Pedro L. Luque-Escamilla

CpGcluster: a distance-based algorithm for CpG-island detection

BackgroundDespite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content.ResultsGiven the higher frequency of CpG dinucleotides at CGIs, as compared to bulk DNA, the distance distributions between neighboring CpGs should differ for bulk and island CpGs. A new algorithm (CpGcluster) is presented, based on the physical distance between neighboring CpGs on the chromosome and able to predict directly clusters of CpGs, while not depending on the subjective criteria mentioned above. By assigning a p-value to each of these clusters, the most statistically significant ones can be predicted as CGIs. CpGcluster was benchmarked against five other CGI finders by using a test sequence set assembled from an experimental CGI library. CpGcluster reached the highest overall accuracy values, while showing the lowest rate of false-positive predictions. Since a minimum-length threshold is not required, CpGcluster can find short but fully functional CGIs usually missed by other algorithms. The CGIs predicted by CpGcluster present the lowest degree of overlap with Alu retrotransposons and, simultaneously, the highest overlap with vertebrate Phylogenetic Conserved Elements (PhastCons). CpGclusters CGIs overlapping with the Transcription Start Site (TSS) show the highest statistical significance, as compared to the islands in other genome locations, thus qualifying CpGcluster as a valuable tool in discriminating functional CGIs from the remaining islands in the bulk genome.ConclusionCpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides. The only search parameter in CpGcluster is the distance between two consecutive CpGs, in contrast to previous algorithms. Therefore, none of the main statistical properties of CpG islands (neither G+C content, CpG fraction nor length threshold) are needed as search parameters, which may lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster predictions.

Removing Noise and Preserving Details with Relaxed Median Filters

In this paper, a median based filter called relaxed median filter is proposed. The filter is obtained by relaxing the order statistic for pixel substitution. Noise attenuation properties as well as edge and line preservation are analyzed statistically. The trade-off between noise elimination and detail preservation is widely analyzed. It is shown that relaxed median filters preserve details better than the standard median filter, and remove noise better than other median type filters.

A measure of quality for evaluating methods of segmentation and edge detection

A new measure of quality is proposed for evaluating the performance of available methods of image segmentation and edge detection. The technique is intended for the evaluation of low error results and features an objective assessment of discrepancy with respect to the theoretical edge, in tandem with subjective visual evaluation using both the neighbourhood and error-interaction criteria. The proposed mathematical model is extremely simple, even from the perspective of computational execution. A training of the measure has been put in practice, which uses visual evaluation of a set of error patterns by a team of observers. Encouraging results were obtained for a selection of test images, especially in relation to other recently proposed and/or currently employed quality measures. ( 2001 Pattern Recognition Society. Published by Elsevier Science Ltd. All rights reserved.

Measurement of surface tension and contact angle using entropic edge detection

This paper presents a new method to measure the surface tension and the contact angle of a liquid. The measurement procedure comprises three steps: acquisition of the liquid drop image, image segmentation to obtain the contour of the drop and surface-tension and contact-angle calculation by the ADSA method. In the second step a new segmentation method is used based on the Jensen-Shannon divergence, an entropic measurement of coherence among distribution probabilities. The advantages of using this entropic edge-detection method are shown; it is especially suitable when the source image of the drop is affected by any kind of noise, blur or low-contrast effect. Results reveal a better performance than other methods used in this field.

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

BackgroundUnmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence.ResultsWe compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains.ConclusionsThe main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands.

XMM-Newton detection of the supernova remnant G304.6 + 0.1 (Kes 17)

Aims. We report the first detailed X-ray study of the supernova remn ant (SNR) G304.6+0.1, achieved with the XMM-Newton mission. Methods. The powerful imaging capability of XMM-Newton was used to study the X-ray characteristics of the remnant at different energy ranges. The X-ray morphology and spectral properties were analyzed. In addittion, radio and mid-infrared data obtained with the Molonglo Observatory Synthesis Telescope and the Spitzer Space Telescope were used to study the association with the detected X-ray emission and to understand the structure of the SNR at differents wavelengths. Results. The SNR shows an extended and arc-like internal structure in the X-ray band with out a compact point-like source inside the remnant. We find a high column density of NH in the range 2.5-3.5� 10 22 cm −2 , which supports a relatively distant location ( d� 9.7 kpc). The X-ray spectrum exhibits at least three emission lines, indicating that the X-ray emission has a thin thermal plasma origin, although a non-thermal contribution cannot be discarded. The spectra of three different regions (north, center and south) are well represented by a combination of a non-equilibrium ionization (PSHOCK) and a power-law (PL) model. The mid-infrared observations show a bright filamentary structure along the n orth-south direction coincident with the NW radio shell. This suggests that Kes 17 is propagating in a non-uniform environment with high density and that the shock front is interacting with several adjacent massive molecular clouds. The good correspondence of radio and mid-infrared emissions suggests that the filamentary fe atures are caused by shock compression. The X-ray characteristics and well-known radio parameters indicate that G304.6+0.1 is a middle-aged SNR (2.8-6.4)� 10 4 yr old and a new member of the recently proposed group of mixed-morphology SNRs.

ARE T TAURI STARS GAMMA-RAY EMITTERS?

T Tauri stars are young, low-mass, pre-main-sequence stars surrounded by an accretion disk. These objects present strong magnetic activity and powerful magnetic reconnection events. Strong shocks are likely associated with fast reconnection in the stellar magnetosphere. Such shocks can accelerate particles up to relativistic energies. We aim at developing a simple model to calculate the radiation produced by non-thermal relativistic particles in the environment of T Tauri stars. We want to establish whether this emission is detectable at high energies with the available or forthcoming γ-ray telescopes. We assume that particles (protons and electrons) pre-accelerated in reconnection events are accelerated at shocks through the Fermi mechanism and we study the high-energy emission produced by the dominant radiative processes. We calculate the spectral energy distribution of T Tauri stars up to high energies and we compare the integrated flux obtained with that from a specific Fermi source, 1FGL J1625.8–2429c, that we tentatively associate with this kind of young stellar object. We suggest that under reasonable general conditions nearby T Tauri stars might be detected at high energies and be responsible for some unidentified Fermi sources on the Galactic plane.

Radio continuum and near-infrared study of the MGRO J2019+37 region

Context. MGRO J2019+37 is an unidentified extended source of very high energy gamm a-rays originally reported by the Milagro Collaboration as the brightest TeV source in the Cygnus region. Its extended emission could be powered by either a single or several sources. The GeV pulsar AGL J2020.5+3653, discovered by AGILE and associated with PSR J2021+3651, could contribute to the emission from MGRO J2019+37. Aims. Our aim is to identify radio and near-infrared sources in the field of the extended TeV source MGRO J2019+37, and study potential counterparts to explain its emission. Methods. We surveyed a region of about 6 square degrees with the Giant Metrewave Radio Telescope (GMRT) at the frequency 610 MHz. We also observed the central square degree of this survey in the near-infrared Ks-band using the 3.5 m telescope in Calar Alto. Archival X-ray observations of some specific fiel ds are included. VLBI observations of an interesting radio source were performed. We explored possible scenarios to produce the multi-TeV emission from MGRO J2019+37 and studied which of the sources could be the main particle accelerator. Results. We present a catalogue of 362 radio sources detected with the GMRT in the field of MGRO J2019+37, and the results of a cross-correlation of this catalog with one obtained at n ear-infrared wavelengths, which contains∼ 3× 10 5 sources, as well as with available X-ray observations of the region. Some peculiar sources inside the∼1 ◦ uncertainty region of the TeV emission from MGRO J2019+37 are discussed in detail, including the pulsar PSR J2021+3651 and its pulsar wind nebula PWN G75.2+0.1, two new radio-jet sources, the Hii region Sh 2-104 containing two star clusters, and the radio source NVSS J202032+363158. We also find that the hadronic scenario is the most likely in case of a s ingle accelerator, and discuss the possible contribution f rom the sources mentioned above. Conclusions. Although the radio and GeV pulsar PSR J2021+3651 / AGL J2020.5+3653 and its associated pulsar wind nebula PWN G75.2+0.1 can contribute to the emission from MGRO J2019+37, extrapolation of the GeV spectrum does not explain the detected multi-TeV flux. Other sources discussed here could contribute to the emission of the Milagro source.

Measurement of ultralow interfacial tension with ADSA using an entropic edge-detector

Abstract The ultralow interfacial tension of the two-liquid phase of a ternary system 1-propanol–n-heptane–water was determined with a pendant drop method using the axisymmetric drop shape analysis (ADSA) methodology. Because the two liquid phases of the ternary system are practically miscible at temperatures near the critical solution temperature, the drops are small and difficult to distinguish from their surroundings. Consequently, some difficulties appear in the automatic drop analysis, mainly in the profile detection step. An entropic edge-detection method based on the Jensen–Shannon divergence is applied for this purpose. To complete the study, the temperature dependence of the interfacial tension of the two-liquid phase of the ternary system was investigated.

Hα observations of the γ-ray-emitting Be/X-ray binary LSI+61 ◦ 303: orbital modulation, disk truncation, and long-term variability ,

We report 138 spectral observations of the Hα emission line of the radio- andγ-ray-emitting Be/X-ray binary LSI+61 ◦ 303 obtained during the period of September 1998 ‐ January 2013. From measuring various Hα parameters, we found that the orbital modulation of the Hα is best visible in the equivalent width ratio EW(B)/EW(R), the equivalent width of the blue hump, and in the radial velocity of the central dip. The periodogram analysis confirmed that t he Hα emission is modulated with the orbital and superorbital periods. For the past 20 years the radius of the circumstellar disk is s imilar to the Roche lobe size at the periastron. It is probabl y truncated by a 6:1 resonance. The orbital maximum of the equivalent width of Hα emission peaks after the periastron and coincides on average with the X-ray andγ-ray maxima. All the spectra are available upon request from the authors and through the CDS.