Characterizing Signal Loss in the 21 cm Reionization Power Spectrum: A Revised Study of PAPER-64

The Epoch of Reionization (EoR) is an uncharted era in our Universe's history during which the birth of the first stars and galaxies led to the ionization of neutral hydrogen in the intergalactic medium. There are many experiments investigating the EoR by tracing the 21cm line of neutral hydrogen. Because this signal is very faint and difficult to isolate, it is crucial to develop analysis techniques that maximize sensitivity and suppress contaminants in data. It is also imperative to understand the trade-offs between different analysis methods and their effects on power spectrum estimates. Specifically, with a statistical power spectrum detection in HERA's foreseeable future, it has become increasingly important to understand how certain analysis choices can lead to the loss of the EoR signal. In this paper, we focus on signal loss associated with power spectrum estimation. We describe the origin of this loss using both toy models and data taken by the 64-element configuration of the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER). In particular, we highlight how detailed investigations of signal loss have led to a revised, higher 21cm power spectrum upper limit from PAPER-64. Additionally, we summarize errors associated with power spectrum error estimation that were previously unaccounted for. We focus on a subset of PAPER-64 data in this paper; revised power spectrum limits from the PAPER experiment are presented in a forthcoming paper by Kolopanis et al. (in prep.) and supersede results from previously published PAPER analyses.Comment: 25 pages, 18 figures, Accepted by Ap

What Next-Generation 21 cm Power Spectrum Measurements Can Teach Us About the Epoch of Reionization

A number of experiments are currently working towards a measurement of the 21 cm signal from the Epoch of Reionization. Whether or not these experiments deliver a detection of cosmological emission, their limited sensitivity will prevent them from providing detailed information about the astrophysics of reionization. In this work, we consider what types of measurements will be enabled by a next-generation of larger 21 cm EoR telescopes. To calculate the type of constraints that will be possible with such arrays, we use simple models for the instrument, foreground emission, and the reionization history. We focus primarily on an instrument modeled after the $\sim 0.1~\rm{km}^2$ collecting area Hydrogen Epoch of Reionization Array (HERA) concept design, and parameterize the uncertainties with regard to foreground emission by considering different limits to the recently described "wedge" footprint in k-space. Uncertainties in the reionization history are accounted for using a series of simulations which vary the ionizing efficiency and minimum virial temperature of the galaxies responsible for reionization, as well as the mean free path of ionizing photons through the IGM. Given various combinations of models, we consider the significance of the possible power spectrum detections, the ability to trace the power spectrum evolution versus redshift, the detectability of salient power spectrum features, and the achievable level of quantitative constraints on astrophysical parameters. Ultimately, we find that $0.1~\rm{km}^2$ of collecting area is enough to ensure a very high significance ($\gtrsim30\sigma$) detection of the reionization power spectrum in even the most pessimistic scenarios. This sensitivity should allow for meaningful constraints on the reionization history and astrophysical parameters, especially if foreground subtraction techniques can be improved and successfully implemented.Comment: 27 pages, 18 figures, updated SKA numbers in appendi

Characterization of THB1, a Chlamydomonas reinhardtii truncated hemoglobin: linkage to nitrogen metabolism and identification of lysine as the distal heme ligand

The nuclear genome of the model organism Chlamydomonas reinhardtii contains genes for a dozen hemoglobins of the truncated lineage. Of those, THB1 is known to be expressed, but the product and its function have not yet been characterized. We present mutagenesis, optical, and nuclear magnetic resonance data for the recombinant protein and show that at pH near neutral in the absence of added ligand, THB1 coordinates the heme iron with the canonical proximal histidine and a distal lysine. In the cyanomet state, THB1 is structurally similar to other known truncated hemoglobins, particularly the heme domain of Chlamydomonas eugametos LI637, a light-induced chloroplastic hemoglobin. Recombinant THB1 is capable of binding nitric oxide (NO(*)) in either the ferric or ferrous state and has efficient NO(*) dioxygenase activity. By using different C. reinhardtii strains and growth conditions, we demonstrate that the expression of THB1 is under the control of the NIT2 regulatory gene and that the hemoglobin is linked to the nitrogen assimilation pathway

Mapping our Universe in 3D with MITEoR

Mapping our universe in 3D by imaging the redshifted 21 cm line from neutral hydrogen has the potential to overtake the cosmic microwave background as our most powerful cosmological probe, because it can map a much larger volume of our Universe, shedding new light on the epoch of reionization, inflation, dark matter, dark energy, and neutrino masses. We report on MITEoR, a pathfinder low-frequency radio interferometer whose goal is to test technologies that greatly reduce the cost of such 3D mapping for a given sensitivity. MITEoR accomplishes this by using massive baseline redundancy both to enable automated precision calibration and to cut the correlator cost scaling from N^2 to NlogN, where N is the number of antennas. The success of MITEoR with its 64 dual-polarization elements bodes well for the more ambitious HERA project, which would incorporate many identical or similar technologies using an order of magnitude more antennas, each with dramatically larger collecting area.Comment: To be published in proceedings of 2013 IEEE International Symposium on Phased Array Systems & Technolog

Segmented Aperture Interferometric Nulling Testbed (SAINT) II: Component Systems Update

"This work presents updates to the coronagraph and telescope components of the Segmented Aperture Interfer-ometric Nulling Testbed (SAINT). The project pairs an actively-controlled macro-scale segmented mirror withthe Visible Nulling Coronagraph (VNC) towards demonstrating capabilities for the future space observatoriesneeded to directly detect and characterize a significant sample of Earth-sized worlds around nearby stars inthe quest for identifying those which may be habitable and possibly harbor life. Efforts to improve the VNCwavefront control optics and mechanisms towards repeating narrowband results are described. A narrative isprovided for the design of new optical components aimed at enabling broadband performance. Initial work withthe hardware and software interface for controlling the segmented telescope mirror is also presented.

Chytrid fungus infection in zebrafish demonstrates that the pathogen can parasitize non-amphibian vertebrate hosts.

Aquatic chytrid fungi threaten amphibian biodiversity worldwide owing to their ability to rapidly expand their geographical distributions and to infect a wide range of hosts. Combating this risk requires an understanding of chytrid host range to identify potential reservoirs of infection and to safeguard uninfected regions through enhanced biosecurity. Here we extend our knowledge on the host range of the chytrid Batrachochytrium dendrobatidis by demonstrating infection of a non-amphibian vertebrate host, the zebrafish. We observe dose-dependent mortality and show that chytrid can infect and proliferate on zebrafish tissue. We also show that infection phenotypes (fin erosion, cell apoptosis and muscle degeneration) are direct symptoms of infection. Successful infection is dependent on disrupting the zebrafish microbiome, highlighting that, as is widely found in amphibians, commensal bacteria confer protection against this pathogen. Collectively, our findings greatly expand the limited tool kit available to study pathogenesis and host response to chytrid infection

Drug-Induced Liver Injury due to Flucloxacillin:Relevance of Multiple Human Leukocyte Antigen Alleles

© 2019 The Authors Clinical Pharmacology & Therapeutics © 2019 American Society for Clinical Pharmacology and Therapeutics Some patients prescribed flucloxacillin (~0.01%) develop drug-induced liver injury (DILI). HLA-B*57:01 is an established genetic risk factor for flucloxacillin DILI. To consolidate this finding, identify additional genetic factors, and assess relevance of risk factors for flucloxacillin DILI in relation to DILI due to other penicillins, we performed a genomewide association study involving 197 flucloxacillin DILI cases and 6,835 controls. We imputed single-nucleotide polymorphism and human leukocyte antigen (HLA) genotypes. HLA-B*57:01 was the major risk factor (allelic odds ratio (OR)=36.62; P=2.67×10−97). HLA-B*57:03 also showed an association (OR=79.21; P=1.2×10−6). Within the HLA-B protein sequence, imputation showed valine97, common to HLA-B*57:01 and HLA-B*57:03, had the largest effect (OR=38.1; P=9.7×10−97). We found no HLA-B*57 association with DILI due to other isoxazolyl penicillins (n=6) or amoxicillin (n=15) and no significant non-HLA signals for any penicillin-related DILI