Precision requirements for interferometric gridding in the analysis of a 21 cm power spectrum

Context. Experiments that try to observe the 21 cm redshifted signals from the epoch of reionisation (EoR) using interferometric low-frequency instruments have stringent requirements on the processing accuracy. Aims. We analyse the accuracy of radio interferometric gridding of visibilities with the aim to quantify the power spectrum bias caused by gridding. We do this ultimately to determine the suitability of different imaging algorithms and gridding settings for an analysis of a 21 cm power spectrum. Methods. We simulated realistic Low-Frequency Array (LOFAR) data and constructed power spectra with convolutional gridding and w stacking, w projection, image-domain gridding, and without w correction. These were compared against data that were directly Fourier transformed. The influence of oversampling, kernel size, w-quantization, kernel windowing function, and image padding were quantified. The gridding excess power was measured with a foreground subtraction strategy, for which foregrounds were subtracted using Gaussian progress regression, as well as with a foreground avoidance strategy. Results. Constructing a power spectrum with a significantly lower bias than the expected EoR signals is possible with the methods we tested, but requires a kernel oversampling factor of at least 4000, and when w-correction is used, at least 500 w-quantization levels. These values are higher than typically used values for imaging, but they are computationally feasible. The kernel size and padding factor parameters are less crucial. Of the tested methods, image-domain gridding shows the highest accuracy with the lowest imaging time. Conclusions. LOFAR 21 cm power spectrum results are not affected by gridding. Image-domain gridding is overall the most suitable algorithm for 21 cm EoR power spectrum experiments, including for future analyses of data from the Square Kilometre Array (SKA) EoR. Nevertheless, convolutional gridding with tuned parameters results in sufficient accuracy for interferometric 21 cm EoR experiments. This also holds for w stacking for wide-field imaging. The w-projection algorithm is less suitable because of the requirements for kernel oversampling, and a faceting approach is unsuitable because it causes spatial discontinuities

Regression analysis of properties of [Au(IPr)(CHR2)] complexes

The European Research Council (ERC) and the Engineering and Physical Sciences Research Council (EPSRC), UK, are gratefully acknowledged for their support. L.C., and S.P.N. thank the King Abdullah University of Science and Technology (KAUST) and Kind Saud University (KSU) for support.New [Au(IPr)(CHR2)] complexes have been synthesised through protonolysis reactions of [Au(IPr)(OH)] with moderately acidic substrates, CH2R2. An array of spectroscopic (IR and NMR), structural (X-ray), electronic (DFT) and experimental (reactivity) parameters was collected to quantify the variation in stereoelectronic properties of these new and previously reported [Au(IPr)(CHR2)] complexes. Variation of the R substituents on the carbanion ligands (CHR2–) was found to have a crucial impact on parameters characterising the resulting gold complexes. A regression analysis of both experimental and modelled parameters, guided by network analysis techniques, produced linear models that supported trends within the [Au(IPr)(CHR2)] complexes.PostprintPeer reviewe

Characterising Radio Telescope Software With the Workload Characterisation Framework

We present a modular framework, the Workload Characterisation Framework (WCF), that is developed to obtain, store and compare key characteristics of radio astronomy processing software in a reproducible way. As a demonstration, we discuss the experiences using the framework to characterise a LOFAR calibration and imaging pipeline.Instrumentatio

TBX2, a Novel Regulator of Labour

Background and Objectives: Therapeutic interventions targeting molecular factors involved in the transition from uterine quiescence to overt labour are not substantially reducing the rate of spontaneous preterm labour. The identification of novel rational therapeutic targets are essential to prevent the most common cause of neonatal mortality. Based on our previous work showing that Tbx2 (T-Box transcription factor 2) is a putative upstream regulator preceding progesterone withdrawal in mouse myometrium, we now investigate the role of TBX2 in human myometrium. Materials and Methods: RNA microarray analysis of (A) preterm human myometrium samples and (B) myometrial cells overexpressing TBX2 in vitro, combined with subsequent analysis of the two publicly available datasets of (C) Chan et al. and (D) Sharp et al. The effect of TBX2 overexpression on cytokines/chemokines secreted to the myometrium cell culture medium were determined by Luminex assay. Results: Analysis shows that overexpression of TBX2 in myometrial cells results in downregulation of TNFα- and interferon signalling. This downregulation is consistent with the decreased expression of cytokines and chemokines of which a subset has been previously associated with the inflammatory pathways relevant for human labour. In contrast, CXCL5 (C-X-C motif chemokine ligand 5), CCL21 and IL-6 (Interleukin 6), previously reported in relation to parturition, do not seem to be under TBX2 control. The combined bioinformatical analysis of the four mRNA datasets identifies a subset of upstream regulators common to both preterm and term labour under control of TBX2. Surprisingly, TBX2 mRNA levels are increased in preterm contractile myometrium. Conclusions: We identified a subset of upstream regulators common to both preterm and term labour that are activated in labour and repressed by TBX2. The increased TBX2 mRNA expression in myometrium collected during a preterm caesarean section while in spontaneous preterm labour compared to tissue harvested during iatrogenic preterm delivery does not fit the bioinformatical model. We can only explain this by speculating that the in vivo activity of TBX2 in human myometrium depends not only on the TBX2 expression levels but also on levels of the accessory proteins necessary for TBX2 activity

Deep sub-arcsecond wide-field imaging of the Lockman Hole field at 144 MHz

Instrumentatio

Fourier-domain dedispersion

We present and implement the concept of the Fourier-domain dedispersion (FDD) algorithm, a brute-force incoherent dedispersion algorithm. This algorithm corrects the frequency-dependent dispersion delays in the arrival time of radio emission from sources such as radio pulsars and fast radio bursts. Where traditional time-domain dedispersion algorithms correct time delays using time shifts, the FDD algorithm performs these shifts by applying phase rotations to the Fourier-transformed time-series data. Incoherent dedispersion to many trial dispersion measures (DMs) is compute-, memory-bandwidth-, and input-output-intensive, and dedispersion algorithms have been implemented on graphics processing units (GPUs) to achieve high computational performance. However, time-domain dedispersion algorithms have low arithmetic intensity and are therefore often memory-bandwidth-limited. The FDD algorithm avoids this limitation and is compute-limited, providing a path to exploit the potential of current and upcoming generations of GPUs. We implement the FDD algorithm as an extension of the DEDIS

Reduced-Precision Acceleration of Radio-Astronomical Imaging on Reconfigurable Hardware

Radio telescopes produce large volumes of data that need to be processed to obtain high-resolution sky images. This is a complex task that requires computing systems that provide both high performance and high energy efficiency. Hardware accelerators such as GPUs (Graphics Processing Units) and FPGAs (Field Programmable Gate Arrays) can provide these two features and are thus an appealing option for this application. Most HPC (High-Performance Computing) systems operate in double precision (64-bit) or in single precision (32-bit), and radio-astronomical imaging is no exception. With reduced precision computing, smaller data types (e.g., 16-bit) are used to improve energy efficiency and throughput performance in noise-tolerant applications. We demonstrate that reduced precision can also be used to produce high-quality sky images. To this end, we analyze the gridding component (Image-Domain Gridding) of the widely-used WSClean imaging application. Gridding is typically one of the most time-consuming steps in the imaging process and, therefore, an excellent candidate for acceleration. We identify the minimum required exponent and mantissa bits for a custom floating-point data type. Then, we propose the first custom floating-point accelerator on a Xilinx Alveo U50 FPGA using High-Level Synthesis. Our reduced-precision implementation improves the throughput and energy efficiency of respectively 1.84\times and 2.03\times compared to the single-precision floating-point baseline on the same FPGA. Our solution is also 2.12\times faster and 3.46\times more energy-efficient than an Intel i9 9900k CPU (Central Processing Unit) and manages to keep up in throughput with an AMD RX 550 GPU

Initial Characterization of C16orf89, A Novel Thyroid-Specific Gene

Background: Thyroid hormone is prerequisite for proper fetal and postnatal neurodevelopment, growth, and metabolism. Although much progress has been made in the characterization of genes implicated in thyroid development and function, the majority of genes involved in this process are still unknown. We have previously applied serial analysis of gene expression (SAGE) to identify novel genes preferentially expressed in the thyroid, and this has resulted in the characterization of DUOX2 and IYD (also known as DEHAL1), two genes encoding essential enzymes in the production of thyroid hormone. In the current study we characterize the gene C16orf89, which is linked to another thyroid-specific SAGE tag CCAGCTGCCT. Methods: We establish tissue-specific expression of C16orf89 using novel tissue-specific SAGE libraries and quantitative polymerase chain reaction. In addition, we characterize the C16orf89 gene and protein, and analyze its mRNA expression in response to thyrotropin and during mouse development. Results: C16orf89 is predominantly expressed in human thyroid tissue with a specificity intermediate between thyroid transcription factors and proteins involved in thyroid hormone synthesis. C16orf89 shows the same expression pattern as Nkx2-1 (thyroid transcription factor 1) from embryonic day (E) 17.5 onward in the developing mouse thyroid and lung. The developmental timing of C16orf89 mRNA expression is similar to that of the iodide transporter Slc5a5 (also known as Nis). Both transcripts are detected from E17.5 in the developing thyroid. This is clearly later than the onset of Tg mRNA expression (from E14.5), while Nkx2-1 and Iyd mRNA can already be detected in the E12.5 thyroid. In in vitro cell culture C16orf89 expression is stimulated by thyrotropin. The major splice variant encodes a 361 amino acid protein that is well conserved between mammals, contains an N-terminal signal peptide, is secreted in a glycosylated form, and does not contain any known functional domain. Conclusions: We present a novel gene highly expressed in thyroid that encodes a currently enigmatic protei