Filter Design for the Detection/Estimation of the Modulus of a Vector. Application to Polarization Data

We consider a set of M images, whose pixel intensities at a common point can be treated as the components of a M-dimensional vector. We are interested in the estimation of the modulus of such a vector associated to a compact source. For instance, the detection/estimation of the polarized signal of compact sources immersed in a noisy background is relevant in some fields like Astrophysics. We develop two different techniques, one based on the Maximum Likelihood Estimator (MLE) applied to the modulus distribution, the modulus filter (ModF) and other based on prefiltering the components before fusion, the filtered fusion (FF), to deal with this problem. We present both methods in the general case of M images and apply them to the particular case of three images (linear plus circular polarization). Numerical simulations have been performed to test these filters considering polarized compact sources immersed in stationary noise. The FF performs better than the ModF in terms of errors in the estimated amplitude and position of the source, especially in the low signal-to-noise case. We also compare both methods with the direct application of a matched filter (MF) on the polarization data. This last technique is clearly outperformed by the new methods.Comment: 18 pages, 3 figures, accepted for publication in Signal Processin

Contributions of point extragalactic sources to the Cosmic Microwave Background bispectrum

All the analyses of Cosmic Microwave Background (CMB) temperature maps up--to--date show that CMB anisotropies follow a Gaussian distribution. On the other hand, astrophysical foregrounds which hamper the detection of the CMB angular power spectrum, are not Gaussian distributed on the sky. Therefore, they should give a sizeable contribution to the CMB bispectrum. In fact, the first year data of the Wilkinson Microwave Anisotropy Probe (WMAP) mission have allowed the {\it first} detection of the extragalactic source contribution to the CMB bispectrum at 41 GHz and, at the same time, much tighter limits than before to non--Gaussian primordial fluctuations. In view of the above and for achieving higher precision in current and future CMB measurements of non--Gaussianity, in this paper we discuss a comprehensive assessment of the bispectrum due to either uncorrelated and clustered extragalactic point sources in the whole frequency interval around the CMB intensity peak. Our calculations, based on current cosmological evolution models for sources, show that the reduced angular bispectrum due to point sources, $b_{ps}$, should be detectable in all WMAP and Planck frequency channels. We also find agreement with the results on $b_{ps}$ at 41 GHz coming from the analysis of the first year WMAP data. Moreover, by comparing $b_{ps}$ with the primordial reduced CMB bispectrum, we find that only the peak value of the primordial bispectrum (which appears at $l\simeq 200$) results greater than $b_{ps}$ in a frequency window around the intensity peak of the CMB. The amplitude of this window basically depends on the capability of the source detection algorithms (i.e., on the achievable flux detection limit, $S_{lim}$, for sources).Comment: 26 pages, 6 Figures, use AasTex5.0, ApJ, in press, Oct. 10, 2003 Issu

Non-blind catalogue of extragalactic point sources from the Wilkinson Microwave Anisotropy Probe (WMAP) first 3--year survey data

We have used the MHW2 filter to obtain estimates of the flux densities at the WMAP frequencies of a complete sample of 2491 sources, mostly brighter than 500 mJy at 5 GHz, distributed over the whole sky excluding a strip around the Galactic equator (b < 5 degrees). After having detected 933 sources above the 3 sigma level in the MHW2 filtered maps - our New Extragalactic WMAP Point Source (NEWPS_3sigma) Catalogue - we are left with 381 sources above 5 sigma in at least one WMAP channel, 369 of which constitute our NEWPS_5sigma catalogue. It is remarkable to note that 98 (i.e. 26%) sources detected above 5 sigma are `new', they are not present in the WMAP catalogue. Source fluxes have been corrected for the Eddington bias. Our flux density estimates before such correction are generally in good agreement with the WMAP ones at 23 GHz. At higher frequencies WMAP fluxes tend to be slightly higher than ours, probably because WMAP estimates neglect the deviations of the point spread function from a Gaussian shape. On the whole, above the estimated completeness limit of 1.1 Jy at 23 GHz we detected 43 sources missed by the blind method adopted by the WMAP team. On the other hand, our low-frequency selection threshold left out 25 WMAP sources, only 12 of which, however, are 5 sigma detections and only 3 have fluxes S at 23 GHz > 1.1 Jy. Thus, our approach proved to be competitive with, and complementary to the WMAP one.Comment: 18 pages, 6 figures, 5 tables. Accepted for publication in ApJ

Genomic analysis of three Bradyrhizobium geno(species) nodulating Lima bean (Phaseolus lunatus L.) in Peru

The Lima bean (Phaseolus lunatus), also known as pallar, ibes, garrofón or butter bean in Peru, México, Spain and USA, respectively, is the second most economically important species of Phaseolus. Peru is a centre of origin and domestication of Lima bean. This crop is cultivated mainly in the Central coast of Peru under a subtropical arid climate. In contrast to the common bean (Phaseolus vulgaris) which forms nodules with fast growing Rhizobium strains, the Lima bean forms nodules with slow growing bacteria of the Bradyrhizobium genus (López-López et al. 2013, Ormeño-Orrillo et al. 2006). We found strains of Bradyrhizobium yuanmingense and of three novel Bradyrhizobium genospecies inside P. lunatus nodules in Peru (Ormeño- Orrillo et al. 2006). Strains of the three novel genospecies were characterized by showing an extra-slow growing phenotype (generation time > 10 h-1) and strong alkali production in yeast extract mannitol medium. Two of the novel genospecies were recently named as Bradyrhizobium paxllaeri and Bradyrhizobium icense (Durán et al. 2014). B. paxllaeri strains dominate nodule occupancy followed by those of B. icense and then the third and yet-unnamed genospecies. With the aim to gain insights into this differential competitive ability, we sequenced the genome of one representative strain of each species. Sequencing was performed with the Illumina HiSeq or MiSeq platform and genome assembly with the SPAdes program. Gene prediction and automated annotation was performed with Prokka and RAST. Annotation of genes putatively involved in competitiveness was manually curated. Assemblies had from 55 to 175 contigs, with N50 sizes > 131 kb. Genome sizes of B. paxllaeri and B. icense were similar (8.2 Mb) and larger than that of the third genospecies (7.8 Mb). Preliminary analysis revealed differences between B. paxllaeri and the other two genospecies such as more genes for type IV pilus and two nodA genes. A comparative genomic analysis of P. lunatus symbionts will be presented at the meeting

The Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and Meiosis

Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1–2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms

A Metalloproteinase Secreted by Streptococcus pneumoniae Removes Membrane Mucin MUC16 from the Epithelial Glycocalyx Barrier

The majority of bacterial infections occur across wet-surfaced mucosal epithelia, including those that cover the eye, respiratory tract, gastrointestinal tract and genitourinary tract. The apical surface of all these mucosal epithelia is covered by a heavily glycosylated glycocalyx, a major component of which are membrane-associated mucins (MAMs). MAMs form a barrier that serves as one of the first lines of defense against invading bacteria. While opportunistic bacteria rely on pre-existing defects or wounds to gain entry to epithelia, non opportunistic bacteria, especially the epidemic disease-causing ones, gain access to epithelial cells without evidence of predisposing injury. The molecular mechanisms employed by these non opportunistic pathogens to breach the MAM barrier remain unknown. To test the hypothesis that disease-causing non opportunistic bacteria gain access to the epithelium by removal of MAMs, corneal, conjunctival, and tracheobronchial epithelial cells, cultured to differentiate to express the MAMs, MUCs 1, 4, and 16, were exposed to a non encapsulated, non typeable strain of Streptococcus pneumoniae (SP168), which causes epidemic conjunctivitis. The ability of strain SP168 to induce MAM ectodomain release from epithelia was compared to that of other strains of S. pneumoniae, as well as the opportunistic pathogen Staphylococcus aureus. The experiments reported herein demonstrate that the epidemic disease-causing S. pneumoniae species secretes a metalloproteinase, ZmpC, which selectively induces ectodomain shedding of the MAM MUC16. Furthermore, ZmpC-induced removal of MUC16 from the epithelium leads to loss of the glycocalyx barrier function and enhanced internalization of the bacterium. These data suggest that removal of MAMs by bacterial enzymes may be an important virulence mechanism employed by disease-causing non opportunistic bacteria to gain access to epithelial cells to cause infection

Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

The increasing ability to sequence and compare multiple individual genomes within a species has highlighted the fact that copy-number variation (CNV) is a substantial and underappreciated source of genetic diversity. Chromosome-scale mutations occur at rates orders of magnitude higher than base substitutions, yet our understanding of the mechanisms leading to CNVs has been lagging. We examined CNV in a region of chromosome 5 (chr5) in haploid and diploid strains of Saccharomyces cerevisiae. We optimized a CNV detection assay based on a reporter cassette containing the SFA1 and CUP1 genes that confer gene dosage-dependent tolerance to formaldehyde and copper, respectively. This optimized reporter allowed the selection of low-order gene amplification events, going from one copy to two copies in haploids and from two to three copies in diploids. In haploid strains, most events involved tandem segmental duplications mediated by nonallelic homologous recombination between flanking direct repeats, primarily Ty1 elements. In diploids, most events involved the formation of a recurrent nonreciprocal translocation between a chr5 Ty1 element and another Ty1 repeat on chr13. In addition to amplification events, a subset of clones displaying elevated resistance to formaldehyde had point mutations within the SFA1 coding sequence. These mutations were all dominant and are proposed to result in hyperactive forms of the formaldehyde dehydrogenase enzyme