ALBERT

Description: In the context of the study of the integrated Sachs–Wolfe (ISW) effect, we construct a template of the projected density distribution up to redshift z ~= 0.7 by using the luminous galaxies (LGs) from the Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8). We use a photometric redshift catalogue trained with more than a hundred thousand galaxies from the Baryon Oscillation Spectroscopic Survey (BOSS) in the SDSS DR8 imaging area covering nearly one-quarter of the sky. We consider two different LG samples whose selection matches that of SDSS-III/BOSS: the low-redshift sample (LOWZ, z [0.15, 0.5]) and the constant mass sample (CMASS, z [0.4, 0.7]). When building the galaxy angular density templates we use the information from star density, survey footprint, seeing conditions, sky emission, dust extinction and airmass to explore the impact of these artefacts on each of the two LG samples. In agreement with previous studies, we find that the CMASS sample is particularly sensitive to Galactic stars, which dominate the contribution to the auto-angular power spectrum below  = 7. Other potential systematics affect mostly the very low multipole range ( [2, 7]), but leave fluctuations on smaller scales practically unchanged. The resulting angular power spectra in the multipole range [2, 100] for the LOWZ, CMASS and LOWZ+CMASS samples are compatible with linear cold dark matter (CDM) expectations and constant bias values of b  = 1.98 ± 0.11, 2.08 ± 0.14 and 1.88 ± 0.11, respectively, with no traces of non-Gaussianity signatures, i.e. $f_{\rm NL}^{\rm local}=59\pm 75$ at 95 per cent confidence level for the full LOWZ+CMASS sample in the multipole range [4, 100]. After cross-correlating Wilkinson Microwave Anisotropy Probe 9-year data with the LOWZ+CMASS LG projected density field, the ISW signal is detected at the level of 1.62–1.69. While this result is in close agreement with theoretical expectations and predictions from realistic Monte Carlo simulations in the concordance CDM model, it cannot rule out by itself an Einstein–de Sitter scenario, and has a moderately low signal compared to previous studies conducted on subsets of this LG sample. We discuss possible reasons for this apparent discrepancy, and point to uncertainties in the galaxy survey systematics as most likely sources of confusion.

Description: SUMMARY Using a numerical approach, we explore wave-induced fluid flow effects in partially saturated porous rocks in which the gas–water saturation patterns are governed by mesoscopic heterogeneities associated with the dry frame properties. The link between the dry frame properties and the gas saturation is defined by the assumption of capillary pressure equilibrium, which in the presence of heterogeneity implies that neighbouring regions can exhibit different levels of saturation. To determine the equivalent attenuation and phase velocity of the synthetic rock samples considered in this study, we apply a numerical upscaling procedure, which permits to take into account mesoscopic heterogeneities associated with the dry frame properties as well as spatially continuous variations of the pore fluid properties. The multiscale nature of the fluid saturation is taken into account by locally computing the physical properties of an effective fluid, which are then used for the larger-scale simulations. We consider two sets of numerical experiments to analyse such effects in heterogeneous partially saturated porous media, where the saturation field is determined by variations in porosity and clay content, respectively. In both cases we also evaluate the seismic responses of corresponding binary, patchy-type saturation patterns. Our results indicate that significant attenuation and modest velocity dispersion effects take place in this kind of media for both binary patchy-type and spatially continuous gas saturation patterns and in particular in the presence of relatively small amounts of gas. The numerical experiments also show that the nature of the gas distribution patterns is a critical parameter controlling the seismic responses of these environments, since attenuation and velocity dispersion effects are much more significant and occur over a broader saturation range for binary patchy-type gas–water distributions. This analysis therefore suggests that the physical mechanisms governing partial saturation should be accounted for when analysing seismic data in a poroelastic framework. In this context, heterogeneities associated with the dry frame properties, which do not play important roles in wave-induced fluid flow processes per se , should be taken into account since they may determine the kind of gas distribution pattern taking place in the porous rock.

Description: SUMMARY In this work, we analyse the role of permeability on the seismic response of sandstone reservoirs characterized by patchy gas–water saturation. We do this in the framework of Johnson’s model, which is a generalization of White’s seminal model allowing for patches of arbitrary geometry. We first assess the seismic attenuation and velocity dispersion characteristics in response to wave-induced fluid flow. To this end, we perform an exhaustive analysis of the sensitivity of attenuation and velocity dispersion of compressional body waves to permeability and explore the roles played by the Johnson parameters T and S / V , which characterize the shape and size of the gas–water patches. Our results indicate that, within the typical frequency range of exploration seismic data, this sensitivity may indeed be particularly strong for a variety of realistic and relevant scenarios. Next, we extend our analysis to the corresponding effects on surface-based reflection seismic data for two pertinent models of typical sandstone reservoirs. In the case of softer and more porous formations and in the presence of relatively low levels of gas saturation we observe that the effects of permeability on seismic reflection data are indeed significant. These prominent permeability effects prevail for normal-incidence and non-normal-incidence seismic data and for a very wide range of sizes and shapes of the gas–water patches. For harder and less porous reservoirs, the normal-incidence seismic responses exhibit little or no sensitivity to permeability, but the corresponding non-normal-incidence responses show a clear dependence on this parameter, again especially so for low gas saturations. The results of this study therefore suggest that, for a range of fairly common and realistic conditions, surface-based seismic reflection data are indeed remarkably sensitive to the permeability of gas reservoirs and thus have the potential of providing corresponding first-order constraints.

Description: The G 4 C 2 -repeat expansion in C9orf72 is a common cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). C9orf72 transcription is reduced in expansion carriers implicating haploinsufficiency as one of the disease mechanisms. Indeed, our recent ALS study revealed that the expansion was associated with hypermethylation of the CpG-island (5'of the repeat) in DNA samples obtained from different tissues (blood, brain and spinal cord). However, the link between FTLD and methylation of the CpG-island is unknown. Hence, we investigated the methylation profile of the same CpG-island by bisulfite sequencing of DNA obtained from blood of 34 FTLD expansion carriers, 166 FTLD non-carriers and 103 controls. Methylation level was significantly higher in FTLD expansion carriers than non-carriers ( P = 7.8E–13). Our results were confirmed by two methods (HhaI-assay and sequencing of cloned bisulfite PCR products). Hypermethylation occurred only in carriers of an allele with 〉50 repeats, and was not detected in non-carriers or individuals with an intermediate allele (22–43 repeats). As expected, the position/number of methylated CpGs was concordant between the sense and anti-sense DNA strand, suggesting that it is a stable epigenetic modification. Analysis of the combined ALS and FTLD datasets (82 expansion carriers) revealed that the degree of methylation of the entire CpG-island or contribution of specific CpGs ( n = 26) is similar in both syndromes, with a trend towards a higher proportion of ALS patients with a high methylation level ( P = 0.09). In conclusion, we demonstrated that hypermethylation of the CpG-island 5'of the G 4 C 2 -repeat is expansion-specific, but not syndrome-specific (ALS versus FTLD).

Description: Article Mutations in the enzyme superoxide dismutase 1 (SOD1) underlie a form of neurodegenerative disease called amyotrophic lateral sclerosis. Here the authors employ in-cell NMR to show that SOD1 mutants adopt unstructured conformations that are unable to bind zinc and may form toxic SOD1 aggregates. Nature Communications doi: 10.1038/ncomms6502 Authors: Enrico Luchinat, Letizia Barbieri, Jeffrey T. Rubino, Tatiana Kozyreva, Francesca Cantini, Lucia Banci

Description: Seismic attenuation and dispersion in layered sedimentary structures are often interpreted in terms of the classical White model for wave-induced pressure diffusion across the layers. However, this interlayer flow is severely dependent on the properties of the interface separating two layers. This interface behaviour can be described by a pressure jump boundary condition involving a non-vanishing interfacial impedance. In this paper, we incorporate the interfacial impedance into the White model by solving a boundary value problem in the framework of quasi-static poroelasticity. We show that the White model predictions for attenuation and dispersion substantially change. These changes can be attributed to petrophysically plausible scenarios such as imperfect hydraulic contacts or the presence of capillarity.

Description: Evolution of H1N1 influenza A outbreaks of the past 100 years is interesting and significantly complex and details of H1N1 genetic drift remains unknown. Here we investigated the clinical characteristics and immune cross-reactivity of significant historical H1N1 strains. We infected ferrets with H1N1 strains from 1943, 1947, 1977, 1986, 1999, and 2009 and showed each produced a unique clinical signature. We found significant cross-reactivity between viruses with similar HA sequences. Interestingly, A/FortMonmouth/1/1947 antisera cross-reacted with A/USSR/90/1977 virus, thought to be a 1947 resurfaced virus. Importantly, our immunological data that didn't show cross-reactivity can be extrapolated to failure of past H1N1 influenza vaccines, ie. 1947, 1986 and 2009. Together, our results help to elucidate H1N1 immuno-genetic alterations that occurred in the past 100 years and immune responses caused by H1N1 evolution. This work will facilitate development of future influenza therapeutics and prophylactics such as influenza vaccines. Scientific Reports 3 doi: 10.1038/srep01698

Description: There is increasing evidence to suggest that the presence of mesoscopic heterogeneities constitutes an important seismic attenuation mechanism in porous rocks. As a consequence, centimetre-scale perturbations of the rock physical properties should be taken into account for seismic modelling whenever detailed and accurate responses of specific target structures are desired, which is, however, computationally prohibitive. A convenient way to circumvent this problem is to use an upscaling procedure to replace each of the heterogeneous porous media composing the geological model by corresponding equivalent visco-elastic solids and to solve the visco-elastic equations of motion for the inferred equivalent model. While the overall qualitative validity of this procedure is well established, there are as of yet no quantitative analyses regarding the equivalence of the seismograms resulting from the original poro-elastic and the corresponding upscaled visco-elastic models. To address this issue, we compare poro-elastic and visco-elastic solutions for a range of marine-type models of increasing complexity. We found that despite the identical dispersion and attenuation behaviour of the heterogeneous poro-elastic and the equivalent visco-elastic media, the seismograms may differ substantially due to diverging boundary conditions, where there exist additional options for the poro-elastic case. In particular, we observe that at the fluid/porous-solid interface, the poro- and visco-elastic seismograms agree for closed-pore boundary conditions, but differ significantly for open-pore boundary conditions. This is an important result which has potentially far-reaching implications for wave-equation-based algorithms in exploration geophysics involving fluid/porous-solid interfaces, such as, for example, wavefield decomposition.

Description: Solitons are of fundamental importance in photonics due to applications in optical data transmission and also as a tool for investigating novel phenomena ranging from light generation at new frequencies and wave-trapping to rogue waves. Solitons are also moving scatterers: they generate refractive index perturbations moving at the speed of light. Here we found that such perturbations scatter light in an unusual way: they amplify light by the mixing of positive and negative frequencies, as we describe using a first Born approximation and numerical simulations. The simplest scenario in which these effects may be observed is within the initial stages of optical soliton propagation: a steep shock front develops that may efficiently scatter a second, weaker probe pulse into relatively intense positive and negative frequency modes with amplification at the expense of the soliton. Our results show a novel all-optical amplification scheme that relies on soliton induced scattering. Scientific Reports 2 doi: 10.1038/srep00932

Description: We obtain constraints on the variation of the fundamental constants from the full shape of the redshift–space correlation function of a sample of luminous galaxies drawn from the Data Release 9 of the Baryonic Oscillations Spectroscopic Survey. We combine this information with additional data from recent cosmic microwave background, baryon acoustic oscillations and H 0 measurements. We focus on possible variations of the fine structure constant α and the electron mass m e in the early Universe, and study the degeneracies between these constants and other cosmological parameters, such as the dark energy equation of state parameter w DE , the massive neutrinos fraction f , the effective number of relativistic species N eff and the primordial helium abundance Y He . In the case when only one of the fundamental constants is varied, our final bounds are $\alpha / \alpha _0 = 0.9957_{-0.0042}^{+0.0041}$ and $m_{\rm e} /(m_{\rm e})_0 = 1.006_{-0.013}^{+0.014}$ . For the joint variation of both fundamental constants, our results are $\alpha / \alpha _0 = 0.9901_{-0.0054}^{+0.0055}$ and m e /( m e ) 0 = 1.028 ± 0.019. The variations of α and m e from their present values affect the bounds on other cosmological parameters. Although when m e is allowed to vary our constraints on w DE are consistent with a cosmological constant, when α is treated as a free parameter we find w DE  = –1.20 ± 0.13; more than 1 away from its standard value. When f and α are allowed to vary simultaneously, we find f  〈 0.043 (95 per cent confidence level, CL), implying a limit of m  〈 0.46 eV (95 per cent CL), while for m e variation, we obtain f  〈 0.086 (95 per cent CL), which implies m  〈 1.1 eV (95 per cent CL). When N eff or Y He are considered as free parameters, their simultaneous variation with α provides constraints close to their standard values (when the H 0 prior is not included in the analysis), while when m e is allowed to vary, their preferred values are significantly higher. In all cases, our results are consistent with no variations of α or m e at the 1 or 2 level.