ALBERT

Description: We introduce a technique to compute exact anelastic sensitivity kernels in the time domain using parsimonious disk storage. The method is based on a reordering of the time loop of time-domain forward/adjoint wave propagation solvers combined with the use of a memory buffer. It avoids instabilities that occur when time-reversing dissipative wave propagation simulations. The total number of required time steps is unchanged compared to usual acoustic or elastic approaches. The cost is reduced by a factor of 4/3 compared to the case in which anelasticity is partially accounted for by accommodating the effects of physical dispersion. We validate our technique by performing a test in which we compare the K α sensitivity kernel to the exact kernel obtained by saving the entire forward calculation. This benchmark confirms that our approach is also exact. We illustrate the importance of including full attenuation in the calculation of sensitivity kernels by showing significant differences with physical-dispersion-only kernels.

Description: The dose effect between nucleoplasmic bridges (NPB) and relatively low doses of ionising radiation remains unknown. Accordingly, this study investigated the NPB frequencies in human peripheral blood lymphocytes exposed to low-dose 60 Co -rays. Complex anomalies, including fused nuclei (FUS), horse-shoe nuclei (HS) and circular nuclei (CIR), which possibly originated from multiple NPBs, were also scored. Human peripheral blood samples were collected from three healthy males and irradiated with 0–1 and 0–0.4 Gy 60 Co -rays. A cytokinesis-block micronucleus cytome assay was then conducted to analyse NPB, PFHC (NPB plus three complex nuclear anomalies) and micronucleus (MN) in binucleated cells. All dose–response curves followed the linear model for both NPB frequency and PFHC cell frequency. The dose–response curves between NPB frequency and absorbed dose at 0–1 and 0–0.4 Gy were y = 0.0037 x + 0.0005 ( R 2 = 0.979, P 〈 0.05) and y = 0.0043 x + 0.0004 ( R 2 = 0.941, P 〈 0.05), respectively. The dose–response curves between PFHC cell frequency and absorbed dose at 0–1 and 0–0.4 Gy were y = 0.0044 x + 0.0007 ( R 2 = 0.982, P 〈 0.05) and y = 0.0059 x + 0.0005 ( R 2 = 0.969, P 〈 0.05), respectively. The statistical significance of differences between the irradiated groups (0–0.4 Gy) and background levels of NPB, PFHC and MN were also analysed. The lowest analysable doses of NPB, PFHC and MN were 0.12, 0.08 and 0.08 Gy, respectively. In conclusion, NPBs and PFHC positively correlated with the absorbed radiation at a relatively low dose.

Description: The conventional finite-difference time-domain (FDTD) method for elastic waves suffers from the staircasing error when applied to model a curved free surface because of its structured grid. In this work, an improved, stable and accurate 3-D FDTD method for elastic wave modelling on a curved free surface is developed based on the finite volume method and enlarged cell technique (ECT). To achieve a sufficiently accurate implementation, a finite volume scheme is applied to the curved free surface to remove the staircasing error; in the mean time, to achieve the same stability as the FDTD method without reducing the time step increment, the ECT is introduced to preserve the solution stability by enlarging small irregular cells into adjacent cells under the condition of conservation of force. This method is verified by several 3-D numerical examples. Results show that the method is stable at the Courant stability limit for a regular FDTD grid, and has much higher accuracy than the conventional FDTD method.

Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.

Description: The Med2, Med3 and Med15 proteins form a heterotrimeric subdomain in the budding yeast Mediator complex. This Med15 module is an important target for many gene specific transcription activators. A previous proteome wide screen in yeast identified Med3 as a protein with priogenic potential. In the present work, we have extended this observation and demonstrate that both Med3 and Med15 form amyloid-like protein aggregates under H 2 O 2 stress conditions. Amyloid formation can also be stimulated by overexpression of Med3 or of a glutamine-rich domain present in Med15, which in turn leads to loss of the entire Med15 module from Mediator and a change in stress response. In combination with genome wide transcription analysis, our data demonstrate that amyloid formation can change the subunit composition of Mediator and thereby influence transcriptional output in budding yeast.

Description: The study of acoustic emissions (AEs) is of paramount importance to understand rock deformation processes. AE recorded during laboratory experiments mimics, in a controlled geometry and environment, natural and induced seismicity. However, these experiments are destructive, time consuming and require a significant amount of resources. Lately, significant progresses have been made in numerical simulations of rock failure processes, providing detailed insights into AE. We utilized the 2-D combined finite-discrete element method to simulate the deformation of Stanstead Granite under varying confining pressure ( P c ) and demonstrated that the increase of confining pressure, P c , (i) shifts failures from tensile towards shear dominated and (ii) enhance the macroscopic ductility. We quantitatively describe the AE activity associated with the fracturing process by assessing the spatial fractal dimension (D-value), the temporal distribution (AE rate) and the slope of the frequency–magnitude distribution (b-value). Based on the evaluation of D-value and AE rate, we defined two distinct deformation phases: Phase I and Phase II. The influence of P c on the spatial distribution of AE varies according to the deformation phase: for increasing P c , D-value decreases and increases during Phases I and II, respectively. In addition, b-value decreases with increasing P c during the entire experiment. Our numerical results show for the first time that variations of D- and b-values as a function of in situ stress can be simulated using the combined finite-discrete element approach. We demonstrate that the examination of seismicity should be carried out carefully, taking into consideration the deformation phase and in situ stress conditions.

Description: The aim of this study is to improve the temporal resolution of seismic wave velocity variations measured using ambient noise correlations. We first reproduce the result obtained by Chen et al. using a network of 21 broad-band stations ideally located around the fault system activated during the Wenchuan earthquake.We measure a velocity drop of 0.07 per cent that was associated with the main shock, with a temporal resolution of 30 days. To determine whether this velocity drop is co-seismic or post-seismic, we attempt to increase the temporal resolution of our observations. By taking advantage of the properties of the curvelet transform, we increase the signal-to-noise ratio of the daily correlations computed between each station pair. It is then possible to measure the velocity drop associated with the Wenchuan earthquake with a temporal resolution of 1 day. This shows that the velocity drop started on 2008 May 12, which was the day of the earthquake, and the velocity reached its lowest value 2 days after the main shock. Moreover, there was a second velocity drop on 2008 May 27, which might relate to strong aftershocks.

Description: Genotype imputation has been widely adopted in the postgenome-wide association studies (GWAS) era. Owing to its ability to accurately predict the genotypes of untyped variants, imputation greatly boosts variant density, allowing fine-mapping studies of GWAS loci and large-scale meta-analysis across different genotyping arrays. By leveraging genotype data from 90 whole-genome deeply sequenced individuals as the evaluation benchmark and the 1000 Genomes Project data as reference panels, we systematically examined four important issues related to genotype imputation practice. First, in a study of imputation accuracy, we found that IMPUTE2 and minimac have the best imputation performance among the three popular imputing software evaluated and that using a multi-population reference panel is beneficial. Second, the optimal imputation quality cutoff for removing poorly imputed variants varies according to the software used. Third, the major contributing factors to consistently poor imputation are low variant heterozygosity, high sequence similarity to other genomic regions, high GC content, segmental duplication and being far from genotyping markers. Lastly, in an evaluation of the imputability of all known GWAS regions, we found that GWAS loci associated with hematological measurements and immune system diseases are harder to impute, as compared with other human traits. Recommendations made based on the above findings may provide practical guidance for imputation exercise in future genetic studies.

Description: Corynebacterium glutamicum , typically used as industrial workhorse for amino acid production, is a moderately salt–alkali-tolerant microorganism with optimal growth at pH 7–9. However, little is known about the mechanisms of salt–alkali tolerance in C. glutamicum . Here, the catalytic capacity of three putative Na + /H + antiporters from C. glutamicum (designated as Cg-Mrp1, Cg-Mrp2 and Cg-NhaP) were characterized in an antiporter-deficient Escherichia coli KNabc strain. Only Cg-Mrp1 was able to effectively complement the Na + -sensitive of E. coli KNabc. Cg-Mrp1 exhibited obvious Na + (Li + )/H + antiport activities with low apparent Km values of 1.08 mM and 1.41 mM for Na + and Li + , respectively. The Na + /H + antiport activity of Cg-Mrp1 was optimal in the alkaline pH range. All three antiporters showed detectable K + /H + antiport activitiy. Cg-NhaP also exhibited Na + (Li + ,Rb + )/H + antiport activities but at lower levels of activity. Interestingly, overexpression of Cg-Mrp2 exhibited clear Na + (K + )/H + antiport activities. These results suggest that C. glutamicum Na + (K + )/H + antiporters may have overlapping roles in coping with salt–alkali and perhaps high-osmolarity stress.

Description: A detailed magnetic analysis has been conducted on the borehole CJ-1 (172.3 m in length) from the Changjiang (Yangtze) River delta. Results show that the dominant magnetic carriers are magnetite and hematite. Palaeomagnetic results reveal that high-frequency changes in palaeomagnetic inclinations are tied significantly to abnormal anisotropy of magnetic susceptibility (AMS) patterns due to effects of the high-energy depositional environment in this region. On the basis of AMS patterns, doubtful palaeomagnetic directional anomalies can be distinguished from authentic palaeomagnetic excursions. Magnetostratigraphic results indicate that the Matuyama–Brunhes boundary (MBB) was recorded at a depth of ~152.5 m. The presence of several short-lived inclination anomalies implied that the sedimentation could be continuous even at the millennial timescale at certain depth intervals bracketing these fast geomagnetic events. In summary, our study provides new insights into constructing reliable magnetostratigraphy in the delta region. Moreover, our new magnetostratigraphy of the Changjiang River delta deposits will facilitate studies on the relevant long-term palaeoenvironmental evolution of the delta.