Inhibition of terminal deoxynucleotidyl transferase by adenine dinucleotides Unique inhibitory action of Ap5A

AbstractTerminal deoxynucleotidyltransferase (TdT) exhibits strong sensitivity to ATP and its dinucleotide analogues, Ap2A, Ap3A, Ap4A, Ap5A and Ap6A. Similar to ATP, all of the dinucleotides appear to be competitive inhibitors of TdT catalysis with respect to substrate deoxynucleoside triphosphates and effectively block the UV-mediated substrate cross-linking to TdT. Among the various dinucleotides, Ap5A and Ap6A (diadenosine 5'-5' penta- and hexaphosphate, respectively) are significantly more effective than dinucleotides containing 2, 3 or 4 phosphate backbones. Furthermore, Ap5A is found to be the only dinucleotide which has reactivity at both substrate- and primer-binding domains in TdT

Adaptive geospatial joins for modern hardware

Geospatial joins are a core building block of connected mobility applications. An especially challenging problem are joins between streaming points and static polygons. Since points are not known beforehand, they cannot be indexed. Nevertheless, points need to be mapped to polygons with low latencies to enable real-time feedback. We present an adaptive geospatial join that uses true hit filtering to avoid expensive geometric computations in most cases. Our technique uses a quadtree-based hierarchical grid to approximate polygons and stores these approximations in a specialized radix tree. We emphasize on an approximate version of our algorithm that guarantees a user-defined precision. The exact version of our algorithm can adapt to the expected point distribution by refining the index. We optimized our implementation for modern hardware architectures with wide SIMD vector processing units, including Intel’s brand new Knights Landing. Overall, our approach can perform up to two orders of magnitude faster than existing techniques

Approximate geospatial joins with precision guarantees

Geospatial joins are a core building block of con- nected mobility applications. An especially challenging problem are joins between streaming points and static polygons. Since points are not known beforehand, they cannot be indexed. Nevertheless, points need to be mapped to polygons with low latencies to enable real-time feedback. We present an approximate geospatial join that guarantees a user-defined precision. Our technique uses a quadtree-based hierarchical grid to approximate polygons and stores these approximations in a specialized radix tree. Our approach can perform up to several orders of magnitude faster than existing techniques while providing sufficiently precise results for many applications

Adaptive main-memory indexing for high-performance point-polygon joins

Connected mobility applications rely heavily on geospatial joins that associate point data, such as locations of Uber cars, to static polygonal regions, such as city neighborhoods. These joins typically involve expensive geometric computations, which makes it hard to provide an interactive user experience. In this paper, we propose an adaptive polygon index that leverages true hit fltering to avoid expensive geometric computations in most cases. In particular, our approach closely approximates polygons by combining quadtrees with true hit filtering, and stores these approximations in a query-effcient radix tree. Based on this index, we introduce two geospatial join algorithms: an approximate one that guarantees a user-defined precision, and an exact one that adapts to the expected point distribution. In summary, our technique outperforms existing CPU-based joins by up to two orders of magnitude and is competitive with state-of-the-art GPU implementations

Linear polarization structures in LOFAR observations of the interstellar medium in the 3C 196 field

This study aims to characterize linear polarization structures in LOFAR observations of the interstellar medium (ISM) in the 3C196 field, one of the primary fields of the LOFAR-Epoch of Reionization key science project. We have used the high band antennas (HBA) of LOFAR to image this region and Rotation Measure (RM) synthesis to unravel the distribution of polarized structures in Faraday depth. The brightness temperature of the detected Galactic emission is 5−15 K in polarized intensity and covers the range from -3 to +8 rad m−2 in Faraday depth. The most interesting morphological feature is a strikingly straight filament at a Faraday depth of +0.5 rad m−2 running from north to south, right through the centre of the field and parallel to the Galactic plane. There is also an interesting system of linear depolarization canals conspicuous in an image showing the peaks of Faraday spectra. We used the Westerbork Synthesis Radio Telescope (WSRT) at 350 MHz to image the same region. For the first time, we see some common morphology in the RM cubes made at 150 and 350~{; ; \rm MHz}; ; . There is no indication of diffuse emission in total intensity in the interferometric data, in line with results at higher frequencies and previous LOFAR observations. Based on our results, we determined physical parameters of the ISM and proposed a simple model that may explain the observed distribution of the intervening magneto- ionic medium. The mean line-of-sight magnetic field component, B∥, is determined to be 0.3±0.1 μG and its spatial variation across the 3C196 field is 0.1 μG. The filamentary structure is probably an ionized filament in the ISM, located somewhere within the Local Bubble. This filamentary structure shows an excess in thermal electron density (neB∥>6.2 cm−3μG) compared to its surroundings

Degree-scale galactic radio emission at 122 MHz around the North Celestial Pole with LOFAR-AARTFAAC

Large scale structure and cosmolog

Cassiopeia A, Cygnus A, Taurus A, and Virgo A at ultra-low radio frequencies

Context. The four persistent radio sources in the northern sky with the highest flux density at metre wavelengths are Cassiopeia A, Cygnus A, Taurus A, and Virgo A; collectively they are called the A-team. Their flux densities at ultra-low frequencies (< 100 MHz) can reach several thousands of janskys, and they often contaminate observations of the low-frequency sky by interfering with image processing. Furthermore, these sources are foreground objects for all-sky observations hampering the study of faint signals, such as the cosmological 21 cm line from the epoch of reionisation. Aims. We aim to produce robust models for the surface brightness emission as a function of frequency for the A-team sources at ultra-low frequencies. These models are needed for the calibration and imaging of wide-area surveys of the sky with low-frequency interferometers. This requires obtaining images at an angular resolution better than 15\u2033 with a high dynamic range and good image fidelity. Methods. We observed the A-team with the Low Frequency Array (LOFAR) at frequencies between 30 MHz and 77 MHz using the Low Band Antenna system. We reduced the datasets and obtained an image for each A-team source. Results. The paper presents the best models to date for the sources Cassiopeia A, Cygnus A, Taurus A, and Virgo A between 30 MHz and 77 MHz. We were able to obtain the aimed resolution and dynamic range in all cases. Owing to its compactness and complexity, observations with the long baselines of the International LOFAR Telescope will be required to improve the source model for Cygnus A further

Sub-arcsecond imaging with the International LOFAR Telescope I. Foundational calibration strategy and pipeline

The International LOFAR Telescope is an interferometer with stations spread across Europe. With baselines of up to ~2000 km, LOFAR has the unique capability of achieving sub-arcsecond resolution at frequencies below 200 MHz. However, it is technically and logistically challenging to process LOFAR data at this resolution. To date only a handful of publications have exploited this capability. Here we present a calibration strategy that builds on previous high-resolution work with LOFAR. It is implemented in a pipeline using mostly dedicated LOFAR software tools and the same processing framework as the LOFAR Two-metre Sky Survey (LoTSS). We give an overview of the calibration strategy and discuss the special challenges inherent to enacting high-resolution imaging with LOFAR, and describe the pipeline, which is publicly available, in detail. We demonstrate the calibration strategy by using the pipeline on P205+55, a typical LoTSS pointing with an 8 h observation and 13 international stations. We perform in-field delay calibration, solution referencing to other calibrators in the field, self-calibration of these calibrators, and imaging of example directions of interest in the field. We find that for this specific field and these ionospheric conditions, dispersive delay solutions can be transferred between calibrators up to ~1.5° away, while phase solution transferral works well over ~1°. We also demonstrate a check of the astrometry and flux density scale with the in-field delay calibrator source. Imaging in 17 directions, we find the restoring beam is typically ~0.3′′ ×0.2′′ although this varies slightly over the entire 5 deg2 field of view. We find we can achieve ~80–300 μJy bm−1 image rms noise, which is dependent on the distance from the phase centre; typical values are ~90 μJy bm−1 for the 8 h observation with 48 MHz of bandwidth. Seventy percent of processed sources are detected, and from this we estimate that we should be able to image roughly 900 sources per LoTSS pointing. This equates to ~ 3 million sources in the northern sky, which LoTSS will entirely cover in the next several years. Future optimisation of the calibration strategy for efficient post-processing of LoTSS at high resolution makes this estimate a lower limit

Constraining the intergalactic medium at z ≈ 9.1 using LOFAR Epoch of Reionization observations

We derive constraints on the thermal and ionization states of the intergalactic medium (IGM) at redshift ≈ 9.1 using new upper limits on the 21-cm power spectrum measured by the LOFAR radio telescope and a prior on the ionized fraction at that redshift estimated from recent cosmic microwave background (CMB) observations. We have used results from the reionization simulation code GRIZZLY and a Bayesian inference framework to constrain the parameters which describe the physical state of the IGM. We find that, if the gas heating remains negligible, an IGM with ionized fraction 0.13 and a distribution of the ionized regions with a characteristic size 8 h−1 comoving megaparsec (Mpc) and a full width at half-maximum (FWHM) 16 h−1 Mpc is ruled out. For an IGM with a uniform spin temperature TS 3 K, no constraints on the ionized component can be computed. If the large-scale fluctuations of the signal are driven by spin temperature fluctuations, an IGM with a volume fraction 0.34 of heated regions with a temperature larger than CMB, average gas temperature 7–160 K, and a distribution of the heated regions with characteristic size 3.5–70 h−1 Mpc and FWHM of 110 h−1 Mpc is ruled out. These constraints are within the 95 per cent credible intervals. With more stringent future upper limits from LOFAR at multiple redshifts, the constraints will become tighter and will exclude an increasingly large region of the parameter space