frame UV and optical light, including the age-sensitive 4000\AA\ break. A lens model is constructed for the system, and results in a robust total magnification of $2.04 \pm 0.16$ for the counter-image; we estimate an average magnification of $17.2 \pm 1.4$ for the giant arc based on the relative physical scales of the arc and counter-image. Fits of single-component spectral energy distribution (SED) models to the photometry result in a moderately young age, $t = 115 \pm 65$\,Myr, small amounts of dust, $E(B-V) \le 0.035$, and an exponentially declining star formation history with \textit{e}-folding time $\tau = 10-100$\,Myr. After correcting for the lensing magnification, we find a stellar mass of $\log(\mathrm{M}/\mathrm{M}_\odot)=10.0 \pm 0.1$. Allowing for episodic star formation, an underlying old burst could contain up to twice the mass inferred from single-component modeling. This stellar mass estimate is consistent with the average stellar mass of a sample of `BM' galaxies ($1.4 < z < 2.0$) studied by Reddy et al. (2006).Comment: 13 pages, 8 figures, abstract abridge

Spectroscopy of Luminous Compact Blue Galaxies in Distant Clusters I. Spectroscopic Data

We used the DEIMOS spectrograph on the Keck II Telescope to obtain spectra of galaxies in the fields of five distant, rich galaxy clusters over the redshift range 0.5 < z < 0.9 in a search for luminous, compact, blue galaxies (LCBGs). Unlike traditional studies of galaxy clusters, we preferentially targeted blue cluster members identified via multi-band photometric pre-selection based on imaging data from the WIYN telescope. Of the 1288 sources that we targeted, we determined secure spectroscopic redshifts for 848 sources, yielding a total success rate of 66%. Our redshift measurements are in good agreement with those previously reported in the literature, except for 11 targets which we believe were previously in error. Within our sample, we confirm the presence of 53 LCBGs in the five galaxy clusters. The clusters all stand out as distinct peaks in the redshift distribution of LCBGs with the average number density of LCBGs ranging from 1.65+-0.25 Mpc^-3 at z=0.55 to 3.13+-0.65 Mpc^-3 at z=0.8. The number density of LCBGs in clustes exceeds the field desnity by a factor of 749+-116 at z=0.55; at z=0.8, the corresponding ratio is E=416+-95. At z=0.55, this enhancement is well above that seen for blue galaxies or the overall cluster population, indicating that LCBGs are preferentially triggered in high-density environments at intermediate redshifts.Comment: 45 pages, 19 figures, accepted to ApJ. For Full resolution figure and data tables, see http://www.salt.ac.za/~crawford/projects/deimos

A panchromatic study of BLAST counterparts: total star-formation rate, morphology, AGN fraction and stellar mass

We carry out a multi-wavelength study of individual galaxies detected by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) and identified at other wavelengths, using data spanning the radio to the ultraviolet (UV). We develop a Monte Carlo method to account for flux boosting, source blending, and correlations among bands, which we use to derive deboosted far-infrared (FIR) luminosities for our sample. We estimate total star-formation rates for BLAST counterparts with z < 0.9 by combining their FIR and UV luminosities. Star formation is heavily obscured at L_FIR > 10^11 L_sun, z > 0.5, but the contribution from unobscured starlight cannot be neglected at L_FIR < 10^11 L_sun, z < 0.25. We assess that about 20% of the galaxies in our sample show indication of a type-1 active galactic nucleus (AGN), but their submillimeter emission is mainly due to star formation in the host galaxy. We compute stellar masses for a subset of 92 BLAST counterparts; these are relatively massive objects, with a median mass of ~10^11 M_sun, which seem to link the 24um and SCUBA populations, in terms of both stellar mass and star-formation activity. The bulk of the BLAST counterparts at z<1 appear to be run-of-the-mill star-forming galaxies, typically spiral in shape, with intermediate stellar masses and practically constant specific star-formation rates. On the other hand, the high-z tail of the BLAST counterparts significantly overlaps with the SCUBA population, in terms of both star-formation rates and stellar masses, with observed trends of specific star-formation rate that support strong evolution and downsizing.Comment: Accepted for publication in the Astrophysical Journal. 44 pages, 11 figures. The SED template for the derivation of L_FIR has changed (added new figure) and the discussion on the stellar masses has been improved. The complete set of full-color postage-stamps can be found at http://blastexperiment.info/results_images/moncelsi

BLAST: the Redshift Survey

The Balloon-borne Large Aperture Submillimeter Telescope (BLAST) has recently surveyed ~8.7 deg^2 centered on GOODS-South at 250, 350, and 500 microns. In Dye et al. (2009) we presented the catalogue of sources detected at 5-sigma in at least one band in this field and the probable counterparts to these sources in other wavebands. In this paper, we present the results of a redshift survey in which we succeeded in measuring redshifts for 82 of these counterparts. The spectra show that the BLAST counterparts are mostly star-forming galaxies but not extreme ones when compared to those found in the Sloan Digital Sky Survey. Roughly one quarter of the BLAST counterparts contain an active nucleus. We have used the spectroscopic redshifts to carry out a test of the ability of photometric redshift methods to estimate the redshifts of dusty galaxies, showing that the standard methods work well even when a galaxy contains a large amount of dust. We have also investigated the cases where there are two possible counterparts to the BLAST source, finding that in at least half of these there is evidence that the two galaxies are physically associated, either because they are interacting or because they are in the same large-scale structure. Finally, we have made the first direct measurements of the luminosity function in the three BLAST bands. We find strong evolution out to z=1, in the sense that there is a large increase in the space-density of the most luminous galaxies. We have also investigated the evolution of the dust-mass function, finding similar strong evolution in the space-density of the galaxies with the largest dust masses, showing that the luminosity evolution seen in many wavebands is associated with an increase in the reservoir of interstellar matter in galaxies.Comment: Accepted for publication in the Astrophysical Journal. Maps and associated results are available at http://blastexperiment.info

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution