A pathfinder version of CHIME (the Canadian Hydrogen Intensity Mapping Experiment) is currently being commissioned at the Dominion Radio Astrophysical Observatory (DRAO) in Penticton, BC. The instrument is a hybrid cylindrical interferometer designed to measure the large scale neutral hydrogen power spectrum across the redshift range 0.8 to 2.5. The power spectrum will be used to measure the baryon acoustic oscillation (BAO) scale across this poorly probed redshift range where dark energy becomes a significant contributor to the evolution of the Universe. The instrument revives the cylinder design in radio astronomy with a wide field survey as a primary goal. Modern low-noise amplifiers and digital processing remove the necessity for the analog beamforming that characterized previous designs. The Pathfinder consists of two cylinders 37 m long by 20 m wide oriented northsouth for a total collecting area of 1,500 square meters. The cylinders are stationary with no moving parts, and form a transit instrument with an instantaneous field of view of ∼100 degrees by 1-2 degrees. Each CHIME Send correspondence to K.Bandura: E-mail: kevin.bandura@mcgill.ca arXiv:1406.2288v1 [astro-ph.IM] 9 Jun 2014Pathfinder cylinder has a feedline with 64 dual polarization feeds placed every ∼30 cm which Nyquist sample the north-south sky over much of the frequency band. The signals from each dual-polarization feed are independently amplified, filtered to 400-800 MHz, and directly sampled at 800 MSps using 8 bits. The correlator is an FX design, where the Fourier transform channelization is performed in FPGAs, which are interfaced to a set of GPUs that compute the correlation matrix. The CHIME Pathfinder is a 1/10th scale prototype version of CHIME and is designed to detect the BAO feature and constrain the distance-redshift relation.The lessons learned from its implementation will be used to inform and improve the final CHIME design.

The Hydrogen Intensity and Real-time Analysis eXperiment (HIRAX) is a new 400-800 MHz radio interferometer under development for deployment in South Africa. HIRAX will comprise 1024 six meter parabolic dishes on a compact grid and will map most of the southern sky over the course of four years. HIRAX has two primary science goals: to constrain Dark Energy and measure structure at high redshift, and to study radio transients and pulsars. HIRAX will observe unresolved sources of neutral hydrogen via their redshifted 21-cm emission line ('hydrogen intensity mapping'). The resulting maps of large-scale structure at redshifts 0.8-2.5 will be used to measure Baryon Acoustic Oscillations (BAO). BAO are a preferential length scale in the matter distribution that can be used to characterize the expansion history of the Universe and thus understand the properties of Dark Energy. HIRAX will improve upon current BAO measurements from galaxy surveys by observing a larger cosmological volume (larger in both survey area and redshift range) and by measuring BAO at higher redshift when the expansion of the universe transitioned to Dark Energy domination. HIRAX will complement CHIME, a hydrogen intensity mapping experiment in the Northern Hemisphere, by completing the sky coverage in the same redshift range. HIRAX's location in the Southern Hemisphere also allows a variety of cross-correlation measurements with large-scale structure surveys at many wavelengths. Daily maps of a few thousand square degrees of the Southern Hemisphere, encompassing much of the Milky Way galaxy, will also open new opportunities for discovering and monitoring radio transients. The HIRAX correlator will have the ability to rapidly and efficiently detect transient events. This new data will shed light on the poorly understood nature of fast radio bursts (FRBs), enable pulsar monitoring to enhance long-wavelength gravitational wave searches, and provide a rich data set for new radio transient phenomena searches. This paper discusses the HIRAX instrument, science goals, and current status.

The detection of the Epoch of Reionization (EoR) delay power spectrum using a ”foreground avoidance method” highly depends on the instrument chromaticity. The systematic effects induced by the radio-telescope spread the foreground signal in the delay domain, which contaminates the EoR window theoretically observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this paper combines detailed electromagnetic and electrical simulations in order to model the chromatic effects of the instrument, and quantify its frequency and time responses. In particular, the effects of the analogue receiver, transmission cables, and mutual coupling are included. These simulations are able to accurately predict the intensity of the reflections occurring in the 150-m cable which links the antenna to the back-end. They also show that electromagnetic waves can propagate from one dish to another one through large sections of the array due to mutual coupling. The simulated system time response is attenuated by a factor 104 after a characteristic delay which depends on the size of the array and on the antenna position. Ultimately, the system response is attenuated by a factor 105 after 1400 ns because of the reflections in the cable, which corresponds to characterizable k∥-modes above 0.7 $h\,\,\rm {Mpc}^{-1}$ at 150 MHz. Thus, this new study shows that the detection of the EoR signal with HERA Phase I will be more challenging than expected. On the other hand, it improves our understanding of the telescope, which is essential to mitigate the instrument chromaticity.

The Canadian Hydrogen Intensity Mapping Experiment (CHIME) is a transit interferometer currently being built at the Dominion Radio Astrophysical Observatory (DRAO) in Penticton, BC, Canada. We will use CHIME to map neutral hydrogen in the frequency range 400 -800 MHz over half of the sky, producing a measurement of baryon acoustic oscillations (BAO) at redshifts between 0.8 -2.5 to probe dark energy. We have deployed a pathfinder version of CHIME that will yield constraints on the BAO power spectrum and provide a test-bed for our calibration scheme. I will discuss the CHIME calibration requirements and describe instrumentation we are developing to meet these requirements.

We present a procedure for efficiently compressing astronomical radio data for high performance applications. Integrated, post-correlation data are first passed through a nearly lossless rounding step which compares the precision of the data to a generalized and calibration-independent form of the radiometer equation. This allows the precision of the data to be reduced in a way that has an insignificant impact on the data. The newly developed Bitshuffle lossless compression algorithm is subsequently applied. When the algorithm is used in conjunction with the HDF5 library and data format, data produced by the CHIME Pathfinder telescope is compressed to 28% of its original size and decompression throughputs in excess of 1 GB/s are obtained on a single core.

Received (to be inserted by publisher); Revised (to be inserted by publisher); Accepted (to be inserted by publisher);We present an overview of the 'ICE' hardware and software framework that implements large arrays of interconnected field programmable gate array (FPGA)-based data acquisition, signal processing and networking nodes economically. The system was conceived for application to radio, millimeter and sub-millimeter telescope readout systems that have requirements beyond typical off-the-shelf processing systems, such as careful control of interference signals produced by the digital electronics, and clocking of all elements in the system from a single precise observatory-derived oscillator. A new generation of telescopes operating at these frequency bands and designed with a vastly increased emphasis on digital signal processing to support their detector multiplexing technology or high-bandwidth correlators-data rates exceeding a terabyte per second-are becoming common. The ICE system is built around a custom FPGA motherboard that makes use of an Xilinx Kintex-7 FPGA and ARMbased co-processor. The system is specialized for specific applications through software, firmware, and custom mezzanine daughter boards that interface to the FPGA through the industry-standard FPGA mezzanine card (FMC) specifications. For high density applications, the motherboards are packaged in 16-slot crates with ICE backplanes that implement a low-cost passive full-mesh network between the motherboards in a crate, allow high bandwidth interconnection between crates, and enable data offload to a computer cluster. A Python-based control software library automatically detects and operates the hardware in the array. Examples of specific telescope applications of the ICE framework are presented, namely the frequency-multiplexed bolometer readout systems used for the South Pole Telescope (SPT) and Simons Array and the digitizer, F-engine, and networking engine for the Canadian Hydrogen Intensity Mapping Experiment (CHIME) and Hydrogen Intensity and Real-time Analysis eXperiment (HIRAX) radio interferometers.

Bacterial pathogens have evolved to regulate virulence gene expression at critical points in the colonization and infection processes to successfully cause disease. The Shigella species infect the epithelial cells lining the colon to result in millions of cases of diarrhea and a significant global health burden. As antibiotic resistance rates increase, understanding the mechanisms of infection is vital to ensure successful vaccine development. Despite significant gains in our understanding of Shigella infection, it remains unknown how the bacteria initiate contact with the colonic epithelium. Most pathogens harbor multiple adherence factors to facilitate this process, but Shigella was thought to have lost the ability to produce these factors. Interestingly, we have identified conditions that mimic some features of gastrointestinal transit and that enable Shigella to express adherence structural genes. This work highlights aspects of genetic regulation for Shigella adherence factors and may have a significant impact on future vaccine development.

Food production in conventional agriculture faces numerous challenges such as reducing waste, meeting demand, maintaining flavor, and providing nutrition. Contained environments under artificial climate control, or cyber-agriculture, could in principle be used to meet many of these challenges. Through such environments, phenotypic expression of the plant—mass, edible yield, flavor, and nutrients—can be actuated through a “climate recipe,” where light, water, nutrients, temperature, and other climate and ecological variables are optimized to achieve a desired result. This paper describes a method for doing this optimization for the desired result of flavor by combining cyber-agriculture, metabolomic phenotype (chemotype) measurements, and machine learning. In a pilot experiment, (1) environmental conditions, i.e. photoperiod and ultraviolet (UV) light (known to affect production of flavor-active molecules in edible plants) were applied under different regimes to basil plants ( Ocimum basilicum ) growing inside a hydroponic farm with an open-source design; (2) flavor-active volatile molecules were measured in each plant using gas chromatography-mass spectrometry (GC-MS); and (3) symbolic regression was used to construct a surrogate model of this chemistry from the input environmental variables, and this model was used to discover new combinations of photoperiod and UV light to increase this chemistry. These new combinations, or climate recipes, were then implemented in the hydroponic farm, and several of them resulted in a marked increase in volatiles over control. The process also led to two important insights: it demonstrated a “dilution effect”, i.e. a negative correlation between weight and desirable chemical species, and it discovered the surprising effect that a 24-hour photoperiod of photosynthetic-active radiation, the equivalent of all-day light, induces the most flavor molecule production in basil. In this manner, surrogate optimization through machine learning can be used to discover effective recipes for cyber-agriculture that would be difficult and time-consuming to find using hand-designed experiments.