ALBERT

Description: We present the results from the Very Large Array radio continuum total power and polarized intensity observations of Stephan's Quintet at 1.43 and 4.86 GHz, along with complementary 4.85- and 8.35-GHz Effelsberg observations. Our study shows a large envelope of radio emission encompassing all the member galaxies and hence a large volume of intergalactic matter. Infall of the galaxy NGC 7318B produces a ridge of intergalactic, polarized emission, for which the magnetic field strength has been estimated as 11.0 ± 2.2 μG, with an ordered component of 2.6 ± 0.8 μG. The energy density of the field within the ridge area is of the same order as estimates of the thermal component, implying that the magnetic field has a significant role in the dynamics of the intergalactic matter. We also report that the tidal dwarf galaxy candidate SQ-B possesses a strong and highly anisotropic magnetic field, with a total strength equal to 6.5 ± 1.9 μG and an ordered component reaching 3.5 ± 1.2 μG, which is comparable to that found in normal-sized galaxies.

Description: Faint undetected sources of radio-frequency interference (RFI) might become visible in long radio observations when they are consistently present over time. Thereby, they might obstruct the detection of the weak astronomical signals of interest. This issue is especially important for Epoch of Reionization (EoR) projects that try to detect the faint redshifted H  i signals from the time of the earliest structures in the Universe. We explore the RFI situation at 30–163 MHz by studying brightness histograms of visibility data observed with Low-Frequency Array (LOFAR), similar to radio-source-count analyses that are used in cosmology. An empirical RFI distribution model is derived that allows the simulation of RFI in radio observations. The brightness histograms show an RFI distribution that follows a power-law distribution with an estimated exponent around –1.5. With several assumptions, this can be explained with a uniform distribution of terrestrial radio sources whose radiation follows existing propagation models. Extrapolation of the power law implies that the current LOFAR EoR observations should be severely RFI limited if the strength of RFI sources remains strong after time integration. This is in contrast with actual observations, which almost reach the thermal noise and are thought not to be limited by RFI. Therefore, we conclude that it is unlikely that there are undetected RFI sources that will become visible in long observations. Consequently, there is no indication that RFI will prevent an EoR detection with LOFAR.

Description: We investigate the effect of propagation of cosmic ray electrons (CRE) on the non-thermal (NTH; synchrotron)–far-infrared correlations in M 31 and M 33. The thermal (TH) and NTH emission components of the radio continuum emission at 1.4 GHz and one higher frequency are compared with dust emission from M 31 and M 33 using Spitzer data. In both galaxies the TH emission is linearly correlated with the emission from warm dust (24 μ m, 70 μ m), but the power laws of the NTH–FIR correlations have exponents b  〈 1 that increase with increasing frequency. Furthermore, the values of b for M 33 are significantly smaller ( b  ~= 0.4) than those for M 31 ( b  ~= 0.6). We interpret the differences in b as differences in the diffusion length of the CRE. We estimate the diffusion length in two ways: (1) by smoothing the NTH emission at the higher frequency until the correlation with NTH emission at 1.4 GHz has b  = 1, and (2) by smoothing the TH emission until the correlation with the NTH emission at the same frequency has b  = 1, assuming that the TH emission represents the source distribution of the CRE. Our smoothing experiments show that M 31 only has a thin NTH disc with a scale height of h  = 0.3–0.4 kpc at 1.4 GHz, whereas M 33 has a similar thin disc as well as a thick disc with scale height h thick  ~= 2 kpc. In the thin discs, the (deprojected) diffusion length at 1.4 GHz is ~=1.5 kpc, yielding a diffusion coefficient of ~=2 10 28 cm 2 s –1 . The structure, strength and regularity of the magnetic field in a galaxy as well as the existence of a thick disc determine the diffusion of the CRE, and hence, the power-law exponent of the NTH–FIR correlations.

Description: Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs. Results: Here we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform. Availability: BMIQ is freely available from http://code.google.com/p/bmiq/ . Contact: a.teschendorff@ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online

Description: Congenital diaphragmatic hernia (CDH) is a common life-threatening birth defect. Recessive mutations in the FRAS1-related extracellular matrix 1 ( FREM1 ) gene have been shown to cause bifid nose with or without anorectal and renal anomalies (BNAR) syndrome and Manitoba oculotrichoanal (MOTA) syndrome, but have not been previously implicated in the development of CDH. We have identified a female child with an isolated left-sided posterolateral CDH covered by a membranous sac who had no features suggestive of BNAR or MOTA syndromes. This child carries a maternally-inherited ~86 kb FREM1 deletion that affects the expression of FREM1 's full-length transcripts and a paternally-inherited splice site mutation that causes activation of a cryptic splice site, leading to a shift in the reading frame and premature termination of all forms of the FREM1 protein. This suggests that recessive FREM1 mutations can cause isolated CDH in humans. Further evidence for the role of FREM1 in the development of CDH comes from an N -ethyl- N -nitrosourea -derived mouse strain, eyes2 , which has a homozygous truncating mutation in Frem1. Frem1 eyes2 mice have eye defects, renal agenesis and develop retrosternal diaphragmatic hernias which are covered by a membranous sac. We confirmed that Frem1 is expressed in the anterior portion of the developing diaphragm and found that Frem1 eyes2 embryos had decreased levels of cell proliferation in their developing diaphragms when compared to wild-type embryos. We conclude that FREM1 plays a critical role in the development of the diaphragm and that FREM1 deficiency can cause CDH in both humans and mice.

Description: We present a model for the seeding and evolution of magnetic fields in protogalaxies. Supernova (SN) explosions during the assembly of a protogalaxy self-consistently provide magnetic seed fields, which are subsequently amplified by compression, shear flows and random motions. Our model explains the origin of strong magnetic fields of μG amplitude within the first star-forming protogalactic structures shortly after the first stars have formed. We implement the model into the magnetohydrodynamics (MHD) version of the cosmological N -body/smoothed-particle hydrodynamics (SPH) simulation code gadget and couple the magnetic seeding directly to the underlying multi-phase description of star formation. We perform simulations of Milky-Way-like galactic halo formation using a standard CDM cosmology and analyse the strength and distribution of the subsequent evolving magnetic field. Within star-forming regions and given typical dimensions and magnetic field strengths in canonical SN remnants, we inject a dipole-shaped magnetic field at a rate of 10 –9  G Gyr –1 . Subsequently, the magnetic field strength increases exponentially on time-scales of a few tens of millions of years within the innermost regions of the halo. Furthermore, turbulent diffusion, shocks and gas motions transport the magnetic field towards the halo outskirts. At redshift z 0, the entire galactic halo is magnetized and the field amplitude is of the order of a few μG in the centre of the halo and 10 –9  G at the virial radius. Additionally, we analyse the intrinsic rotation measure (RM) of the forming galactic halo over a range of redshift. The mean halo intrinsic RM peaks between redshifts z 4 and z 2 and reaches absolute values around 1000 rad m –2 . While the halo virializes towards redshift z 0, the intrinsic RM values decline to a mean value below 10 rad m –2 . At high redshifts, the distribution of individual star-forming and thus magnetized regions is widespread. This leads to a widespread distribution of large intrinsic RM values. In our model for the evolution of galactic magnetic fields, the seed magnetic field amplitude and distribution are no longer free parameters, but determined self-consistently by the star formation process occurring during the formation of cosmic structures. Thus, this model provides a solution to the seed field problem.

Description: Although the interaction between interleukin-8 (IL-8) and glycosaminoglycans (GAGs) is crucial for the mediation of inflammatory effects, little is known about the site specificity of this interaction. Therefore, we studied complexes of IL-8 and heparin (HEP) as well as other GAGs in a multidisciplinary approach, involving site-directed mutagenesis, mass spectrometry, fluorescence and solution NMR spectroscopy as well as computer modeling. The interaction between GAG and IL-8 is largely driven by the amine groups of the lysine and the guanidinium groups of arginine side chains. However, due to fast exchange with the solvent, it is typically not possible to detect NMR signals of those groups. Here, we applied reductive 13 C-methylation of the lysine side chains providing sensitive NMR probes for monitoring directly the sites of GAG interaction in 1 H- 13 C correlation experiments. We focused on the lysine side chains K25, K28, K59, K69 and K72 of IL-8 (1–77), which were reported to be involved in the binding to GAGs. The NMR signals of these residues were assigned in 1 H- 13 C HSQC spectra through the help of site-directed mutagenesis. NMR and fluorescence titration experiments in combination with molecular docking and molecular dynamics simulations were applied to investigate the involvement of each lysine in the binding with HEP and various GAG hexasaccharides. We identified K25, K69 and K72 to be the most relevant binding anchors of IL-8(1–77) for the analyzed GAGs.

Description: This work describes a novel approach for the reduction of energy consumption in data centres (DCs) that will yield benefits both in terms of running costs and its environmental impact. The method is based on the introduction of collaborative interactions and flexibility clauses in contracts between all the DC ecosystem entities. The included entities are all the actors along the energy production–consumption chain, from the energy provider to the Information Technology customer. The collaborative approach also integrates the interaction between federated DCs. In this paper, we find a detailed description of the architecture that enables interaction between the DC ecosystem parties, which is designed to be progressively deployed, allowing traditional and ‘greened’ services to coexist, and without modification of the existing DC automation and framework systems.

Description: Chronic periodontitis (CP) is a common oral disease that confers substantial systemic inflammatory and microbial burden and is a major cause of tooth loss. Here, we present the results of a genome-wide association study of CP that was carried out in a cohort of 4504 European Americans (EA) participating in the Atherosclerosis Risk in Communities (ARIC) Study (mean age—62 years, moderate CP—43% and severe CP—17%). We detected no genome-wide significant association signals for CP; however, we found suggestive evidence of association ( P 〈 5 x 10 –6 ) for six loci, including NIN , NPY , WNT5A for severe CP and NCR2 , EMR1 , 10p15 for moderate CP. Three of these loci had concordant effect size and direction in an independent sample of 656 adult EA participants of the Health, Aging, and Body Composition (Health ABC) Study. Meta-analysis pooled estimates were severe CP ( n = 958 versus health: n = 1909)— NPY , rs2521634 [G]: odds ratio [OR = 1.49 (95% confidence interval (CI = 1.28–1.73, P = 3.5 x 10 –7 ))]; moderate CP ( n = 2293)— NCR2 , rs7762544 [G]: OR = 1.40 (95% CI = 1.24–1.59, P = 7.5 x 10 –8 ), EMR1 , rs3826782 [A]: OR = 2.01 (95% CI = 1.52–2.65, P = 8.2 x 10 –7 ). Canonical pathway analysis indicated significant enrichment of nervous system signaling, cellular immune response and cytokine signaling pathways. A significant interaction of NUAK1 (rs11112872, interaction P = 2.9 x 10 –9 ) with smoking in ARIC was not replicated in Health ABC, although estimates of heritable variance in severe CP explained by all single nucleotide polymorphisms increased from 18 to 52% with the inclusion of a genome-wide interaction term with smoking. These genome-wide association results provide information on multiple candidate regions and pathways for interrogation in future genetic studies of CP.

Description: A photometric and spectral study of the variable star V2494 Cyg in the L 1003 dark cloud is presented. The brightness of the star, formerly known as HH 381 IRS, increased by 2.5 mag in R (probably in the 1980s) and since then has remained nearly constant. Since the brightness increase, V2494 Cyg has illuminated a bipolar cometary nebula. The stellar spectrum has several features typical of the FU Ori (FUor) type, plus it exhibits very strong Hα and forbidden emission lines with high-velocity components. These emission lines originate in the Herbig–Haro (HH) jet near the star. The kinematic age of the jet is consistent with it forming at the time of the outburst leading to the luminosity increase. V2494 Cyg also produces a rather extended outflow; it is the first known FUor with both an observed outburst and a parsec-sized HH flow. The nebula, illuminated by V2494 Cyg, possesses similar morphological and spectral characteristics to Hubble's variable nebula (R Monocerotis/NGC 2261).