The meso-genomic era

A report from HGM2001, the sixth annual International Human Genome Meeting organized by The Human Genome Organisation (HUGO), Edinburgh, UK, 19-22 April 2001

Simulation of Laser Propagation in a Plasma with a Frequency Wave Equation

The aim of this work is to perform numerical simulations of the propagation of a laser in a plasma. At each time step, one has to solve a Helmholtz equation in a domain which consists in some hundreds of millions of cells. To solve this huge linear system, one uses a iterative Krylov method with a preconditioning by a separable matrix. The corresponding linear system is solved with a block cyclic reduction method. Some enlightments on the parallel implementation are also given. Lastly, numerical results are presented including some features concerning the scalability of the numerical method on a parallel architecture

TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres.

Shorter telomeres have been associated with increased risk of malignancy, including colorectal cancer (CRC). Telomere length is heritable and may be an intermediate phenotype linked to genetic susceptibility to CRC

The Remarkable Be Star HD110432

HD110432 has gained considerable attention because it is a hard, variable X-ray source similar to gamma Cas. From time-serial echelle data obtained over two weeks during 2005 January and February, we find several remarkable characteristics in the star's optical spectrum. The line profiles show rapid variations on some nights which can be most likely be attributed to irregularly occurring and short-lived migrating subfeatures. Such features have only been observed to date in gamma Cas and AB Dor, two stars for which it is believed magnetic fields force circumstellar clouds to corotate over the stellar surface. The star's optical spectrum also exhibits a number of mainly FeII and HeI emission features with profiles typical of an optically thin disk viewed edge-on. Using spectral synthesis techniques, we find that its temperature is 9800K +/-300K, that its projected area is a remarkably large 100 stellar areas, and its emitting volume resides at a distance of 1 AU from the star. We also find that the star's absorption profiles extend to +/-1000 km/s, a fact which we cannot explain. Otherwise, HD110432 and gamma Cas share similarly peculiar X-ray and optical characteristics such as high X-ray temperature, erratic X-ray variability on timescales of a few hours, optical emission lines, and submigrating features in optical line profiles. Because of these similarities, we suggest that this star is a new member of a select class of "gamma Cas analogs."Comment: 31 pages, 9 figures, accepted by ApJ (3/20/06

Identification of the Mass Donor Star's Spectrum in SS 433

We present spectroscopy of the microquasar SS 433 obtained near primary eclipse and disk precessional phase Psi = 0.0, when the accretion disk is expected to be most ``face-on''. The likelihood of observing the spectrum of the mass donor is maximized at this combination of orbital and precessional phases since the donor is in the foreground and above the extended disk believed to be present in the system. The spectra were obtained over four different runs centered on these special phases. The blue spectra show clear evidence of absorption features consistent with a classification of A3-7 I. The behavior of the observed lines indicates an origin in the mass donor. The observed radial velocity variations are in anti-phase to the disk, the absorption lines strengthen at mid-eclipse when the donor star is expected to contribute its maximum percentage of the total flux, and the line widths are consistent with lines created in an A supergiant photosphere. We discuss and cast doubt on the possibility that these lines represent a shell spectrum rather than the mass donor itself. We re-evaluate the mass ratio of the system and derive masses of 10.9 +/- 3.1 Msun and 2.9 +/- 0.7 Msun for the mass donor and compact object plus disk, respectively. We suggest that the compact object is a low mass black hole. In addition, we review the behavior of the observed emission lines from both the disk/wind and high velocity jets.Comment: submitted to ApJ, 24 pages, 7 figure

A 10-hour period revealed in optical spectra of the highly variable WN8 Wolf-Rayet star WR 123

Aims. What is the origin of the large-amplitude variability in Wolf-Rayet WN8 stars in general and WR123 in particular? A dedicated spectroscopic campaign targets the ten-hour period previously found in the high-precision photometric data obtained by the MOST satellite. Methods. In June-August 2003 we obtained a series of high signal-to-noise, mid-resolution spectra from several sites in the {\lambda}{\lambda} 4000 - 6940 A^{\circ} domain. We also followed the star with occasional broadband (Johnson V) photometry. The acquired spectroscopy allowed a detailed study of spectral variability on timescales from \sim 5 minutes to months. Results. We find that all observed spectral lines of a given chemical element tend to show similar variations and that there is a good correlation between the lines of different elements, without any significant time delays, save the strong absorption components of the Hei lines, which tend to vary differently from the emission parts. We find a single sustained periodicity, P \sim 9.8 h, which is likely related to the relatively stable pulsations found in MOST photometry obtained one year later. In addition, seemingly stochastic, large-amplitude variations are also seen in all spectral lines on timescales of several hours to several days.Comment: 6 pages, 4 figures, 2 tables, data available on-line, accepted in A&A Research Note

The Seroepidemiology of Haemophilus influenzae Type B Prior to Introduction of an Immunization Programme in Kathmandu, Nepal.

Haemophilus influenzae type b (Hib) is now recognized as an important pathogen in Asia. To evaluate disease susceptibility, and as a marker of Hib transmission before routine immunization was introduced in Kathmandu, 71 participants aged 7 months-77 years were recruited and 15 cord blood samples were collected for analysis of anti-polyribosylribitol phosphate antibody levels by enzyme-linked immunosorbent assay. Only 20% of children under 5 years old had levels considered protective (>0.15 µg/ml), rising to 83% of 15-54 year-olds. Prior to introduction of Hib vaccine in Kathmandu, the majority of young children were susceptible to disease

Recombination dynamics of a human Y-chromosomal palindrome:rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions

The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9-8.4×10(-4) events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages

Using honey to heal diabetic foot ulcers

Diabetic ulcers seem to be arrested in the inflammatory/proliferative stage of the healing process, allowing infection and inflammation to preclude healing. Antibiotic-resistant bacteria have become a major cause of infections, including diabetic foot infections. It is proposed here that the modern developments of an ancient and traditional treatment for wounds, dressing them with honey, provide the solution to the problem of getting diabetic ulcers to move on from the arrested state of healing. Honeys selected to have a high level of antibacterial activity have been shown to be very effective against antibiotic-resistant strains of bacteria in laboratory and clinical studies. The potent anti-inflammatory action of honey is also likely to play an important part in overcoming the impediment to healing that inflammation causes in diabetic ulcers, as is the antioxidant activity of honey. The action of honey in promotion of tissue regeneration through stimulation of angiogenesis and the growth of fibroblasts and epithelial cells, and its insulin-mimetic effect, would also be of benefit in stimulating the healing of diabetic ulcers. The availability of honey-impregnated dressings which conveniently hold honey in place on ulcers has provided a means of rapidly debriding ulcers and removing the bacterial burden so that good healing rates can be achieved with neuropathic ulcers. With ischemic ulcers, where healing cannot occur because of lack of tissue viability, these honey dressings keep the ulcers clean and prevent infection occurring

Abundance analysis of targets for the COROT / MONS asteroseimology missions I. Semi-automatic abundance analysis of the gamma Dor star HD 49434

One of the goals of the ground-based support program for the COROT and MONS/Roemer satellite missions is to select and characterise suitable target stars for the part of the missions dedicated to asteroseismology. While the global atmospheric parameters may be determined with good accuracy from the Stromgren indices, careful abundance analysis must be made for the proposed main targets. This is a time consuming process considering the long list of primary and secondary targets. We have therefore developed new software called VWA for this task. The VWA automatically selects the least blended lines from the atomic line database VALD, and consequently adjusts the abundance in order to find the best match between the calculated and observed spectra. The variability of HD 49434 was discovered as part of COROT ground-based support observations. Here we present a detailed abundance analysis of HD 49434 using VWA. For most elements we find abundances somewhat below the Solar values, in particular we find [Fe/H] = -0.13(14). We also present the results from the study of the variability that is seen in spectroscopic and photometric time series observations. From the characteristics of the variation seen in photometry and in the line profiles we propose that HD 49434 is a variable star of the gamma Doradus type.Comment: 10 pages, 6 figure