MYOD-1 in normal colonic mucosa : role as a putative biomarker?

Background DNA methylation of promoter-associated CpG islands of certain genes may play a role in the development of colorectal cancer. The MYOD-1 gene which is a muscle differentiation gene has been showed to be significantly methylated in colorectal cancer which, is an age related event. However the role of this gene in the colonic mucosa is not understood and whether methylation occurs in subjects without colon cancer. In this study, we have determined the frequency of methylation of the MYOD-1 gene in normal colonic mucosa and investigated to see if this is associated with established colorectal cancer risk factors primarily ageing. Results We analysed colonic mucosal biopsies in 218 normal individuals and demonstrated that in most individuals promoter hypermethylation was not quantified for MYOD-1. However, promoter hypermethylation increased significantly with age (p < 0.001 using regression analysis) and this was gender independent. We also showed that gene promoter methylation increased positively with an increase in waist to hip (WHR) ratio – the latter is also a known risk factor for colon cancer development. Conclusions Our study suggests that promoter gene hypermethylation of the MYOD-1 gene increases significantly with age in normal individuals and thus may offer potential as a putative biomarker for colorectal cancer

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces

The adsorption of a collagen fragment on both a hydrophobic, hydrogen-terminated and a hydrophilic, natively oxidised Si surface is investigated using all-atom molecular dynamics. While favourable direct protein-surface interactions via localised contact points characterise adhesion to the hydrophilic surface, evenly spread surface/molecule contacts and stabilisation of the helical structure occurs upon adsorption on the hydrophobic surface. In the latter case, we find that adhesion is accompanied by a mutual fit between the hydrophilic/hydrophobic pattern within the protein and the layered water structure at the solid/liquid interface, which may provide an additional driving force to the classic hydrophobic effect

Bash2py: A bash to Python translator

Abstract—Shell scripting is the primary way for programmers to interact at a high level with operating systems. For decades bash shell scripts have thus been used to accomplish various tasks. But Bash has a counter-intuitive syntax that is not well understood by modern programmers and is no longer adequately supported, making it now difficult to maintain. Bash also suffers from poor performance, memory leakage problems, and limited functionality which make continued dependence on it problematic. At the request of our industrial partner, we therefore developed a source-to-source translator, bash2py, which converts bash scripts into Python. Bash2py leverages the open source bash code, and the internal parser employed by Bash to parse any bash script. However, bash2py re-implements the variable expansion that occurs in Bash to better generate correct Python code. Bash2py correctly converts most Bash into Python, but does require human intervention to handle constructs that cannot easily be automatically translated. In our experiments on real-world open source bash scripts bash2py successfully translates 90 % of the code. Feedback from our industrial partner confirms the usefulness of bash2py in practice

The WiggleZ Dark Energy Survey: Star-formation in UV-luminous galaxies from their luminosity functions

We present the ultraviolet (UV) luminosity function of galaxies from the GALEX Medium Imaging Survey with measured spectroscopic redshifts from the first data release of the WiggleZ Dark Energy Survey. This sample selects galaxies with high star formation rates: at 0.6 < z < 0.9 the median star formation rate is at the upper 95th percentile of optically-selected (r<22.5) galaxies and the sample contains about 50 per cent of all NUV < 22.8, 0.6 < z < 0.9 starburst galaxies within the volume sampled. The most luminous galaxies in our sample (-21.0>M_NUV>-22.5) evolve very rapidly with a number density declining as (1+z)^{5\pm 1} from redshift z = 0.9 to z = 0.6. These starburst galaxies (M_NUV<-21 is approximately a star formation rate of 30 \msuny) contribute about 1 per cent of cosmic star formation over the redshift range z=0.6 to z=0.9. The star formation rate density of these very luminous galaxies evolves rapidly, as (1+z)^{4\pm 1}. Such a rapid evolution implies the majority of star formation in these large galaxies must have occurred before z = 0.9. We measure the UV luminosity function in 0.05 redshift intervals spanning 0.1<z<0.9, and provide analytic fits to the results. At all redshifts greater than z=0.55 we find that the bright end of the luminosity function is not well described by a pure Schechter function due to an excess of very luminous (M_NUV<-22) galaxies. These luminosity functions can be used to create a radial selection function for the WiggleZ survey or test models of galaxy formation and evolution. Here we test the AGN feedback model in Scannapieco et al. (2005), and find that this AGN feedback model requires AGN feedback efficiency to vary with one or more of the following: stellar mass, star formation rate and redshift.Comment: 27 pages; 13 pages without appendices. 22 figures; 11 figures in the main tex

The WiggleZ Dark Energy Survey: improved distance measurements to z = 1 with reconstruction of the baryonic acoustic feature

We present significant improvements in cosmic distance measurements from the WiggleZ Dark Energy Survey, achieved by applying the reconstruction of the baryonic acoustic feature technique. We show using both data and simulations that the reconstruction technique can often be effective despite patchiness of the survey, significant edge effects and shot-noise. We investigate three redshift bins in the redshift range 0.2 < z < 1, and in all three find improvement after reconstruction in the detection of the baryonic acoustic feature and its usage as a standard ruler. We measure model-independent distance measures DV(rsfid/rs) of 1716 ± 83, 2221 ± 101, 2516 ± 86 Mpc (68 per cent CL) at effective redshifts z = 0.44, 0.6, 0.73, respectively, where DV is the volume-averaged distance, and rs is the sound horizon at the end of the baryon drag epoch. These significantly improved 4.8, 4.5 and 3.4 per cent accuracy measurements are equivalent to those expected from surveys with up to 2.5 times the volume of WiggleZ without reconstruction applied. These measurements are fully consistent with cosmologies allowed by the analyses of the Planck Collaboration and the Sloan Digital Sky Survey. We provide the DV(rsfid/rs) posterior probability distributions and their covariances. When combining these measurements with temperature fluctuations measurements of Planck, the polarization of Wilkinson Microwave Anisotropy Probe 9, and the 6dF Galaxy Survey baryonic acoustic feature, we do not detect deviations from a flat Λ cold dark matter (ΛCDM) model. Assuming this model, we constrain the current expansion rate to H₀ = 67.15 ± 0.98 km s⁻¹Mpc⁻¹. Allowing the equation of state of dark energy to vary, we obtain wDE = −1.080 ± 0.135. When assuming a curved ΛCDM model we obtain a curvature value of ΩK = −0.0043 ± 0.0047

The WiggleZ Dark Energy Survey: the growth rate of cosmic structure since redshift z=0.9

We present precise measurements of the growth rate of cosmic structure for the redshift range 0.1 < z < 0.9, using redshift-space distortions in the galaxy power spectrum of the WiggleZ Dark Energy Survey. Our results, which have a precision of around 10% in four independent redshift bins, are well-fit by a flat LCDM cosmological model with matter density parameter Omega_m = 0.27. Our analysis hence indicates that this model provides a self-consistent description of the growth of cosmic structure through large-scale perturbations and the homogeneous cosmic expansion mapped by supernovae and baryon acoustic oscillations. We achieve robust results by systematically comparing our data with several different models of the quasi-linear growth of structure including empirical models, fitting formulae calibrated to N-body simulations, and perturbation theory techniques. We extract the first measurements of the power spectrum of the velocity divergence field, P_vv(k), as a function of redshift (under the assumption that P_gv(k) = -sqrt[P_gg(k) P_vv(k)] where g is the galaxy overdensity field), and demonstrate that the WiggleZ galaxy-mass cross-correlation is consistent with a deterministic (rather than stochastic) scale-independent bias model for WiggleZ galaxies for scales k < 0.3 h/Mpc. Measurements of the cosmic growth rate from the WiggleZ Survey and other current and future observations offer a powerful test of the physical nature of dark energy that is complementary to distance-redshift measures such as supernovae and baryon acoustic oscillations.Comment: 17 pages, 11 figures, accepted for publication by MNRA

Prospectus, December 2, 1975

PC NEWS IN BRIEF: 1975 FALL SEMESTER GRADS, PRESIDENT REPORTS, TRAFFIC STUDY AT PARKLAND; Campus FM Radio A Reality; StuGo proposes $18,000 cut: Emergency meeting slashes$$$; editorials; Letters to the Editor; Roots & Radicals; Forum; Seniors visit P/C; Far Out Planet; Counseling Services Available at P/C; Questions, Just ask Bob; Karate Club; Phi Beta Lambda; Parkland, Sangamon combination; Library Report; Baby born to Reids; Distaff Side; Skylines: Secrets of Life; Parkland teacher stars in musical; Snow Queen contest, dance planned by StuGo; Wright accepts new Chevy; Christmas Music; Swingles Swing; Aw, c\u27mon, Denice; Public StuGo Meeting set for Dec. 6; Cardwell reports to Faculty Senate; Library Security System; Senator Resigns; Parkland Events; Dinner set for December 4; Staerkel scores lack of state funding; If Snow comes, can flu be far behind?; Library Hours; Prospectus Photo Contest; Attend StuGo Meeting: Students protest further cuts in StuGo budget; Ooops!; Two Plays set for Dec. 4 and &; Fly Navy; Snow Queen Candidates named; Good News; Vinyl Love; Foto-Funny\u27s; Country Bouquet: Chicano country ; Dear Bonnie; Art Works for P/C; Classified; U.S. returns vs. Illini; Cobras host Wabash in season opener; Sports Views: Parkland football may be in danger; 1975-76 Cobras Parkland Basketball Roster; 1975-1976 Parkland College Basketball Schedulehttps://spark.parkland.edu/prospectus_1975/1001/thumbnail.jp

The Allen Telescope Array Twenty-centimeter Survey - A 690-Square-Degree, 12-Epoch Radio Dataset - I: Catalog and Long-Duration Transient Statistics

We present the Allen Telescope Array Twenty-centimeter Survey (ATATS), a multi-epoch (12 visits), 690 square degree radio image and catalog at 1.4GHz. The survey is designed to detect rare, very bright transients as well as to verify the capabilities of the ATA to form large mosaics. The combined image using data from all 12 ATATS epochs has RMS noise sigma = 3.94mJy / beam and dynamic range 180, with a circular beam of 150 arcsec FWHM. It contains 4408 sources to a limiting sensitivity of S = 20 mJy / beam. We compare the catalog generated from this 12-epoch combined image to the NRAO VLA Sky Survey (NVSS), a legacy survey at the same frequency, and find that we can measure source positions to better than ~20 arcsec. For sources above the ATATS completeness limit, the median flux density is 97% of the median value for matched NVSS sources, indicative of an accurate overall flux calibration. We examine the effects of source confusion due to the effects of differing resolution between ATATS and NVSS on our ability to compare flux densities. We detect no transients at flux densities greater than 40 mJy in comparison with NVSS, and place a 2-sigma upper limit on the transient rate for such sources of 0.004 per square degree. These results suggest that the > 1 Jy transients reported by Matsumura et al. (2009) may not be true transients, but rather variable sources at their flux density threshold.Comment: 41 pages, 19 figures, ApJ accepted; corrected minor typo in Table