The Luminosity Function of Lyman alpha Emitters at Redshift z=7.7

Lyman alpha (Lya) emission lines should be attenuated in a neutral intergalactic medium (IGM). Therefore the visibility of Lya emitters at high redshifts can serve as a valuable probe of reionization at about the 50% level. We present an imaging search for z=7.7 Lya emitting galaxies using an ultra-narrowband filter (filter width= 9A) on the NEWFIRM imager at the Kitt Peak National Observatory. We found four candidate Lya emitters in a survey volume of 1.4 x 10^4 Mpc^3, with a line flux brighter than 6x10^-18 erg/cm^2/s (5 sigma in 2" aperture). We also performed a detailed Monte-Carlo simulation incorporating the instrumental effects to estimate the expected number of Lya emitters in our survey, and found that we should expect to detect one Lya emitter, assuming a non-evolving Lya luminosity function (LF) between z=6.5 and z=7.7. Even if one of the present candidates is spectroscopically confirmed as a z~8 Lya emitter, it would indicate that there is no significant evolution of the Lya LF from z=3.1 to z~8. While firm conclusions would need both spectroscopic confirmations and larger surveys to boost the number counts of galaxies, we successfully demonstrate the feasibility of sensitive near-infrared (1.06 um) narrow-band searches using custom filters designed to avoid the OH emission lines that make up most of the sky background.Comment: Published in ApJ, 3 figure

Searching for z~7.7 Lyman Alpha Emitters in the COSMOS Field with NEWFIRM

The study of Ly-alpha emission in the high-redshift universe is a useful probe of the epoch of reionization, as the Ly-alpha line should be attenuated by the intergalactic medium (IGM) at low to moderate neutral hydrogen fractions. Here we present the results of a deep and wide imaging search for Ly-alpha emitters in the COSMOS field. We have used two ultra-narrowband filters (filter width of ~8-9 {\deg}A) on the NEWFIRM camera, installed on the Mayall 4m telescope at Kitt Peak National Observatory, in order to isolate Ly-alpha emitters at z = 7.7; such ultra-narrowband imaging searches have proved to be excellent at detecting Ly-alpha emitters. We found 5-sigma detections of four candidate Ly-alpha emitters in a survey volume of 2.8 x 10^4 Mpc^3 (total survey area ~760 arcmin^2). Each candidate has a line flux greater than 8 x 10^-18 erg s^-1 cm^-2. Using these results to construct a luminosity function and comparing to previously established Ly-alpha luminosity functions at z = 5.7 and z = 6.5, we find no conclusive evidence for evolution of the luminosity function between z = 5.7 and z = 7.7. Statistical Monte Carlo simulations suggest that half of these candidates are real z = 7.7 targets, and spectroscopic follow-up will be required to verify the redshift of these candidates. However, our results are consistent with no strong evolution in the neutral hydrogen fraction of the IGM between z = 5.7 and z = 7.7, even if only one or two of the z = 7.7 candidates are spectroscopically confirmed.Comment: 29 pages, 5 figures, accepted to ApJ (12/11

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

SCAPP: An algorithm for improved plasmid assembly in metagenomes

Background: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.</jats:p