Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, ...phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.
Context. In the past decade, sensitive, resolved Sunyaev-Zel’dovich (SZ) studies of galaxy clusters have become common. Whereas many previous SZ studies have parameterized the pressure profiles of ...galaxy clusters, non-parametric reconstructions will provide insights into the thermodynamic state of the intracluster medium. Aim. We seek to recover the non-parametric pressure profiles of the high redshift (z = 0.89) galaxy cluster CLJ 1226.9+3332 as inferred from SZ data from the MUSTANG, NIKA, Bolocam, and Planck instruments, which all probe different angular scales. Methods. Our non-parametric algorithm makes use of logarithmic interpolation, which under the assumption of ellipsoidal symmetry is analytically integrable. For MUSTANG, NIKA, and Bolocam we derive a non-parametric pressure profile independently and find good agreement among the instruments. In particular, we find that the non-parametric profiles are consistent with a fitted generalized Navaro-Frenk-White (gNFW) profile. Given the ability of Planck to constrain the total signal, we include a prior on the integrated Compton Y parameter as determined by Planck. Results. For a given instrument, constraints on the pressure profile diminish rapidly beyond the field of view. The overlap in spatial scales probed by these four datasets is therefore critical in checking for consistency between instruments. By using multiple instruments, our analysis of CLJ 1226.9+3332 covers a large radial range, from the central regions to the cluster outskirts: 0.05 R500 < r < 1.1 R500. This is a wider range of spatial scales than is typically recovered by SZ instruments. Similar analyses will be possible with the new generation of SZ instruments such as NIKA2 and MUSTANG2.
Screening for germline mutations in breast cancer‐associated genes BRCA1 and BRCA2 is indicated for patients with breast cancer from high‐risk breast cancer families and influences both treatment ...options and clinical management. However, only 25% of selected patients test positive for BRCA1/2 mutation, indicating that additional diagnostic biomarkers are necessary. We analyzed 124 formalin‐fixed paraffin‐embedded (FFPE) tumor samples from patients with hereditary (104) and sporadic (20) invasive breast cancer, divided into two series (A and B). Microarray expression profiling of 829 human miRNAs was performed on 76 samples (Series A), and bioinformatics tool Prophet was used to develop and test a microarray classifier. Samples were stratified into a training set (n = 38) for microarray classifier generation and a test set (n = 38) for signature validation. A 35‐miRNA microarray classifier was generated for the prediction of BRCA1/2 mutation status with a reported 95% (95% CI = 0.88–1.0) and 92% (95% CI: 0.84–1.0) accuracy in the training and the test set, respectively. Differential expression of 12 miRNAs between BRCA1/2 mutation carriers versus noncarriers was validated by qPCR in an independent tumor series B (n = 48). Logistic regression model based on the expression of six miRNAs (miR‐142‐3p, miR‐505*, miR‐1248, miR‐181a‐2*, miR‐25* and miR‐340*) discriminated between tumors from BRCA1/2 mutation carriers and noncarriers with 92% (95% CI: 0.84–0.99) accuracy. In conclusion, we identified miRNA expression signatures predictive of BRCA1/2 mutation status in routinely available FFPE breast tumor samples, which may be useful to complement current patient selection criteria for gene testing by identifying individuals with high likelihood of being BRCA1/2 mutation carriers.
What's New?
Screening for germline mutations in BRCA1 and BRCA2 genes is indicated for breast cancer patients from high‐risk breast cancer families to inform both treatment options and clinical management. However, currently only 25% of selected patients test positive for BRCA1/2 mutation, calling for additional diagnostic biomarkers. Here, BRCA1 and BRCA2 breast tumors presented highly homogeneous miRNA expression profiles and could be differentiated from familial non‐BRCA1/2 (BRCAX) and sporadic breast tumors based on unique miRNA expression signatures with 92% accuracy, in routinely available FFPE breast tumors samples. These signatures may be useful for complementing current patient selection criteria for BRCA1/2 gene testing.
We propose a method to map the temperature distribution of the hot gas in galaxy clusters that uses resolved images of the thermal Sunyaev-Zel’dovich (tSZ) effect in combination with X-ray data. ...Application to images from the New IRAM KIDs Array (NIKA) and XMM-Newton allows us to measure and determine the spatial distribution of the gas temperature in the merging cluster MACS J0717.5+3745, at z = 0.55. Despite the complexity of the target object, we find a good morphological agreement between the temperature maps derived from X-ray spectroscopy only – using XMM-Newton (TXMM) and Chandra (TCXO) – and the new gas-mass-weighted tSZ+X-ray imaging method (TSZX). We correlate the temperatures from tSZ+X-ray imaging and those from X-ray spectroscopy alone and find that TSZX is higher than TXMM and lower than TCXO by ~ 10% in both cases. Our results are limited by uncertainties in the geometry of the cluster gas, contamination from kinetic SZ (~10%), and the absolute calibration of the tSZ map (7%). Investigation using a larger sample of clusters would help minimise these effects.
We extend the theory of astrophysical maser propagation through a medium with a Zeeman-split molecular response to the case of a non-uniform magnetic field, and allow a component of the electric ...field of the radiation in the direction of propagation: a characteristic of radiation with orbital angular momentum. A classical reduction of the governing equations leads to a set of nine differential equations for the evolution of intensity-like parameters for each Fourier component of the radiation. Four of these parameters correspond to the standard Stokes parameters, whilst the other five represent the z-component of the electric field, and its coupling to the conventional components in the x–y-plane. A restricted analytical solution of the governing equations demonstrates a non-trivial coupling of the Stokes parameters to those representing orbital angular momentum: the z-component of the electric field can grow from a background in which only Stokes-I is non-zero. A numerical solution of the governing equations reveals radiation patterns with a radial and angular structure for the case of an ideal quadrupole magnetic field perpendicular to the propagation direction. In this ideal case, generation of radiation orbital angular momentum, like polarization, can approach 100 per cent.
The Crab nebula is a supernova remnant exhibiting a highly polarized synchrotron radiation at radio and millimetre wavelengths. It is the brightest source in the microwave sky with an extension of 7 ...by 5 arcmin, and is commonly used as a standard candle for any experiment which aims to measure the polarization of the sky. Though its spectral energy distribution has been well characterized in total intensity, polarization data are still lacking at millimetre wavelengths. We report in this paper high resolution observations (18′′ FWHM) of the Crab nebula in total intensity and linear polarization at 150 GHz with the NIKA camera. NIKA, operated at the IRAM 30 m telescope from 2012 to 2015, is a camera made of Lumped Element Kinetic Inductance Detectors (LEKIDs) observing the sky at 150 and 260 GHz. From these observations we are able to reconstruct the spatial distribution of the polarization degree and angle of the Crab nebula, which is found to be compatible with previous observations at lower and higher frequencies. Averaging across the source and using other existing data sets we find that the Crab nebula polarization angle is consistent with being constant over a wide range of frequencies with a value of − 87.7° ± 0.3 in Galactic coordinates. We also present the first estimation of the Crab nebula spectral energy distribution polarized flux in a wide frequency range: 30–353 GHz. Assuming a single power law emission model we find that the polarization spectral index βpol = – 0.347 ± 0.026 is compatible with the intensity spectral index β = – 0.323 ± 0.001.
The characterization of the Intracluster Medium (ICM) properties of high-redshift galaxy clusters is fundamental to our understanding of large-scale structure formation processes. We present the ...results of a multiwavelength analysis of the very massive cluster MOO J1142+1527 at a redshift z = 1.2 discovered as part of the Massive and Distant Clusters of WISE Survey. This analysis is based on high angular resolution Chandra X-ray and NIKA2 Sunyaev-Zel'dovich (SZ) data. The cluster thermodynamic radial profiles have been obtained with unprecedented precision at this redshift and up to 0.7R500, thanks to the combination of high-resolution X-ray and SZ data. The comparison between the galaxy distribution mapped in infrared by Spitzer and the morphological properties of the ICM derived from the combined analysis of the Chandra and NIKA2 data leads us to the conclusion that the cluster is an ongoing merger. We have estimated a systematic uncertainty on the cluster total mass that characterizes both the impact of the observed deviations from spherical symmetry and of the core dynamics on the mass profile. We further combine the X-ray and SZ data at the pixel level to obtain maps of the temperature and entropy distributions. We find a relatively low-entropy core at the position of the X-ray peak and high-temperature regions located on its south and west sides. This work demonstrates that the addition of spatially resolved SZ observations to low signal-to-noise X-ray data brings a high information gain on the characterization of the evolution of ICM thermodynamic properties at z > 1.
We designed, fabricated, and characterized four arrays of horn-coupled, lumped element kinetic inductance detectors (LEKIDs), optimized to work in the spectral bands of the balloon-borne OLIMPO ...experiment. OLIMPO is a 2.6 m aperture telescope, aimed at spectroscopic measurements of the Sunyaev-Zel'dovich (SZ) effect. OLIMPO will also validate the LEKID technology in a representative space environment. The corrected focal plane is filled with diffraction limited horn-coupled KID arrays, with 19, 37, 23, 41 active pixels respectively at 150, 250, 350, and 460 GHz. Here we report on the full electrical and optical characterization performed on these detector arrays before the flight. In a dark laboratory cryostat, we measured the resonator electrical parameters, such as the quality factors and the electrical responsivities, at a base temperature of 300 mK. The measured average resonator Qs are 1.7×104, 7.0×103, 1.0×104, and 1.0×104 for the 150, 250, 350, and 460 GHz arrays, respectively. The average electrical phase responsivities on resonance are 1.4 rad/pW, 1.5 rad/pW, 2.1 rad/pW, and 2.1 rad/pW; the electrical noise equivalent powers are 45 aW/ Hz, 160 aW/ Hz, 80 aW/ Hz, and 140 aW/ Hz, at 12 Hz. In the OLIMPO cryostat, we measured the optical properties, such as the noise equivalent temperatures (NET) and the spectral responses. The measured NETRJs are 200 μK. s, 240 μK s, 240 μK s, and 340 μK s, at 12 Hz; under 78, 88, 92, and 90 mK Rayleigh-Jeans blackbody load changes respectively for the 150, 250, 350, and 460 GHz arrays. The spectral responses were characterized with the OLIMPO differential Fourier transform spectrometer (DFTS) up to THz frequencies, with a resolution of 1.8 GHz.
Purpose
A meta-analysis was performed to asses whether antibiotic prophylaxis is effective in reducing the incidence of surgical site infection (SSI) after open mesh repair of groin hernia.
Methods
A ...literature search for randomized controlled trials (RCT) evaluating the effectiveness of antibiotic prophylaxis in adult patients undergoing open mesh repair of groin hernia was performed in November 2015. Incidence of overall and deep SSI was considered as primary and secondary outcome measures, respectively. Only studies with a clear definition of SSI and a follow-up of at least 1 month were included. Effect size from each RCT was computed as odds ratio (OR) and 95 % confidence interval (CI) and then data were pooled using a random-effects model.
Results
Sixteen RCTs with a total number of 5519 patients were included in the meta-analysis. Considering all the RCTs, antibiotic prophylaxis significantly reduced the overall incidence of SSI from 4.8 % to 3.2 % OR 0.68, 95 % CI (0.51–0.91). However, after removal of two outlier studies, which were identified by evaluating the standardized residual, the result of the meta-analysis became non-significant OR 0.76, 95 % CI (0.56–1.02). The incidence of deep SSI was very low (0–0.7 %) and the effect of antibiotic prophylaxis was not significant OR 0.80, 95 % CI (0.32–1.99).
Conclusions
The results of this meta-analysis do not support the routine use of antibiotic prophylaxis for the open mesh repair of groin hernia. In clinical settings with unexpectedly high rates of SSIs, the appropriateness of surgical asepsis should be carefully checked.
Substructures in the hot gas atmosphere of galaxy clusters are related to their formation history and to the astrophysical processes at play in the intracluster medium (ICM). The thermal ...Sunyaev-Zel’dovich (tSZ) effect is directly sensitive to the line-of-sight integrated ICM pressure, and is thus particularly adapted to study ICM substructures. In this paper, we apply structure-enhancement filtering algorithms to high-resolution tSZ observations (e.g., NIKA) of distant clusters in order to search for pressure discontinuities, compressions, and secondary peaks in the ICM. The same filters are applied to toy-model images and to synthetic tSZ images extracted from RHAPSODY-G cosmological hydrodynamic simulations, in order to better interpret the extracted features. We also study the noise propagation through the filters and quantify the impact of systematic effects, such as data-processing-induced artifacts and point-source residuals, the latter being identified as the dominant potential contaminant. In three of our six NIKA-observed clusters we identify features at high signal-to-noise ratio that show clear evidence for merger events. In MACS J0717.5+3745 (z = 0.55), three strong pressure gradients are observed on the east, southeast, and west sectors, and two main peaks in the pressure distribution are identified. We observe a lack of tSZ compact structure in the cool-core cluster PSZ1 G045.85+57.71 (z = 0.61), and a tSZ gradient ridge dominates in the southeast. In the highest redshift cluster, CL J1226.9+3332 (z = 0.89), we detect a ridge pressure gradient of ~45 arcsec (360 kpc) in length associated with a secondary pressure peak in the west region. Our results show that current tSZ facilities have now reached the angular resolution and sensitivity to allow an exploration of the details of pressure substructures in clusters, even at high redshift. This opens the possibility to quantify the impact of the dynamical state on the relation between the tSZ signal and the mass of clusters, which is important when using tSZ clusters to test cosmological models. This work also marks the first NIKA cluster sample data release.
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