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The MeerKAT Exploration of Relics, Giant Halos, and Extragalactic Radio Sources (MERGHERS) survey is a planned project to study a large statistical sample of galaxy clusters with the MeerKAT observatory. Here we present the results of a 16-h pilot project, observed in response to the 2019 MeerKAT Shared Risk proposal call, to test the feasibility of using MeerKAT for a large cluster study using short (0.2–2.1 h) integration times. The pilot focuses on 1.28-GHz observations of 13 massive, low-to-intermediate redshift (0.22 < z < 0.65) clusters from the Sunyaev–Zel'dovich-selected Atacama Cosmology Telescope (ACT) DR5 catalogue that show multiwavelength indications of dynamical disturbance. With a 70 per cent detection rate (9/13 clusters), this pilot study validates our proposed MERGHERS observing strategy and provides twelve detections of diffuse emission, eleven of them new, indicating the strength of MeerKAT for such types of studies. The detections (signal-to-noise ratio ≳ 6) are summarized as follows: two systems host both relic(s) and a giant radio halo, five systems host radio haloes, and two have candidate radio haloes. Power values, k -corrected to 1.4 GHz, assuming a fiducial spectral index of α = −1.3 ± 0.4, are consistent with known radio halo and relic scaling relations. [ABSTRACT FROM AUTHOR]

We present a fully parallelized grid-based parameter estimation algorithm for investigating multidimensional likelihoods called Snake, and apply it to cosmological parameter estimation. The basic idea is to map out the likelihood grid-cell by grid-cell according to decreasing likelihood, and stop when a certain threshold has been reached. This approach improves vastly on the “curse of dimensionality” problem plaguing standard grid-based parameter estimation simply by disregarding grid cells with negligible likelihood. The main advantages of this method compared to standard Metropolis-Hastings Markov Chain Monte Carlo methods include (1) trivial extraction of arbitrary conditional distributions; (2) direct access to Bayesian evidences; (3) better sampling of the tails of the distribution; and (4) nearly perfect parallelization scaling. The main disadvantage is, as in the case of brute-force grid-based evaluation, a dependency on the number of parameters, Npar. One of the main goals of the present paper is to determine how large Npar can be, while still maintaining reasonable computational efficiency; we find that Npar = 12 is well within the capabilities of the method. The performance of the code is tested by comparing cosmological parameters estimated using Snake and the WMAP-7 data with those obtained using CosmoMC, the current standard code in the field. We find fully consistent results, with similar computational expenses, but shorter wall time due to the perfect parallelization scheme. [ABSTRACT FROM AUTHOR]

We investigate sets of random variables that can be arranged sequentially such that a given variable only depends conditionally on its immediate predecessor. For such sets, we show that the full joint probability distribution may be expressed exclusively in terms of uni- and bivariate marginals. Under the assumption that the cosmic microwave background (CMB) power spectrum likelihood only exhibits correlations within a banded multipole range, ΔℓC, we apply this expression to two outstanding problems in CMB likelihood analysis. First, we derive a statistically well-defined hybrid likelihood estimator, merging two independent (e.g., low- and high-ℓ) likelihoods into a single expression that properly accounts for correlations between the two. Applying this expression to the Wilkinson Microwave Anisotropy Probe (WMAP) likelihood, we verify that the effect of correlations on cosmological parameters in the transition region is negligible in terms of cosmological parameters for WMAP; the largest relative shift seen for any parameter is 0.06σ. However, because this may not hold for other experimental setups (e.g., for different instrumental noise properties or analysis masks), but must rather be verified on a case-by-case basis, we recommend our new hybridization scheme for future experiments for statistical self-consistency reasons. Second, we use the same expression to improve the convergence rate of the Blackwell-Rao likelihood estimator, reducing the required number of Monte Carlo samples by several orders of magnitude, and thereby extend it to high-ℓ applications. [ABSTRACT FROM AUTHOR]

The Q/U Imaging ExperimenT (QUIET) is designed to measure polarization in the cosmic microwave background, targeting the imprint of inflationary gravitational waves at large angular scales(~1°). Between 2008 October and 2010 December, two independent receiver arrays were deployed sequentially on a 1.4m side-fed Dragonian telescope. The polarimeters that form the focal planes use a compact design based on high electron mobility transistors (HEMTs) that provides simultaneous measurements of the Stokes parameters Q, U, and I in a single module. The 17-element Q-band polarimeter array, with a central frequency of 43.1 GHz, has the best sensitivity (69 μKs½) and the lowest instrumental systematic errors ever achieved in this band, contributing to the tensor-to-scalar ratio at r < 0.1. The 84-element W-band polarimeter array has a sensitivity of 87 μKs½ at a central frequency of 94.5 GHz. It has the lowest systematic errors to date, contributing at r < 0.01. The two arrays together cover multipoles in the range l ~ 25-975. These are the largest HEMT-based arrays deployed to date. This article describes the design, calibration, performance, and sources of systematic error of the instrument. [ABSTRACT FROM AUTHOR]

A recent application of the Kolmogorov-Smirnov test to the WMAP 7 year W-band maps claims evidence that the CMB is "weakly random", and that only 20% of the signal can be explained as a random Gaussian field. I here repeat this analysis, and in contrast to the original result find no evidence for deviation from the standard ∧CDM model. Instead, the results of the original analysis are consistent with not properly taking into account the correlations of the ∧CDM power spectrum. [ABSTRACT FROM AUTHOR]

The Q/U Imaging ExperimenT (QUIET) employs coherent receivers at 43 GHz and 94 GHz, operating on the Chajnantor plateau in the Atacama Desert in Chile, to measure the anisotropy in the polarization of the cosmic microwave background (CMB). QUIET primarily targets the B modes from primordial gravitational waves. The combination of these frequencies gives sensitivity to foreground contributions from diffuse Galactic synchrotron radiation. Between 2008 October and 2010 December, over 10,000 hr of data were collected, first with the 19 element 43 GHz array (3458 hr) and then with the 90 element 94 GHz array. Each array observes the same four fields, selected for low foregrounds, together covering %1000 deg². This paper reports initial results from the 43 GHz receiver, which has an array sensitivity to CMB fluctuations of 69 µK√s. The data were extensively studied with a large suite of null tests before the power spectra, determined with two independent pipelines, were examined. Analysis choices, including data selection, were modified until the null tests passed. Cross-correlating maps with different telescope pointings is used to eliminate a bias. This paper reports the EE, BB, and EB power spectra in the multipole range ℓ = 25-475. With the exception of the lowest multipole bin for one of the fields, where a polarized foreground, consistent with Galactic synchrotron radiation, is detected with 3cr significance, the E-mode spectrum is consistent with the ACDM model, confirming the only previous detection of the first acoustic peak. The B-mode spectrum is consistent with zero, leading to a measurement of the tensor-to-scalar ratio of Due to image rights restrictions, multiple line equation(s) cannot be graphically displayed. The combination of a new time-stream "double-demodulation" technique, side-fed Dragoman optics, natural sky rotation, and frequent boresight rotation leads to the lowest level of systematic contamination in the B-mode power so far reported, below the level of r = 0.1. [ABSTRACT FROM AUTHOR]

Future cosmic microwave background (CMB) polarization experiments aim to measure an unprecedentedly small signal – the primordial gravity wave component of the polarization field B mode. To achieve this, they will analyse huge data sets, involving years of time-ordered data (TOD) from massively multi-detector focal planes. This creates the need for fast and precise methods to complement the maximum-likelihood (ML) approach in analysis pipelines. In this paper, we investigate fast map-making methods as applied to long duration, massively multi-detector, ground-based experiments, in the context of the search for B modes. We focus on two alternative map-making approaches: destriping and TOD filtering, comparing their performance on simulated multi-detector polarization data. We have written an optimized, parallel destriping code, the DEStriping CARTographer (descart), that is generalized for massive focal planes, including the potential effect of cross-correlated TOD noise. We also determine the scaling of computing time for destriping as applied to a simulated full-season data set for a realistic experiment. We find that destriping can outperform filtering in estimating both the large-scale E- and B-mode angular power spectra. In particular, filtering can produce significant spurious B-mode power via EB mixing. Whilst this can be removed, it contributes to the variance of B-mode bandpower estimates at scales near the primordial B-mode peak. For the experimental configuration we simulate, this has an effect on the possible detection significance for primordial B modes. Destriping is a viable alternative fast method to the full ML approach that does not cause the problems associated with filtering, and is flexible enough to fit into both ML and Monte Carlo pseudo- pipelines. [ABSTRACT FROM AUTHOR]

Development of efficient methods to transfer large DNA fragments into plants will greatly facilitate the map-based cloning of genes. The recently developed BIBAC and TAC vectors have shown potential to deliver large DNA fragments into plants via Agrobacterium-mediated transformation. Here we report that BIBAC and TAC clones containing potato genomic DNA fragments larger than 100 kb are not stable in Agrobacterium. We tested the possible factors that may cause instability, including the insert sizes of the BIBAC and TAC constructs, potato DNA fragments consisting of highly repetitive or largely single-copy DNA sequences, different Agrobacterium transformation methods and different Agrobacterium strains. The insert sizes of the potato BIBAC and TAC constructs were found to be critical to their stability in Agrobacterium. All constructs containing a potato DNA fragment larger than 100 kb were not stable in any of the four tested Agrobacterium strains, including two recA deficient strains. We developed a transposon-based technique that can be used to efficiently subclone a BAC insert into two to three BIBAC/TAC constructs to circumvent the instability problem. [ABSTRACT FROM AUTHOR]

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating potato disease in the world. Control of late blight in the United States and other developed countries relies extensively on fungicide application. We previously demonstrated that the wild diploid potato species Solanum bulbocastanum is highly resistant to all known races of P. infestans. Potato germplasm derived from S. bulbocastanum has shown durable and effective resistance in the field. Here we report the cloning of the major resistance gene RB in S. bulbocastanum by using a map-based approach in combination with a long-range (LR)-PCR strategy. A cluster of four resistance genes of the CC-NBSLRR (coiled coil-nucleotide binding site-Leu-rich repeat) class was found within the genetically mapped RB region. Transgenic plants containing a LR-PCR product of one of these four genes displayed broad spectrum late blight resistance. The cloned RB gene provides a new resource for developing late blight-resistant potato varieties. Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system. [ABSTRACT FROM AUTHOR]

Reliable and easy to use techniques for chromosome identification are critical for many aspects of cytogenetic research. Unfortunately, such techniques are not available in many plant species, especially those with a large number of small chromosomes. Here we demonstrate that fluorescence in situ hybridization (FISH) signals derived from bacterial artificial chromosomes (BACs) can be used as chromosome-specific cytogenetic DNA markers for chromosome identification in potato. We screened a potato BAC library using genetically mapped restriction fragment length polymorphism markers as probes. The identified BAC clones were then labeled as probes for FISH analysis. A set of 12 chromosome-specific BAC clones were isolated and the FISH signals derived from these BAC clones serve as convenient and reliable cytological markers for potato chromosome identification. We mapped the 5S rRNA genes, the 45S rRNA genes, and a potato late blight resistance gene to three specific potato chromosomes using the chromosome-specific BAC clones. [ABSTRACT FROM AUTHOR]

Somatic hybrids between potato and Solanum bulbocastanum, a wild diploid (2n=2x=24) Mexican species, are highly resistant to late blight, caused by Phytophthora infestans. Both randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers that are closely linked to the resistance have been noted by analysis of three different backcross-2 populations derived from two different somatic hybrids. With reference to previously published potato and tomato maps, resistance appears to be on the long arm of chromosome 8 and is flanked by RFLP markers CP53 and CT64. In a population of BC2 plants derived from a cross between the BC1 line J10lK6 [(S. tuberosum PI 203900+S. bulbocastanum PI 243510) ×Katahdin)]×Atlantic, late blight resistance cosegregated with RFLP marker CT88 and RAPD marker OPG02–625. [ABSTRACT FROM AUTHOR]

RAPD analysis was performed on 40 species of Rubus. Seventy-three percent of the bands produced were polymorphic. These data were sufficient to construct a dendrogram. The results are generally in agreement with the traditional classification of the genus Rubus. The exceptions, three species of the subgenus Malachobatus clustered with species of the subgenus Idaeobatus and one species of the subgenus Idaeobatus classified with the Malachobatus species, could not be accounted for based on morphology or breeding behavior. Neither classical nor RAPD-based taxonomy could explain breeding behavior exhibited between interspecific crosses within a subgenus. [ABSTRACT FROM PUBLISHER]

Mental distress may entail increased risk of hip fracture, but it is uncertain whether the effect consists solely of an indirect effect through use of medication, or whether it is also mediated through other mechanism. The purpose of this study was to examine the association between mental distress and risk of hip fracture in women, adjusted for medication (that is, use of tranquillisers/sedatives or hypnotics). A three year follow up of hip fracture was conducted on 18,612 women, consisting of 92.5% of all women aged 50 years or older in a Norwegian county. Three hundred and twenty nine suffered a hip fracture. A mental distress index was based on questions about life dissatisfaction, nervousness, loneliness, sleep disorders, troubled and uneasy feelings, depression and impairment attributable to psychological complaints. Relative risk with 95% confidence intervals (CI) of hip fracture with respect to mental distress were controlled for medication, age, body mass index (BMI), smoking, physical inactivity, and physical illness by means of Cox regression. The 10% of women with the highest mental distress had more than twofold increased risk of hip fracture compared with the 10% of women with the lowest mental distress, after adjustment for age and medication. The relative risk was 1.95 (95% CI 1.2, 3.3) after additional control for BMI, smoking, physical inactivity, and physical illness. The relative risk of hip fracture for daily users of medication compared with never users was 2.1 (95% CI 1.6, 2.9). After adjusting for mental distress it was 1.5 (95% CI 1.0, 2.2). Risk of hip fracture was positively related to mental distress, also after adjustment for medication use. The effect of tranquillisers/sedatives or hypnotics on hip fracture risk may be overestimated in studies with no adjustments for mental distress. [ABSTRACT FROM AUTHOR]

Polyploidy in blackberries and ploidy differences between Rubus species are obstacles to the efficient introduction of valuable germplasm, both intra- and interspecific, into blackberry breeding programs. Expansion of the germplasm base would be facilitated by reducing the ploidy level of blackberry cultivars to the diploid level. In this report selection of twin seed, interspecific hybridization, and pollen irradiation were compared as methods in the recovery of dihaploids from tetraploid blackberry cultivars. One dihaploid was obtained through selection of twin seed and several were obtained following interspecific hybridization. The infrequency of twinning and difficulty in detecting twin seed in Rubus reduced the efficiency of this method. The efficiency with which dihaploids could be obtained following interspecific hybridization varied with the pollen parent. Reduced seed set and seed quality following pollinations with respectively R. parvifolius and R. hirsutus could be used to advantage in the recovery of dihaploids from blackberries. Ploidy reduction in several tetraploid blackberry cultivars was obtained following pollinations with 100 and 150 kR gamma irradiated pollen. Most of the seedlings obtained at the 50 kR dosage were aneuploid. Pollen irradiation at 150 kR was the most efficient method of obtaining dihaploids from tetraploid blackberries. Twenty percent of the seedlings obtained following this treatment were dihaploid. [ABSTRACT FROM AUTHOR]

We estimate the spectral index, β, of polarized synchrotron emission as observed in the 9 yr Wilkinson Microwave Anisotropy Probe sky maps using two methods, linear regression (“T-T plot”) and maximum likelihood. We partition the sky into 24 disjoint sky regions and evaluate the spectral index for all polarization angles between 0° and 85° in steps of 5°. Averaging over polarization angles, we derive a mean spectral index of βall-sky = –2.99 ± 0.01 in the frequency range of 23-33 GHz. We find that the synchrotron spectral index steepens by 0.14 from low to high Galactic latitudes, in agreement with previous studies, with mean spectral indices of βplane = –2.98 ± 0.01 and βhigh-lat = –3.12 ± 0.04. In addition, we find a significant longitudinal variation along the Galactic plane with a steeper spectral index toward the Galactic center and anticenter than toward the Galactic spiral arms. This can be well modeled by an offset sinusoidal, β(l) = –2.85 + 0.17sin (2l – 90°). Finally, we study synchrotron emission in the BICEP2 field, in an attempt to understand whether the claimed detection of large-scale B-mode polarization could be explained in terms of synchrotron contamination. Adopting a spectral index of β = –3.12, typical for high Galactic latitudes, we find that the most likely bias corresponds to about 2% of the reported signal (r = 0.003). The flattest index allowed by the data in this region is β = –2.5, and under the assumption of a straight power-law frequency spectrum, we find that synchrotron emission can account for at most 20% of the reported BICEP2 signal. [ABSTRACT FROM AUTHOR]

The Q/U Imaging ExperimenT (QUIET) has observed the cosmic microwave background (CMB) at 43 and 95 GHz. The 43 GHz results have been published in a previous paper, and here we report the measurement of CMB polarization power spectra using the 95 GHz data. This data set comprises 5337 hr of observations recorded by an array of 84 polarized coherent receivers with a total array sensitivity of 87 μK. Four low-foreground fields were observed, covering a total of ∼1000 deg2 with an effective angular resolution of 12.′8, allowing for constraints on primordial gravitational waves and high signal-to-noise measurements of the E-modes across three acoustic peaks. The data reduction was performed using two independent analysis pipelines, one based on a pseudo-Cℓ (PCL) cross-correlation approach, and the other on a maximum-likelihood (ML) approach. All data selection criteria and filters were modified until a predefined set of null tests had been satisfied before inspecting any non-null power spectrum. The results derived by the two pipelines are in good agreement. We characterize the EE, EB, and BB power spectra between ℓ = 25 and 975 and find that the EE spectrum is consistent with ΛCDM, while the BB power spectrum is consistent with zero. Based on these measurements, we constrain the tensor-to-scalar ratio to r = 1.1+0.9– 0.8 (r < 2.8 at 95% C.L.) as derived by the ML pipeline, and r = 1.2+0.9– 0.8 (r < 2.7 at 95% C.L.) as derived by the PCL pipeline. In one of the fields, we find a correlation with the dust component of the Planck Sky Model, though the corresponding excess power is small compared to statistical errors. Finally, we derive limits on all known systematic errors, and demonstrate that these correspond to a tensor-to-scalar ratio smaller than r = 0.01, the lowest level yet reported in the literature. [ABSTRACT FROM AUTHOR]