ALBERT

Description: Seismic waves sensitive to the outermost part of the Earth's liquid core seem to be affected by a stably stratified layer at the core–mantle boundary. Such a layer could have an observable signature in both long-term and short-term variations of the magnetic field of the Earth, which are used to probe the flow at the top of the core. Indeed, with the recent SWARM mission, it seems reasonable to be able to identify waves propagating in the core with period of several months, which may play an important role in the large-scale dynamics. In this paper, we characterize the influence of a stratified layer at the top of the core on deep quasi-geostrophic (Rossby) waves. We compute numerically the quasi-geostrophic eigenmodes of a rapidly rotating spherical shell, with a stably stratified layer near the outer boundary. Two simple models of stratification are taken into account, which are scaled with commonly adopted values of the Brunt–Väisälä frequency in the Earth's core. In the absence of magnetic field, we find that both azimuthal wavelength and frequency of the eigenmodes control their penetration into the stratified layer: the higher the phase speed, the higher the permeability of the stratified layer to the wave motion. We also show that the theory developed by Takehiro & Lister for thermal convection extends to the whole family of Rossby waves in the core. Adding a magnetic field, the penetrative behaviour of the quasi-geostrophic modes (the so-called fast branch) is insensitive to the imposed magnetic field and only weakly sensitive to the precise shape of the stratification. Based on these results, the large-scale and high-frequency modes (1–2 month periods) may be detectable in the geomagnetic data measured at the Earth's surface, especially in the equatorial area where the modes can be trapped.

Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Description: Data on biological mechanisms of aging are mostly obtained from cross-sectional study designs. An inherent disadvantage of this design is that inter-individual differences can mask small but biologically significant age-dependent changes. A serially sampled design (same individual at different time points) would overcome this problem but is often limited by the relatively small numbers of available paired samples and the statistics being used. To overcome these limitations, we have developed a new vector-based approach, termed three-component analysis, which incorporates temporal distance, signal intensity and variance into one single score for gene ranking and is combined with gene set enrichment analysis. We tested our method on a unique age-based sample set of human skin fibroblasts and combined genome-wide transcription, DNA methylation and histone methylation (H3K4me3 and H3K27me3) data. Importantly, our method can now for the first time demonstrate a clear age-dependent decrease in expression of genes coding for proteins involved in translation and ribosome function. Using analogies with data from lower organisms, we propose a model where age-dependent down-regulation of protein translation-related components contributes to extend human lifespan.

Description: A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines G enomic O rigins T hrough T axonomic CHA llenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.

Description: A 3-D magnetotelluric (MT) inversion code using unstructured tetrahedral elements has been developed in order to correct the topographic effect by directly incorporating it into computational grids. The electromagnetic field and response functions get distorted at the observation sites of MT surveys because of the undulating surface topography, and without correcting this distortion, the subsurface structure can be misinterpreted. Of the two methods proposed to correct the topographic effect, the method incorporating topography explicitly in the inversion is applicable to a wider range of surveys. For forward problems, it has been shown that the finite element method using unstructured tetrahedral elements is useful for the incorporation of topography. Therefore, this paper shows the applicability of unstructured tetrahedral elements in MT inversion using the newly developed code. The inversion code is capable of using the impedance tensor, the vertical magnetic transfer function (VMTF), and the phase tensor as observational data, and it estimates the subsurface resistivity values and the distortion tensor of each observation site. The forward part of the code was verified using two test models, one incorporating topographic effect and one without, and the verifications showed that the results were almost the same as those of previous works. The developed inversion code was then applied to synthetic data from a MT survey, and was verified as being able to recover the resistivity structure as well as other inversion codes. Finally, to confirm its applicability to the data affected by topography, inversion was performed using the synthetic data of the model that included two overlapping mountains. In each of the cases using the impedance tensor, the VMTF and the phase tensor, by including the topography in the mesh, the subsurface resistivity was determined more proficiently than in the case using the flat-surface mesh. Although the locations of the anomalies were not accurately estimated by the inversion using distorted impedance tensors due to the slightly undervalued gain, these locations were correctly estimated by using undistorted impedance tensors or adding VMTFs in the data. Therefore, it can be concluded that the inversion using the unstructured tetrahedral element effectively prevents the misinterpretation of subsurface resistivity and recovers subsurface resistivity proficiently by representing the topography in the computational mesh.

Description: Separating the contribution of different hematite coercivity grains to the magnetic fabric is a standing problem in rock magnetism because of the common occurrence of thermochemical alterations when measuring the anisotropy of thermal remanence. A technique that eliminates this bias is presented, which is useful when there is a need to separate the fabric of detrital from pigmentary hematite, for example. The method is based on stepwise thermal demagnetization of saturation isothermal remanent magnetizations (IRMs) applied orthogonally on three sister specimens, allowing calculation of the anisotropy tensor from the three components of each demagnetized IRM vector, avoiding the necessity of having to apply IRMs to thermochemically altered specimens. Vector subtraction allows determining the anisotropy tensor for specific unblocking-temperature ranges. The anisotropies of the pigmentary, specular and total hematite of the Mauch Chunk Formation red beds of Pennsylvania have been measured from an oriented block sample and results are compared to previous anisotropy measurements performed using the high-field anisotropy of isothermal remanence technique (hf-AIR), which measures total undifferentiated hematite. Experiments were conducted using non-saturating 1 T and fully saturating 5.5 T fields: both experimental sets seem capable of measuring the orientation of the specularite anisotropy principal axes, but 5.5 T are needed to capture the orientation of the higher coercivity pigmentary grains. The magnitudes of the principal axes, instead, are only faithfully measured using 5.5 T fields and yield somewhat higher anisotropies than those measured by hf-AIR. The fundamental requirement for this technique is homogeneous material among the three sister specimens, which is a significant limitation; homogeneity tests allow assessment of applicability of the method and reliability of the results.

Description: Archaeomagnetic field models cover longer timescales than historical models and may therefore resolve the motion of geomagnetic features on the core–mantle boundary (CMB) in a more meaningful statistical sense. Here we perform a detailed appraisal of archaeomagnetic field models to infer some aspects of the physics of the outer core. We characterize and compare the identification and tracking of reversed flux patches (RFPs) in order to assess the RFPs robustness. We find similar behaviour within a family of models but differences among different families, suggesting that modelling strategy is more influential than data set. Similarities involve recurrent positions of RFPs, but no preferred direction of motion is found. The tracking of normal flux patches shows similar qualitative behaviour confirming that RFPs identification and tracking is not strongly biased by their relative weakness. We also compare the tracking of RFPs with that of the historical field model gufm1 and with seismic anomalies of the lowermost mantle to explore the possibility that RFPs have preferred locations prescribed by lower mantle lateral heterogeneity. The archaeomagnetic field model that most resembles the historical field is interpreted in terms of core dynamics and core–mantle thermal interactions. This model exhibits correlation between RFPs and low seismic shear velocity in co-latitude and a shift in longitude. These results shed light on core processes, in particular we infer toroidal field lines with azimuthal orientation below the CMB and large fluid upwelling structures with a width of about 80° (Africa) and 110° (Pacific) at the top of the core. Finally, similar preferred locations of RFPs in the past 9 and 3 kyr of the same archaeomagnetic field model suggest that a 3 kyr period is sufficiently long to reliably detect mantle control on core dynamics. This allows estimating an upper bound of 220–310 km for the magnetic boundary layer thickness below the CMB.

Description: Post-depositional reductive diagenesis usually results in partial or entire cleansing of the pristine palaeomagnetic signal, therefore, its intensity is important to be assessed for sediments that are in the purpose of retrieving palaeomagnetic information. Grain size, rock magnetic and geochemical studies on the entire core, along with scanning electron microscope observations and X-ray diffraction analyses for representative samples were carried out on a Holocene sediment core retrieved from the deep water part of Huguangyan maar lake (HGY), southeast China. The pristine magnetic mineral assemblage of the studied core is domianted by superparamagnetic (SP) and stable single domain titanomagnetite, and high coercivity minerals are not detectable. Based on down-core variations of the average grain size ( M Z ), total organic carbon (TOC), detrital elements (Al, Ti, Fe and Mn) and the concentration and mineralogy of magnetic minerals, the studied core could be divided into three subsections. The uppermost subsection is the least affected by diagenesis, with detrital titanomagnetite as the dominant magnetic mineral. This is owing to low TOC contents, but high detrital input generated by weak Asian summer monsoon intensity during the late Holocene. The intermediate subsection shows down-core progressively enhanced dissolution of detrital titanomagnetite, and concomitant formation of authigenic pyrite and siderite, which indicates down-core progressively enhanced diagenesis generated by down-core progressive increasing TOC content, but decreasing detrital input as the result of down-core progressively strengthened Asian summer monsoon intensity. The pristine magnetic mineral assemblage has been profoundly modified in the lowermost subsection. At certain positions of the lowermost subsection, detrital titanomagnetite has been even completely dissolved via diagenesis, giving place to authigenic pyrite and siderite. High TOC content, but low detrital input generated from strong Asian summer monsoon intensity during the early Holocene are accountable for intensive diagenesis in the lowermost subsection. Complete erasing of detrital magnetic input signal at certain positions of the lowermost subsection, and considerable formation of authigenic siderite indicate that palaeomagnetic records of the studied core have been significantly compromised. The studied core has relatively higher TOC content, lower detrital matter content, calmer sedimentary environments, and less DO available at its water–sediment interface than the cores retrieved at relatively shallower water depths, which all contribute to its relatively stronger diagenesis. Progressive thickening of the upper two subsections with increasing water depth is owing to progressive increase in sedimentation rate with increasing water depth, which is the key factor in determining the thickness of each diagenetic subsection of cores from HGY. It would be better that lake sediments for palaeomagnetic investigations collected at a water depth shallower than the depth of its thermocline.

Description: The rocks in the crust and the upper mantle of the Earth are believed to exhibit electrical anisotropy to some extent. It is beneficial to further understand and recognize the propagation of the electromagnetic waves in the Earth by investigating the magnetotelluric (which is one of the main geophysical techniques to probe the deep structures in the Earth) responses of the media with anisotropic conductivity structures. In this study, we examine the magnetotelluric fields over an idealized 2-D model consisting of two segments with axially anisotropic conductivity structures overlying a perfect conductor basement by a quasi-static analytic approach. The resulting analytic solution could not only contribute to the electromagnetic induction theory in the anisotropic Earth but also serve as at least an initial standard solution which could be used to validate the reliability and accuracy of the numerical algorithms developed for modelling the magnetotelluric responses of the 2-D media with much more general anisotropic conductivity.

Description: Several works have reported that haematite has non-linear initial susceptibility at room temperature, like pyrrhotite or titanomagnetite, but there is no explanation for the observed behaviours yet. This study sets out to determine which physical property (grain size, foreign cations content and domain walls displacements) controls the initial susceptibility. The performed measurements include microprobe analysis to determine magnetic phases different to haematite; initial susceptibility (300 K); hysteresis loops, SIRM and backfield curves at 77 and 300 K to calculate magnetic parameters and minor loops at 77 K, to analyse initial susceptibility and magnetization behaviours below Morin transition. The magnetic moment study at low temperature is completed with measurements of zero field cooled–field cooled and AC susceptibility in a range from 5 to 300 K. The minor loops show that the non-linearity of initial susceptibility is closely related to Barkhausen jumps. Because of initial magnetic susceptibility is controlled by domain structure it is difficult to establish a mathematical model to separate magnetic subfabrics in haematite-bearing rocks.