ALBERT

Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.

Description: We studied ionospheric responses to the 2012 April 11 M w 8.6 North Sumatra earthquake using total electron content (TEC) measurements with the regional Global Navigation Satellite System network. This earthquake ruptured the oceanic lithosphere off the Indian Ocean coast of North Sumatra, and is known as the largest strike-slip earthquake ever recorded. Coseismic ionospheric disturbances (CIDs) with rapid TEC enhancement of a few TEC units propagated northward with a speed of acoustic waves (~1 km s –1 ). Resonant atmospheric oscillation with a frequency ~4 mHz have been found as monochromatic oscillation of TEC lasting for an hour after the main shock and the largest aftershock. We compared CID amplitudes of 21 earthquakes world-wide with moment magnitudes ( M w ) 6.6–9.2. They roughly obeyed a law such that CID amplitude increases by two orders of magnitude for the M w increase of three. The 2012 North Sumatra earthquakes slightly deviated negatively from the trend possibly reflecting their strike-slip mechanisms, that is small vertical crustal movements for their magnitudes.

Description: Several bioinformatics methods have been proposed for the detection and characterization of genomic structural variation (SV) from ultra high-throughput genome resequencing data. Recent surveys show that comprehensive detection of SV events of different types between an individual resequenced genome and a reference sequence is best achieved through the combination of methods based on different principles (split mapping, reassembly, read depth, insert size, etc.). The improvement of individual predictors is thus an important objective. In this study, we propose a new method that combines deviations from expected library insert sizes and additional information from local patterns of read mapping and uses supervised learning to predict the position and nature of structural variants. We show that our approach provides greatly increased sensitivity with respect to other tools based on paired end read mapping at no cost in specificity, and it makes reliable predictions of very short insertions and deletions in repetitive and low-complexity genomic contexts that can confound tools based on split mapping of reads.

Description: Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework, implemented in a user-friendly software package, named KGGSeq ( http://statgenpro.psychiatry.hku.hk/kggseq ), will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes.

Description: Small RNAs (sRNAs) are a class of short (20–25 nt) non-coding RNAs that play important regulatory roles in gene expression. An essential first step in understanding their function is to confidently identify sRNA targets. In plants, several classes of sRNAs such as microRNAs (miRNAs) and trans-acting small interfering RNAs have been shown to bind with near-perfect complementarity to their messenger RNA (mRNA) targets, generally leading to cleavage of the mRNA. Recently, a high-throughput technique known as Parallel Analysis of RNA Ends (PARE) has made it possible to sequence mRNA cleavage products on a large-scale. Computational methods now exist to use these data to find targets of conserved and newly identified miRNAs. Due to speed limitations such methods rely on the user knowing which sRNA sequences are likely to target a transcript. By limiting the search to a tiny subset of sRNAs it is likely that many other sRNA/mRNA interactions will be missed. Here, we describe a new software tool called PAREsnip that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments. By searching for targets of a complete ‘sRNAome’ we can facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.

Description: Gene fusions are common driver events in leukaemias and solid tumours; here we present FusionAnalyser, a tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end high-throughput transcriptome sequencing data. We initially tested FusionAnalyser by using a set of in silico randomly generated sequencing data from 20 known human translocations occurring in cancer and subsequently using transcriptome data from three chronic and three acute myeloid leukaemia samples. in all the cases our tool was invariably able to detect the presence of the correct driver fusion event(s) with high specificity. In one of the acute myeloid leukaemia samples, FusionAnalyser identified a novel, cryptic, in-frame ETS2–ERG fusion. A fully event-driven graphical interface and a flexible filtering system allow complex analyses to be run in the absence of any a priori programming or scripting knowledge. Therefore, we propose FusionAnalyser as an efficient and robust graphical tool for the identification of functional rearrangements in the context of high-throughput transcriptome sequencing data.

Description: The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (~92%).

Description: We introduce Grinder ( http://sourceforge.net/projects/biogrinder/ ), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Description: The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith–Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.

Description: Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (multivariate analysis of transcript splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P -value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT–PCR validation rate of 86% for differential exon skipping events with a MATS FDR of 〈10%. Additionally, over the full list of RT–PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.

Description: Numerous algorithms have been developed to analyze ChIP-Seq data. However, the complexity of analyzing diverse patterns of ChIP-Seq signals, especially for epigenetic marks, still calls for the development of new algorithms and objective comparisons of existing methods. We developed Qeseq, an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length. To objectively assess its performance relative to other 14 ChIP-Seq peak finders, we designed a novel protocol based on Validation Discriminant Analysis (VDA) to optimally select validation sites and generated two validation datasets, which are the most comprehensive to date for algorithmic benchmarking of key epigenetic marks. In addition, we systematically explored a total of 315 diverse parameter configurations from these algorithms and found that typically optimal parameters in one dataset do not generalize to other datasets. Nevertheless, default parameters show the most stable performance, suggesting that they should be used. This study also provides a reproducible and generalizable methodology for unbiased comparative analysis of high-throughput sequencing tools that can facilitate future algorithmic development.

Description: The informational content of RNA sequencing is currently far from being completely explored. Most of the analyses focus on processing tables of counts or finding isoform deconvolution via exon junctions. This article presents a comparison of several techniques that can be used to estimate differential expression of exons or small genomic regions of expression, based on their coverage function shapes. The problem is defined as finding the differentially expressed exons between two samples using local expression profile normalization and statistical measures to spot the differences between two profile shapes. Initial experiments have been done using synthetic data, and real data modified with synthetically created differential patterns. Then, 160 pipelines (5 types of generator x 4 normalizations x 8 difference measures) are compared. As a result, the best analysis pipelines are selected based on linearity of the differential expression estimation and the area under the ROC curve. These platform-independent techniques have been implemented in the Bioconductor package rnaSeqMap. They point out the exons with differential expression or internal splicing, even if the counts of reads may not show this. The areas of application include significant difference searches, splicing identification algorithms and finding suitable regions for QPCR primers.

Description: The rapid expansion in the quantity and quality of RNA-Seq data requires the development of sophisticated high-performance bioinformatics tools capable of rapidly transforming this data into meaningful information that is easily interpretable by biologists. Currently available analysis tools are often not easily installed by the general biologist and most of them lack inherent parallel processing capabilities widely recognized as an essential feature of next-generation bioinformatics tools. We present here a user-friendly and fully automated R NA- S eq a nalysis p ipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-throughput RNA-Seq datasets. R-SAP follows a hierarchical decision making procedure to accurately characterize various classes of transcripts and achieves a near linear decrease in data processing time as a result of increased multi-threading. In addition, RNA expression level estimates obtained using R-SAP display high concordance with levels measured by microarrays.

Description: Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein–DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.

Description: A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and blocking variables while still taking full account of biological variation. Biological variation between RNA samples is estimated separately from the technical variation associated with sequencing technologies. Novel empirical Bayes methods allow each gene to have its own specific variability, even when there are relatively few biological replicates from which to estimate such variability. The pipeline is implemented in the edgeR package of the Bioconductor project. A case study analysis of carcinoma data demonstrates the ability of generalized linear model methods (GLMs) to detect differential expression in a paired design, and even to detect tumour-specific expression changes. The case study demonstrates the need to allow for gene-specific variability, rather than assuming a common dispersion across genes or a fixed relationship between abundance and variability. Genewise dispersions de-prioritize genes with inconsistent results and allow the main analysis to focus on changes that are consistent between biological replicates. Parallel computational approaches are developed to make non-linear model fitting faster and more reliable, making the application of GLMs to genomic data more convenient and practical. Simulations demonstrate the ability of adjusted profile likelihood estimators to return accurate estimators of biological variability in complex situations. When variation is gene-specific, empirical Bayes estimators provide an advantageous compromise between the extremes of assuming common dispersion or separate genewise dispersion. The methods developed here can also be applied to count data arising from DNA-Seq applications, including ChIP-Seq for epigenetic marks and DNA methylation analyses.

Description: ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available to extract binding motifs from peak data sets. However, most approaches are only available as command-line programs, or via a website but with size restrictions. We present peak-motifs , a computational pipeline that discovers motifs in peak sequences, compares them with databases, exports putative binding sites for visualization in the UCSC genome browser and generates an extensive report suited for both naive and expert users. It relies on time- and memory-efficient algorithms enabling the treatment of several thousand peaks within minutes. Regarding time efficiency, peak-motifs outperforms all comparable tools by several orders of magnitude. We demonstrate its accuracy by analyzing data sets ranging from 4000 to 1 28 000 peaks for 12 embryonic stem cell-specific transcription factors. In all cases, the program finds the expected motifs and returns additional motifs potentially bound by cofactors. We further apply peak-motifs to discover tissue-specific motifs in peak collections for the p300 transcriptional co-activator. To our knowledge, peak-motifs is the only tool that performs a complete motif analysis and offers a user-friendly web interface without any restriction on sequence size or number of peaks.

Description: Genetic disorders can be detected by prenatal diagnosis using Chorionic Villus Sampling, but the 1:100 chance to result in miscarriage restricts the use to fetuses that are suspected to have an aberration. Detection of trisomy 21 cases noninvasively is now possible owing to the upswing of next-generation sequencing (NGS) because a small percentage of fetal DNA is present in maternal plasma. However, detecting other trisomies and smaller aberrations can only be realized using high-coverage NGS, making it too expensive for routine practice. We present a method, WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR), which detects small aberrations using low-coverage NGS. The increased detection resolution was achieved by comparing read counts within the tested sample of each genomic region with regions on other chromosomes that behave similarly in control samples. This within-sample comparison avoids the need to re-sequence control samples. WISECONDOR correctly identified all T13, T18 and T21 cases while coverages were as low as 0.15–1.66. No false positives were identified. Moreover, WISECONDOR also identified smaller aberrations, down to 20 Mb, such as del(13)(q12.3q14.3), +i(12)(p10) and i(18)(q10). This shows that prevalent fetal copy number aberrations can be detected accurately and affordably by shallow sequencing maternal plasma. WISECONDOR is available at bioinformatics.tudelft.nl/wisecondor.

Description: Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon–exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F 1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/ .

Description: Combinatorial interactions among transcription factors (TFs) are critical for integrating diverse intrinsic and extrinsic signals, fine-tuning regulatory output and increasing the robustness and plasticity of regulatory systems. Current knowledge about combinatorial regulation is rather limited due to the lack of suitable experimental technologies and bioinformatics tools. The rapid accumulation of ChIP-Seq data has provided genome-wide occupancy maps for a large number of TFs and chromatin modification marks for identifying enhancers without knowing individual TF binding sites. Integration of the two data types has not been researched extensively, resulting in underused data and missed opportunities. We describe a novel method for discovering frequent combinatorial occupancy patterns by multiple TFs at enhancers. Our method is based on probabilistic item set mining and takes into account uncertainty in both types of ChIP-Seq data. By joint analysis of 108 TFs in four human cell types, we found that cell–type-specific interactions among TFs are abundant and that the majority of enhancers have flexible architecture. We show that several families of transposable elements disproportionally overlap with enhancers with combinatorial patterns, suggesting that these transposable element families play an important role in the evolution of combinatorial regulation.

Description: Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.

Description: Next-generation sequencing (NGS) technologies-based transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.

Description: Broad-band magnetic susceptibility (MS) measurement, a novel magnetic method capable of quantifying a narrow grain size distribution (GSD) of superparamagnetic (SP) particles by measuring low-field MS at a number of frequency steps spanning four orders of magnitude, has been tested in a loess/palaeosol section at Luochuan in the Chinese Loess Plateau. The studied succession consists of sequences from the latest palaeosol unit (S0) to the upper part of the loess unit (L2), spanning the last glacial–interglacial cycle. Reconstructed GSDs consist of volume fractions on the order of 10 –24 m 3 , and the mean GSDs are modal but with distinctive skewness among the loess, the weakly developed palaeosols (weak palaeosols), and the mature palaeosols. This indicates that the mean volume of SP particles in this loess/palaeosol sequence tends to increase during the transition from loess -〉 weak palaeosol -〉 palaeosol, an indication of grain growth as pedogenesis progresses. Total frequency dependence, or TFD(per cent), the difference between 130 at the lowest (130 Hz) and 500k at the highest (500 kHz) frequencies normalized to 130 , is judged to be a more suitable index than previous frequency dependence parameters for the concentration of SP particles. TFD(per cent) has a strong correlation with 130 , showing a continuous ‘growth curve’ with the rate of increase being highest for the loess, moderate for the weak palaeosols, and saturated for the palaeosols. The characteristic curve suggests that smaller SP particles are preferentially formed in the earlier stage of pedogenesis rather than the later phase when even larger particles are formed in mature palaeosols. These results demonstrate that the broad-band MS measurement method will be useful for the quantitative assessment of magnetic nanoparticles in soils and sediments.

Description: Environmental magnetism can provide simple and fast methods to semi-quantify the contamination levels by heavy metals in urban areas from the relationships between the magnetic properties and the heavy metal concentrations. The aim of this study is to explore the interpretation of selected magnetic parameters as proxies for the evaluation of heavy metal contamination in urban dusts. Dust samples were collected from different districts of Nanjing, Southeast China. The magnetic properties of dusts were analysed and heavy metal (Fe, Al, As, Ba, Cd, Cr, Co, Cu, Hg, Mn, Mo, Ni, Pb, Sr, V and Zn) concentrations were measured. Magnetic minerals, mainly from anthropogenic activities, are dominated by coarse stable single domain-grained ferrimagnetic minerals. The – T curves indicated that the main magnetic minerals are magnetite and hematite. Magnetic properties exhibited similar spatial distribution and significant positive correlations with the concentrations of most metals and with the pollution load index. Magnetic properties had a strong link with the abundance of heavy metals derived from industrial emission and traffic activities, whereas there was a poor correlation with the concentrations of metals from multi-sources such as commercial/domestic sources and natural processes. Besides the low-frequency magnetic susceptibility ( LF ) and the saturation isothermal remanent magnetization, other magnetic parameters can be considered as efficient indicators in the assessment of heavy metal contamination. The linkage between the magnetic properties and heavy metal concentrations in street dusts depends on the sources and nature of their magnetic fraction. Environmental magnetism analyses may provide simple and rapid methods for the assessment of heavy metal contamination in urban street dusts.

Description: We present in this paper an alternative approach to modelling and inversion of surface nuclear magnetic resonance (sNMR) data that has numerous attractive characteristics. By considering the forward and inverse problem in the frequency-domain (FD) it is possible to heavily truncate the band-limited data set with no appreciable loss of information. Furthermore, it introduces a natural method of signal demodulating and sidesteps the rotating frame transformation, which can be difficult to apply to large volumes. By instead remaining in the laboratory frame, phase shifts due to off-resonance transmission and static variation in the Larmor frequencies become simpler to account for. For these reasons, we present the first practical scheme for comprehensively inverting the complex sNMR data set. The use of complex data allows for improved depth and decay constant resolution. However, it requires the knowledge of subsurface electrical conductivity, and by corollary the ability to accurately model those effects in the sNMR record. Finally, the complex FD signal is sensitive to dephasing of the sNMR record due to static magnetic field inhomogeneity. We illustrate the ability to detect dephasing in synthetic and field data and demonstrate an effective inversion which is able to solve for static dephasing effects. This results in better estimation of meaningful decay constants as well as reduced error in extrapolated initial signal amplitude. Both of these parameters are critical for using sNMR in applications requiring estimation of hydraulic parameters.

Description: We report a palaeomagnetic investigation of the last full geomagnetic field reversal, the Matuyama-Brunhes (M-B) transition, as preserved in a continuous sequence of exposed lacustrine sediments in the Apennines of Central Italy. The palaeomagnetic record provides the most direct evidence for the tempo of transitional field behaviour yet obtained for the M-B transition. 40 Ar/ 39 Ar dating of tephra layers bracketing the M-B transition provides high-accuracy age constraints and indicates a mean sediment accumulation rate of about 0.2 mm yr –1 during the transition. Two relative palaeointensity (RPI) minima are present in the M-B transition. During the terminus of the upper RPI minimum, a directional change of about 180 ° occurred at an extremely fast rate, estimated to be less than 2 ° per year, with no intermediate virtual geomagnetic poles (VGPs) documented during the transit from the southern to northern hemisphere. Thus, the entry into the Brunhes Normal Chron as represented by the palaeomagnetic directions and VGPs developed in a time interval comparable to the duration of an average human life, which is an order of magnitude more rapid than suggested by current models. The reported investigation therefore provides high-resolution integrated palaeomagnetic and radioisotopic data that document the fine details of the anatomy and tempo of the M-B transition in Central Italy that in turn are crucial for a better understanding of Earth's magnetic field, and for the development of more sophisticated models that are able to describe its global structure and behaviour.

Description: The anisotropy of magnetic susceptibility (AMS) of soft rocks was measured in order to distinguish between the effect of remote and local strain fields, determine the size of the related inelastic damage zone and resolve the fault-plane solutions of past earthquakes. The AMS fabrics were explored next to late Pleistocene syndepositional normal faults (total displacement up to ~3.5 m) that cross soft lacustrine rocks within the seismically active Dead Sea basin. ‘Deposition fabrics’ prevail meters away from the fault planes and are characterized by scattered maximum and intermediate principal AMS axes. ‘Deformation fabrics’ are detected up to tens of centimetres from the fault planes and are characterized by well-grouped AMS axes, in which one of the principal axes is parallel to the strike of the nearby fault. Variations in the AMS fabrics and magnetic lineations define the size of the inelastic damage zone around the faults. The results demonstrate that the deformation-driven magnetic fabrics and the associated inelastic damage zones are compatible with coseismic dynamic faulting and the effects of the local strain field during earthquakes. Most of the AMS fabrics show a conspicuous similarity to that of the fault-plane solutions, i.e., the principal AMS axes and instantaneous strain ellipsoids are coaxial. These results suggest a novel application of the AMS method for defining the shape and size of the damage zones surrounding dynamic faults and determining the full tensor of the local strain field.

Description: Very low frequency (VLF) electromagnetic waves that penetrate conductive magma-filled dykes generate secondary fields on the surface that can be used to invert for dyke properties. The model used for the interpretation calculates currents induced in a conductive strip by an inducing field that decays exponentially with depth due to the conductivity of the surrounding medium. The differential equations are integrated to give an inhomogeneous Fredholm equation of the second kind with a kernel consisting of a modified Bessel function of the second kind. Numerical methods are typically used to solve for the induced currents in the strip. In this paper, we apply a modified Galerkin–Chebyshev method, which involves separating the kernel into source and field spectra and integrating the source terms to obtain a matrix equation for the unknown coefficients. The incident wave is expressed as a Chebyshev series. The modified Bessel function is separated into a logarithmic singularity and a non-singular remainder, both of which are expanded in complex Chebyshev polynomials. The Chebyshev coefficients for the remainder are evaluated using a fast Fourier transform, while the logarithmic term and incident field have analytic series. The deconvolution then involves a matrix inversion. The results depend on the ratio of strip-size to skin-depth. For infinite skin-depth and a singular conductivity distribution given by $\tau _0 a/\sqrt{a^2 - z^2 }$ (where 0 is the conductance, a is the half-length and z the distance from the centre), Parker gives an analytic solution. We present a similar analytic series solution for the finite skin-depth case, where the size to skin depth ratio is small. Results are presented for different ratios of size to skin depth that can be compared with numerical solutions. We compare full-space and half-space solutions. A fit of the model to VLF data taken above a magma filled dykes in Hawaii and Mt Etna demonstrates that while properties such as depth to top, conductivity ratio, tilt and dip can be determined, the depth to bottom is indeterminate due to the exponential decay of the inducing field.

Description: Correlated data errors (noise) are common in magnetotelluric (MT) data, but MT inversions typically neglect error correlations without investigating the impact of this simplification on inversion results. This paper examines effects of neglecting frequency- and spatially correlated noise on MT inversion, based on a nonlinear Bayesian formulation which quantifies the uncertainties of inversion results in terms of marginal posterior probability densities and credibility intervals. To do so, data with frequency- and spatially correlated noise of differing degrees are generated for several layered (1-D) synthetic cases. Bayesian MT inversions are carried out for these data sets with and without accounting for error correlation (i.e. applying full and diagonal covariance matrices, respectively, in the inversion), and the results are compared. For cases with noise that is strongly correlated over frequency or space, parameter uncertainties estimated using the diagonal-covariance simplification (neglecting error correlations) are found to often be significantly underestimated compared with results computed using the full covariance matrix.

Description: We report a new method to infer continuous time-series of the declination, inclination and intensity of the magnetic field from archaeomagnetic data. Adopting a Bayesian perspective, we need to specify a priori knowledge about the time evolution of the magnetic field. It consists in a time correlation function that we choose to be compatible with present knowledge about the geomagnetic time spectra. The results are presented as distributions of possible values for the declination, inclination or intensity. We find that the methodology can be adapted to account for the age uncertainties of archaeological artefacts and we use Markov chain Monte Carlo to explore the possible dates of observations. We apply the method to intensity data sets from Mari, Syria and to intensity and directional data sets from Paris, France. Our reconstructions display more rapid variations than previous studies and we find that the possible values of geomagnetic field elements are not necessarily normally distributed. Another output of the model is better age estimates of archaeological artefacts.

Description: We present a rigorous method for interpolation of electric and magnetic fields close to an interface with a conductivity contrast. The method takes into account not only a well-known discontinuity in the normal electric field, but also discontinuity in all the normal derivatives of electric and magnetic tangential fields. The proposed method is applied to marine 3-D controlled-source electromagnetic modelling (CSEM) where sources and receivers are located close to the seafloor separating conductive seawater and resistive formation. For the finite-difference scheme based on the Yee grid, the new interpolation is demonstrated to be much more accurate than alternative methods (interpolation using nodes on one side of the interface or interpolation using nodes on both sides, but ignoring the derivative jumps). The rigorous interpolation can handle arbitrary orientation of interface with respect to the grid, which is demonstrated on a marine CSEM example with a dipping seafloor. The interpolation coefficients are computed by minimizing a misfit between values at the nearest nodes and linear expansions of the continuous field components in the coordinate system aligned with the interface. The proposed interpolation operators can handle either uniform or non-uniform grids and can be applied to interpolation for both sources and receivers.

Description: According to field observations, electromagnetic (EM) signals accompanying seismic waves can be recorded. The orders of magnitude of observed coseismic electric and magnetic signals associated with earthquakes are usually around 1 to 10 1 mV km –1 and 10 –2 to 1 nT, respectively. In this paper, we carry out numerical simulation of coseismic EM signals associated with seismic waves due to electrokinetic effect and compare with field observations. The seismic source is represented by a finite fault measuring 15 x 9 km 2 with a max slip displacement 1.5 m, corresponding to a M w 5.9 earthquake. While using the EM surface boundary condition of continuous horizontal EM components, the magnetic signals only accompany the late-arriving S waves at receiver near the ground surface. This is obviously different from field observations. Thus, we adopt another EM surface boundary condition which assumes the ground surface carries surface charge. For the used half-space model, a surface-charge density magnitude | Q sc | in excess of 10 –4 C m –2 is sufficient to make horizontal magnetic components clearly show up at the whole time duration of seismic waves. When | Q sc | increases, the contribution of surface-charge density to coseismic EM signals becomes more and more dominant comparing with that of the seismically induced streaming-current. We estimate the Q sc expected at the Earth's surface might be a value between –5 x 10 –4 and –0.1 C m –2 by the comparison between numerical results and field observations. The vertical magnetic signals only accompany the late-arriving seismic waves, because they are theoretically only induced by SH wave. The field observation results of vertical magnetic signals may be resulted from the scattering effect or the seismic dynamo effect. We conclude that electrokinetic effect combined with surface-charge assumption is one possible generation mechanism of the observed coseismic EM signals.

Description: Fifteen sites of lava flows from Martinique Island (FWI) have been selected to document the geomagnetic field in the Caribbean area over the past 2.5 Ma and further constrain the time-averaged field during this period. Identical characteristic directions were isolated using both AF and thermal stepwise demagnetization techniques in all flows. Nine mean-site directions have a normal polarity, while three others are reversed. The mean geomagnetic pole position obtained after reducing all directions to the same polarity is indistinguishable from the present north geographic pole. The dispersion is at least 8° larger than the values derived from the time-averaged field models and remains unexplained otherwise than resulting from the relatively small number of directions. The other three flows are characterized by large deviations from the expected north–south direction. One lava flow dated at 1.69 Ma (±0.02 Ma) is likely associated with a transitional field during the Gilsà subchron. The lava flow dated at 770 ka (±11 ka) coincides with the age of the Brunhes-Matuyama geomagnetic reversal and is also coeval with another intermediate flow of the same age found at Guadeloupe Island. The 617 ka (±52 ka) old unit is characterized by reversed directions that are evidently not related to the last reversal, but with other reversed polarity and transitional lava flows of the same age recorded, respectively at Mexico and La Palma island. We infer that the presence of reversed directions with the same age at distinct localities confirms that a short episode of reversed polarity has occurred during this period.

Description: Presently, most loess/palaeosol magnetic susceptibility records are interpreted as following either the wind-vigour model or the pedogenic enhancement model. However redoxomorphic processes induced by waterlogging, often referred to gleying in the loess literature, are also known to alter loess deposits but their impact on loess/palaeosol magnetic susceptibility records has received little attention. The reported rock magnetic study aims to characterize the mineral magnetic response of loess to waterlogging-induced redoxomorphic processes, thus improving our understanding of mineral magnetic changes within loess deposits with respect to environmental and climate conditions. The Nussloch loess-palaeosol deposit (Rhine Valley, Germany) was targeted because it is one of the best-studied Pleniglacial deposits for Western Europe in which numerous tundra gley intervals have been identified. Moreover, a comprehensive high-resolution environmental magnetism study has never been undertaken for this site. Various rock magnetism experiments were conducted at both room and low temperatures to characterise the composition, concentration and relative magnetic grain size of the mineral magnetic assemblage. The relative changes in magnetic parameters within the investigated loess interval are primarily controlled by (1) varying concentrations of coarse-grained ferrimagnetic particles of detrital (aeolian) origin and (2) dissolution of fine-grained ferrimagnetic particles related to in situ post-depositional alteration promoted by waterlogging-induced redoxomorphic processes. Goethite is found to be ubiquitous throughout the studied interval and is argued to have both a primary (aeolian) and secondary ( in situ ) origin. We conclude, that redoxomorphic processes induced by waterlogging, if present, will hinder the interpretation of magnetic susceptibility variations within loess and palaeosol deposits following the expected relationships dictated by the wind-vigour and the pedogenic enhancement magnetism models.

Description: Palaeosecular variation (PSV), as estimated from the scatter of remanent magnetization directions or poles, can be used to shed light to processes in the geodynamo, and potentially, to model the growth of the solid inner core. To understand the temporal aspects of the geomagnetic field behavior in the far past, we have calculated the scatter of palaeomagnetic poles (S) from a set of 55 high-quality observations derived from a new Precambrian paleomagnetic data compilation. Our analysis supports former Phanerozoic and Precambrian analyses of PSV, which favour a lower reversal rate, a higher stability of the geodynamo and a substantially smaller size of the inner core prior to 1.5 billion years ago.

Description: A palaeomagnetic study has been carried out in 29 cores drilled at six different sites from the volcanic products of Lomo Negro eruption (El Hierro, Canary Islands, Spain). Systematic thermal and alternating field demagnetization of the samples’ natural remanent magnetization revealed a northward, stable palaeomagnetic direction similar in all the samples. Rock magnetic experiments indicate that this palaeomagnetic component is carried by a mixture of high-Ti and low-Ti titanomagnetite crystals typical of basaltic lithologies that have experienced a significant degree of oxyexsolution during subaerial cooling. The well constrained palaeomagnetic direction of Lomo Negro lavas was used to perform a palaeomagnetic dating of the volcanic event, using the SHA.DIF.14k global geomagnetic model restricted for the last 3000 yr. It can be unambiguously concluded that Lomo Negro eruption occurred well before the previously proposed date of 1793 AD, with three different age ranges being statistically possible during the last 3 ka: 115 BC-7 AD, 410–626 AD and 1499–1602 AD. The calibration of a previously published non-calibrated 14 C dating suggests a XVI c. date for Lomo Negro eruption. This conclusion leaves open the possibility that the seismic crisis occurred at El Hierro in 1793 AD was related to an intrusive magmatic event that either did not reach the surface or either culminated in an unregistered submarine eruption similar to the one occurred in 2011–2012 at the southern off-shore ridge of the island.

Description: We have performed an extended palaeomagnetic study of the Oslo Graben volcanics, compared to the study of half a century ago by van Everdingen, using modern techniques and a four times larger amount of sites, plus additional rock magnetic experiments. We conclude that the average direction ( D = 204.0, I = –37.9, k = 46.9, α 95 = 2.0) and associated palaeomagnetic pole ( = 48.3, = 155.5, K = 52.2, A 95 = 1.9) of the Krokskogen and Vestfold volcanics together are statistically identical to those of the earlier study. This gives confidence in the fact that older palaeomagnetic studies can be reliable and robust, even though methods have improved. Our larger number of samples, and better age constraints, enable us to separate the data into two major intervals: the younger, on average, Krokskogen area and the older Vestfold area. The results show firstly that palaeolatitudes are slightly higher than predicted by the latest apparent polar wander path (APWP) for Eurasia by Torsvik et al. These data support an early Permian Pangaea A configuration and do not necessitate a Pangaea B configuration. The larger data set also allows us to assess the distribution of the characteristic remanent magnetization directions of the Oslo Graben in terms of geomagnetic field behaviour, which were acquired during a long period of dominantly single polarity the Permo-Carboniferous Reversed Superchron (PCRS). The distributions show a significantly lower virtual geomagnetic pole (VGP) scatter at the observed (low) latitudes than expected from a compilation from lavas of the last 5 Myr. The data do however show excellent agreement with the scatter observed both during the Cretaceous Normal Superchron and the PCRS. A comparison of the directional distributions in terms of elongation is less discriminating, since the large errors in all cases allow a fit to the predicted elongation/inclination behaviour of the TK03.GAD model.

Description: We illustrate a new imaging method to estimate the depth to the sources of potential fields and the structural index. The method consists of applying the Depth from EXtreme Point (DEXP) transformation to the ratio (R) between two different-order partial derivatives of the field. While the scaling function of the potential field depends on the structural index, we show that the scaling function of R merely depends on the difference between the two used orders of differentiation. This allows three main features to be established for the DEXP transformation of R: (1) it is independent from the structural index; (2) the estimation of the source depths is fully automatic, simply consisting in the search of position of the extreme points of the DEXP image and (3) the structural index of each source is finally determined from the scaling function or the extreme points using the estimated depth. Besides the well-known characteristics of the DEXP transformation, such as high-resolution and stability, the DEXP transformation of R enjoys one more relevant feature: it can be applied to multisource cases, yielding simultaneously correct estimations of structural index and depth for each source in the same image. However, while the DEXP transformation is a linear transformation of the field, the DEXP transformation of R is non-linear, and a procedure is described to circumvent the non-linear effects. The method is tested with synthetic examples and the estimated source parameters show a good agreement with the true values. The method was applied also to real magnetic data from the Pima copper mine, Arizona, USA, Hamrawien area, Egypt and Cataldere, Bala district of Turkey. The results are consistent with the known information about the causative sources.

Description: Variational data assimilation (4DVar) is a powerful technique for tuning dynamic models to observations, in order not only to forecast future time evolution of the system, but to make inferences about quantities that are otherwise unconstrained by observation. We apply this technique, well-grounded in meteorology and oceanography, to the Earth's core where incompressible fluid motions in an electrically conducting medium are responsible for magnetic field generation. Our dynamic model's momentum equation neglects inertia such that the entire evolution depends only on the structure of the initial magnetic field; time evolution of the system is solely governed by the equation of magnetic induction. Nevertheless the dynamic system encompasses the effects of rotation, Lorentz forces and viscosity and aims to mimic a reasonable force-balance in the Earth's core. Building on the work of Li et al. , in order to optimize the data-fit subject to the dynamics, we further develop the mathematical structure of the adjoint equations of the system. We address the feasibility of recovering 3-D spatial properties of the system using only time-varying 2-D observations of different character. Using closed-loop testing, we demonstrate the retrievability of the initial state (and thus the entire trajectory) of the system over convective timescales, when sampling in regions in which magnetic induction dominates over diffusion. The results suggest the possibility of retrieving the entire trajectory of the dynamo system of the Earth using the 400-yr model of secular variation gufm1 .

Description: We investigate polarity reversals in the geodynamo using a rotating, convection-driven dynamo model. As the flow in rapidly rotating convection is dominated by columns aligned with the axis of rotation, the focus is on the dynamics of columnar vortices. By studying the growth of a seed magnetic field to a stable axial dipole field, we show that the magnetic field acts in ways that significantly enhance the relative helicity between cyclonic and anticyclonic vortices. This flow asymmetry is the hallmark of a dipolar dynamo. Strong buoyancy, on the other hand, offsets the effect of the magnetic field, establishing parity between positive and negative vortices. As the dipole field is deprived of the helicity required to support itself, the dynamo is pushed into a reversing state. This is a likely regime for polarity reversals in the Earth's core. The integral lengthscale at which buoyancy injects energy is not significantly different from the convective flow lengthscale, which implies that buoyancy does not feed vortices at the small scales where non-linear inertia is present. The lengthscale at which the Lorentz force acts in the reversing dynamo is small, which may allow the passive presence of non-linear inertia in the small scales.

Description: A new methodology to estimate magnetotelluric (MT) tensor relationships, called Estimation of Local transfer-functIons by Combining Interstation Transfer-functions (ELICIT), is proposed whereby the MT tensor relationships of the local site are derived using only interstation transfer functions. The MT impedance tensor and the geomagnetic transfer function at the local site are characterised by combining interstation tensor relationships between electric and magnetic fields at the local site with the horizontal magnetic fields acquired at a neighbouring site. The main property of the proposed method is that the employed interstation transfer functions are independently constrained, without the need to acquire the electric and the magnetic fields at the local site simultaneously to recover the local MT tensor relationships. Due to this property, the ELICIT method offers new possibilities for MT data acquisition and processing, providing significant improvements when the magnetic time-series at the local site are affected by local noise or are truncated. Error analysis shows that, even when magnetic fields are truncated, the quality of the results obtained following the ELICIT method are similar to those we would obtain if the magnetic fields had not been truncated. Another important property is that different neighbouring sites can be used to recover the tensor relationships at the local site. Averaging of results obtained using different neighbouring sites can be performed to improve the statistics. For our example data, when the ELICIT method is used to improve the statistics, errors of the estimates for periods between 1000 and 20 000 s periodicities are clearly reduced. All interstation transfer functions are calculated doing remote reference and the bootstrap method is used to compute the errors, when necessary. Long period magnetotelluric data acquired in the Pyrenees and in the Atlas Mountains in Morocco, and magnetic data provided by Fürstenfeldbruck magnetic observatory have been used to test the proposed ELICIT method, with positive results. Due to the lack of requirement that the electric and the magnetic fields of the local site be acquired simultaneously, the proposed method also offers new possibilities for MT data acquisition, optimizing the available instrumentation.

Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc , being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.

Description: Broad-band and long period magnetotelluric (MT) data were acquired at 39 stations along five NNW-SSE profiles crossing the Iapetus Suture Zone (ISZ) in Ireland. Regional strike analyses indicate that the vast majority of the MT data is consistent with an assumption of a 2-D geo-electric strike direction. Strike is N52°E for the three easternmost profiles and N75°E for the two westernmost profiles; these directions correlate well with the observed predominant geological strike of the study region. 2-D inversions of the galvanic distortion-corrected TE and TM mode data from each profile are shown and discussed. As mapped geological variations between the neighbouring profiles suggest a heterogeneous subsurface, it is important to verify the robustness of the presence and geometries of prominent conductivity anomalies by employing 3-D forward and inverse modelling. A high conductivity layer (resistivity of 1–10 m), found at middle to lower crustal depths and presumed to be indicative of metamorphosed graphitic sediments rich in sulphides deposited during the convergence of the Laurentian and Avalonian continents, essentially constitutes the electrical signature of the ISZ. Shallow conductors observed are probably due to black shales that were widely deposited within the sedimentary accretionary wedge during Ordovician time. We interpret the moderately low resistivity at shallow depths from west to east across Ireland as indicative of an increase in maturity of the black shales in the easterly direction. From our conductivity models the southern extent of the ISZ is inferred to lie between the Navan Silvermines Fault and the Navan Tipperary Line, and shows clear resistivity contrast along all the profiles at the southern MT stations. The change in resistivity deduced from the 2-D models is spatially related to the composition of Lower Palaeozoic Ordovician, Silurian, Devonian and Carboniferous rocks. At upper mantle depths of about 60 km, a high conductivity block below the central MT stations is found to lie within the accretionary wedge of the Iapetus suture, and the location of the conductive anomaly corroborates reasonably well with the inferred spreading head of the putative Iceland plume-related magmatic intrusion. The low resistivity upper crust beneath the ISZ is indeed rich in Ordovician rocks with black shale content in the eastern as well as the central part; the western part is largely underlain by a highly resistive block of volcanic and metamorphosed rocks forming crystalline basement.

Description: This paper presents new directional archeomagnetic data from nine Meso-/Neolithic fireplaces, sampled in a cave shelter, at Arconciel, in western Switzerland. Rock magnetic measurements indicate a homogenous magnetic mineralogy in all fireplaces, with magnetite as the main magnetic carrier. The remanent magnetization is stable and generally shows one characteristic directional component. Nine new directions, which were obtained from Arconciel, are combined with 356 other archeomagnetic data from a circular area with a radius of 700 km around this site, to obtain a penalized least square spline fit for the past 9000 yr. We found in general good agreement with other local compilations, such as the Balkan curve, the regional SCHA.DIF.8k model and with lake sediments from UK, Fennoscandia and Switzerland. Nevertheless, a time lag of several centuries is observed for a declination maximum between the archeomagnetic spline fit and the other European data records around 5900 BC. This time lag is also observed in the Swiss lake sediment record; therefore we interpret this shift as a local feature of the Earth's magnetic field.

Description: In Christian religion the sunrise is of great symbolic importance. Therefore, many churches constructed in the Middle Ages point towards geographic East. Although ‘easting’ of churches actually refers to the alignment towards the azimuth of sunrise on the individual churches’ patron's day, deviation of nave alignment from the geographic East direction is often assumed to be caused by the use of magnetic compasses. Therefore, the church alignment could provide information about historical magnetic declination. We investigate 124 churches in Lower Austria and 68 in northern Germany to clarify this question as well as the ‘easting’ hypothesis. Church orientations are determined from georeferenced satellite images. Metadata such as the construction year, possible reconstructions and the church patron are gathered to determine the date when current church direction was appointed, and to perform sunrise calculations. However, due to uncertainties of construction years and the declining importance of orientation tradition after the 15th century several churches are excluded from the study. Thus, 32 churches with reliable metadata remain for evaluation in each region. The analysis reveals a preferred alignment of naves towards geographic East in Lower Austria and northern Germany. The construction and alignment of churches was often affected by the pre-existing buildings and streets or topography and natural surroundings. Therefore, deviations from geographic East are more likely caused by town or landscape. The mean deviations from magnetic East in both regions are large compared to the mean deviations from geographic East and sunrise azimuths. Hence, the use of compasses cannot be confirmed. Despite a few churches indicating orientation according to their patron's day, a general trend cannot be observed in the data reviewed.

Description: A new finite difference solution to the global geomagnetic induction problem is developed and tested, based on a modified Lorenz gauge of the magnetic vector and electric scalar potentials and implementing a novel, overset ‘Yin-Yang’ grid that avoids unnecessary mesh refinement at the geographic poles. Previously used in whole-earth mantle convection models, the overset grid is built from a pair of partially overlapping mid-latitude latitude–longitude (lat/lon) grids, one of which is rotated with respect to the other for complete coverage of the sphere. Because of this symmetry, only one set of finite difference templates is required for global discretization of the governing Maxwell equations, a redundancy that is exploited for computational efficiency and multithreaded parallelization. Comparisons between solutions obtained by the proposed method show excellent agreement with those obtained by independent integral equation methods for 1-D, 2-D and 3-D problem geometries. The computational footprint of the method is minimized through a (non-symmetric) matrix-free BiCG-STAB iterative solver which computes finite difference matrix coefficients ‘on the fly’ as needed, rather than pulling stored values from memory. Scaling of the matrix-free BiCG-STAB algorithm with problem size shows behaviour similar to that seen with the (symmetric) QMR algorithm used in the Cartesian case from which the present algorithm is based. The proposed method may therefore provide a competitive addition to the existing body of global-scale geomagnetic induction modelling algorithms, allowing for resource-efficient forward modelling as the kernel for large-scale computing such as inversion of geomagnetic response functions, computational hypothesis testing and parametric studies of mantle geodynamics and physiochemical state.

Description: We present a robust and scalable solver for time-harmonic Maxwell's equations for problems with large conductivity contrasts, wide range of frequencies, stretched grids and locally refined meshes. The solver is part of the fully distributed adaptive 3-D electromagnetic modelling scheme which employs the finite element method and unstructured non-conforming hexahedral meshes for spatial discretization using the open-source software deal.II. We use the complex-valued electric field formulation and split it into two real-valued equations for which we utilize an optimal block-diagonal pre-conditioner. Application of this pre-conditioner requires the solution of two smaller real-valued symmetric problems. We solve them by using either a direct solver or the conjugate gradient method pre-conditioned with the recently introduced auxiliary space technique. The auxiliary space pre-conditioner reformulates the original problem in form of several simpler ones, which are then solved using highly efficient algebraic multigrid methods. In this paper, we consider the magnetotelluric case and verify our numerical scheme by using COMMEMI 3-D models. Afterwards, we run a series of numerical experiments and demonstrate that the solver converges in a small number of iterations for a wide frequency range and variable problem sizes. The number of iterations is independent of the problem size, but exhibits a mild dependency on frequency. To test the stability of the method on locally refined meshes, we have implemented a residual-based a posteriori error estimator and compared it with uniform mesh refinement for problems up to 200 million unknowns. We test the scalability of the most time consuming parts of our code and show that they fulfill the strong scaling assumption as long as each MPI process possesses enough degrees of freedom to alleviate communication overburden. Finally, we refer back to a direct solver-based pre-conditioner and analyse its complexity in time. The results show that for multiple right-hand sides the direct solver-based pre-conditioner can still be faster for problems of medium size. On the other hand, it also shows non-linear growth in memory, whereas the auxiliary space method increases only linearly.

Description: The configuration of the Pangea supercontinent has been a topic of intense debate for almost half a century, a controversy that stems from discrepancies between the geology-based Pangea-A and the palaeomagnetically based Pangea-B. Recent palaeomagnetic compilations aimed at resolving this controversy have identified the poor quality of palaeomagnetic data from Gondwana for Permian times as a major obstacle. Specifically, the vast majority of Gondwanan poles come from sedimentary rocks that are prone to biases from compaction or are poorly dated. Here, we present a new palaeomagnetic pole for cratonic South America based on impact melts from the 254.7 ± 2.5 Ma Araguainha impact structure (AIS). The granite basement, the impact-generated melt sheet and veins were sampled at 28 sites (169 specimens) and provided a reliable palaeomagnetic record similar to that of volcanic rocks. Alternating field and thermal demagnetization indicate a stable characteristic remanent magnetization carried by both magnetite and haematite. All sites but one show a single palaeomagnetic direction of normal polarity with a mean direction of Dec = 357.4°; Inc = –38.9°; N  = 28; k  = 62.35; α 95  = 3.5°, yielding a palaeomagnetic pole (AIS) at Lat = –84.2; Lon = 326.6; K  = 83.5; A 95  = 3.6°; S B  = 9.6°. The new pole provides a firm constraint on the position of Gondwana which is consistent with the Pangea A configuration.

Description: Reconstructions of the Holocene geomagnetic field and how it varies on millennial timescales are important for understanding processes in the core but may also be used to study long-term solar-terrestrial relationships and as relative dating tools for geological and archaeological archives. Here, we present a new family of spherical harmonic geomagnetic field models spanning the past 9000 yr based on magnetic field directions and intensity stored in archaeological artefacts, igneous rocks and sediment records. A new modelling strategy introduces alternative data treatments with a focus on extracting more information from sedimentary data. To reduce the influence of a few individual records all sedimentary data are resampled in 50-yr bins, which also means that more weight is given to archaeomagnetic data during the inversion. The sedimentary declination data are treated as relative values and adjusted iteratively based on prior information. Finally, an alternative way of treating the sediment data chronologies has enabled us to both assess the likely range of age uncertainties, often up to and possibly exceeding 500 yr and adjust the timescale of each record based on comparisons with predictions from a preliminary model. As a result of the data adjustments, power has been shifted from quadrupole and octupole to higher degrees compared with previous Holocene geomagnetic field models. We find evidence for dominantly westward drift of northern high latitude high intensity flux patches at the core mantle boundary for the last 4000 yr. The new models also show intermittent occurrence of reversed flux at the edge of or inside the inner core tangent cylinder, possibly originating from the equator.

Description: Several recent studies have used palaeomagnetic estimates of the virtual axial dipole moment to construct a quantitative stochastic model for fluctuations and reversals in the Earth's dipole field. We investigate the physical significance of the terms in a standard stochastic (Langevin) model using output from a numerical geodynamo model. The first term, known as the drift term, characterizes the slow adjustment of the dipole field toward a time-averaged state. We find that the timescale for this slow adjustment is set by the magnetic decay time of dipole fluctuations. These fluctuations are typically be represented by the first few decay modes. The second term is often called the noise term because it characterizes the influence of short-period convective fluctuations in the core. We establish a connection between the noise term and the rms variation in magnetic induction. Applying these results to the palaeomagnetic field suggests that the rms variation in dipole generation exceeds the mean rate of generation. Such large fluctuations may be necessary to permit magnetic reversals. Palaeomagnetic estimates of the drift term favour a high electrical conductivity in the core. A lower bound on electrical conductivity is 0.6 x 10 6 S m –1 . Similarly, we establish an upper bound on turbulent magnetic diffusivity (0.8 m 2 s –1 ), although realistic estimates may be much less.

Description: We demonstrate that first differences of polar orbiting satellite magnetic data in the along-track direction can be used to obtain high resolution models of the lithospheric field. Along-track differences approximate the north–south magnetic field gradients for non-polar latitudes. In a test case, using 2 yr of low altitude data from the CHAMP satellite, we show that use of along-track differences of vector field data results in an enhanced recovery of the small scale lithospheric field, compared to the use of the vector field data themselves. We show that the along-track technique performs especially well in the estimation of near zonal spherical harmonic coefficients. Moreover, lithospheric field models determined using along-track differences are found to be less sensitive to the presence of unmodelled external field contributions and problems associated with the polar gap are ameliorated. Experiments in modelling the Earth's lithospheric magnetic field with along-track differences are presented here as a proof of concept. We anticipate that use of such along-track differences in combination with east–west field differences, as are now provided by the Swarm satellite constellation, will be important in building the next generation of lithospheric field models.

Description: We develop an singular value decomposition-based compression of the Green's function matrix of an electromagnetic integral equation forward solver for global geomagnetic induction, on top of an fast Fourier transform reduction of the system to a block-diagonal form. With this approach, the memory usage and CPU time of Krylov subspace iterative solutions are significantly reduced at a very small cost of accuracy, making the accelerated forward solver well suited for 3-D inversions as well as forward simulations with multiple sources.

Description: The Fisher distribution is central to palaeomagnetism but presents several problems when used to characterize geomagnetic field directions as observed in sequences of volcanic rocks. First, it introduces a shallowing effect when used to define the mean of any group of directional unit vectors. This is problematic because it can suggest the presence of persistent non-axial dipole components when none are present. More importantly, it fails to capture the observed ‘long tail’ in distributions of both directions and associated virtual geomagnetic poles in terms of angular distance from a central direction. To achieve a good fit to data, it therefore requires the introduction of a second distribution (and therefore the estimation of additional parameters) or the arbitrary removal of data. Here we present a new distribution to describe palaeomagnetic directions and demonstrate that it overcomes both of these problems, generating robust indicators of both the central direction (or pole position) and the spread of palaeomagnetic data as defined by unit vectors. Starting from the assumption that poles (or directions) have an expected colatitude, rather than a mean location, we derive the spherical exponential distribution. We demonstrate that this new distribution provides a good fit to palaeomagnetic data sets from seven large igneous provinces between 15 and 65 Ma and also those produced by numerical dynamo models. We also use it to derive a new shape parameter which may be used as a diagnostic tool for testing goodness of fit of models to data and use this to argue for a shift in geomagnetic behaviour between 5 and 15 Ma. Furthermore, we point out that this new statistic can be used to determine the most appropriate distribution to be used when constructing confidence limits for poles.

Description: Haematite pigment is a common constituent of sedimentary rocks, but its contribution to the natural remanent magnetization of rocks is poorly understood. Here, we describe magnetic properties of two distinct pigment types that produce a characteristic decorative ‘print stone’ found in the ~2.5 Ga Mount McRae Shale Formation, Hamersley Province, Western Australia. Distinct magnetic remanence directions observed in the Print Stone can be correlated to each pigment type. By comparison with the Australian apparent polar wander path, the remanence carried by uniformly distributed pigment can be dated to ~15–25 Ma, while two age options, the Mesoproterozoic (~1.5 Ga) or the middle Carboniferous (~320–310 Ma), are permissible for the remanence carried by the pigment responsible for the distinctive ‘newsprint’ pattern. Magnetic properties and demagnetization characteristics of the different pigment types overlap significantly, and thus are not predictive of the dominant remanence carrier. Magnetic characteristics of the uniformly distributed pigment vary significantly on short spatial scales. Strong local control on pigment formation raises the possibility that a primary remanent magnetization may survive locally in pockets within sedimentary red bed formations.

Description: Remanent magnetizations of magnetites between single-domain (SD) threshold size (0.1 μm) and 20 μm have SD-like intensities and coercivities. This paper shows for the first time that magnetite's induced magnetization also has pseudo-single-domain behaviour. The first part of the paper reports temperature-dependent initial susceptibility data, k 0 ( T ), of sized magnetites and assesses their granulometric potential. The second part transforms coercive force data, H c ( T ), for the same magnetites into simulated k 0 ( T ) curves. The third part considers k 0 ( T ) results of coarse-grained mafic rocks as candidate sources of deep-seated magnetic anomalies. High-temperature susceptibility k 0 measured with a Kappabridge for eight fractions of crushed natural magnetites (median sizes of 0.6, 1, 3, 6, 9, 14, 110 and 135 μm) shows a progressive increase in the height of the Hopkinson peak below the Curie point as grain size decreases. The trend is systematic and has granulometric potential in the 1–14 μm range. Self-demagnetization should produce almost flat k 0 ( T ) in grains larger than SD size but experimentally, well-defined Hopkinson peaks are not limited to the finest grains. 1-μm magnetites have a peak 1.5 times k 0 at 20 °C and 14-μm grains have a peak of 1.25. Only 110 and 135 μm grains have T -independent k 0 . Using an empirical relationship between coercive force H c and k 0 , H c ( T ) data for the sized magnetites were used to simulate k 0 ( T ) results. A hump in the k 0 heating curve around 250 °C was traced to annealing out internal strains, evident in H c data measured in first heatings. For sizes ≤6 μm, observed Hopkinson peaks were smaller than predicted, possibly because of a previously unrecognized grain-size dependence of the empirical constant relating H c and k 0 . Two crystalline rocks, a gabbro and a diabase, combine SD-like Hopkinson peaks and multidomain (MD) flat ramps in their k 0 ( T ) data. In the diabase, a Hopkinson peak is prominent in separated plagioclase grains containing submicron magnetite, but is masked in whole-rock data. The gabbro has a clear superposition of SD and MD k 0 ( T ) functions in its whole-rock data, with a Hopkinson peak of 1.35. If oceanic layer-3 gabbros have similar susceptibility enhancement above 500 °C, they could be more important magnetic anomaly sources than room-temperature k 0 measurements on dredged or fault-uplifted samples would suggest.

Description: Conventionally, overall gene expressions from microarrays are used to infer gene networks, but it is challenging to account splicing isoforms. High-throughput RNA Sequencing has made splice variant profiling practical. However, its true merit in quantifying splicing isoforms and isoform-specific exon expressions is not well explored in inferring gene networks. This study demonstrates SpliceNet, a method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using large dimensional trace. It goes beyond differentially expressed genes and infers splicing isoform network changes between normal and diseased samples. It eases the sample size bottleneck; evaluations on simulated data and lung cancer-specific ERBB2 and MAPK signaling pathways, with varying number of samples, evince the merit in handling high exon to sample size ratio datasets. Inferred network rewiring of well established Bcl-x and EGFR centered networks from lung adenocarcinoma expression data is in good agreement with literature. Gene level evaluations demonstrate a substantial performance of SpliceNet over canonical correlation analysis, a method that is currently applied to exon level RNA-Seq data. SpliceNet can also be applied to exon array data. SpliceNet is distributed as an R package available at http://www.jjwanglab.org/SpliceNet .

Description: We present a new approach to automatic training of a eukaryotic ab initio gene finding algorithm. With the advent of Next-Generation Sequencing, automatic training has become paramount, allowing genome annotation pipelines to keep pace with the speed of genome sequencing. Earlier we developed GeneMark-ES, currently the only gene finding algorithm for eukaryotic genomes that performs automatic training in unsupervised ab initio mode. The new algorithm, GeneMark-ET augments GeneMark-ES with a novel method that integrates RNA-Seq read alignments into the self-training procedure. Use of ‘assembled’ RNA-Seq transcripts is far from trivial; significant error rate of assembly was revealed in recent assessments. We demonstrated in computational experiments that the proposed method of incorporation of ‘unassembled’ RNA-Seq reads improves the accuracy of gene prediction; particularly, for the 1.3 GB genome of Aedes aegypti the mean value of prediction Sensitivity and Specificity at the gene level increased over GeneMark-ES by 24.5%. In the current surge of genomic data when the need for accurate sequence annotation is higher than ever, GeneMark-ET will be a valuable addition to the narrow arsenal of automatic gene prediction tools.

Description: We investigate the influence of different thermal and velocity boundary conditions on numerical geodynamo models. We concentrate on the implications for magnetic field morphology, heat transport scaling laws, force balances and generation mechanisms. The field morphology most strongly depends on the local Rossby number, but there is some variation in the dipolarity of the field with boundary condition. Scaling laws also depend on the boundary conditions, but a diffusivity-free scaling is a good first order approximation for all our dipolar models. Our multipolar models, however, obey different scaling laws from dipolar models implying a different force balance in these models. We find that our dipolar models have a stronger degree of Lorentz–Coriolis balance compared to our multipolar models which have a stronger degree of Lorentz-inertial balance.The models with a stronger Lorentz–Coriolis dominance can be generated by either α, α 2 or α 2 mechanisms whereas the models with a stronger Lorentz-inertial balance are all α 2 dynamos. These results imply that some caution is necessary when extrapolating results from dynamo models to Earth-like parameters since the choice of boundary conditions can have important effects.

Description: Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ~8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.

Description: Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. The recent expansion of sequenced genomes offers the opportunity to study ISs comprehensively, but this requires efficient and accurate tools for IS annotation. We have developed an open-source program called OASIS, or Optimized Annotation System for Insertion Sequences, which automatically annotates ISs within sequenced genomes. OASIS annotations of 1737 bacterial and archaeal genomes offered an unprecedented opportunity to examine IS evolution. At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa. This may indicate differential loss, barriers to exchange and/or insufficient time to equilibrate across clades. The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes 〉2 Mb. At the finer scale of recently diverged genomes, the proportion of shared IS content falls sharply, suggesting loss and/or emergence of barriers to successful cross-infection occurs rapidly. Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.

Description: The study of cell-population heterogeneity in a range of biological systems, from viruses to bacterial isolates to tumor samples, has been transformed by recent advances in sequencing throughput. While the high-coverage afforded can be used, in principle, to identify very rare variants in a population, existing ad hoc approaches frequently fail to distinguish true variants from sequencing errors. We report a method (LoFreq) that models sequencing run-specific error rates to accurately call variants occurring in 〈0.05% of a population. Using simulated and real datasets (viral, bacterial and human), we show that LoFreq has near-perfect specificity, with significantly improved sensitivity compared with existing methods and can efficiently analyze deep Illumina sequencing datasets without resorting to approximations or heuristics. We also present experimental validation for LoFreq on two different platforms (Fluidigm and Sequenom) and its application to call rare somatic variants from exome sequencing datasets for gastric cancer. Source code and executables for LoFreq are freely available at http://sourceforge.net/projects/lofreq/ .

Description: Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling data enable identification of novel isoforms, quantification of known isoforms and detection of changes in transcriptional or RNA-processing activity. Existing approaches to detect differential isoform abundance between samples either require a complete isoform annotation or fall short in providing statistically robust and calibrated significance estimates. Here, we propose a suite of statistical tests to address these open needs: a parametric test that uses known isoform annotations to detect changes in relative isoform abundance and a non-parametric test that detects differential read coverages and can be applied when isoform annotations are not available. Both methods account for the discrete nature of read counts and the inherent biological variability. We demonstrate that these tests compare favorably to previous methods, both in terms of accuracy and statistical calibrations. We use these techniques to analyze RNA-Seq libraries from Arabidopsis thaliana and Drosophila melanogaster. The identified differential RNA processing events were consistent with RT–qPCR measurements and previous studies. The proposed toolkit is available from http://bioweb.me/rdiff and enables in-depth analyses of transcriptomes, with or without available isoform annotation.

Description: The absence of a quality control (QC) system is a major weakness for the comparative analysis of genome-wide profiles generated by next-generation sequencing (NGS). This concerns particularly genome binding/occupancy profiling assays like chromatin immunoprecipitation (ChIP-seq) but also related enrichment-based studies like methylated DNA immunoprecipitation/methylated DNA binding domain sequencing, global run on sequencing or RNA-seq. Importantly, QC assessment may significantly improve multidimensional comparisons that have great promise for extracting information from combinatorial analyses of the global profiles established for chromatin modifications, the bindings of epigenetic and chromatin-modifying enzymes/machineries, RNA polymerases and transcription factors and total, nascent or ribosome-bound RNAs. Here we present an approach that associates global and local QC indicators to ChIP-seq data sets as well as to a variety of enrichment-based studies by NGS. This QC system was used to certify 〉5600 publicly available data sets, hosted in a database for data mining and comparative QC analyses.

Description: Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.

Description: The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments. Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth. We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions. Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line comparisons among various chromatin regions for four human cell-lines (K562, GM12878, IMR90 and H1hESC), which shows that the openness of chromatin region is well correlated with chromatin function. This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used.

Description: Lake sediments are excellent sources of palaeoenvironmental and palaeoclimatic information because they provide continuous and high-resolution records. South America is of particular interest because it is the only landmass that stretches southward into the Pacific and Atlantic Oceans towards Antarctica. The aim of this study is to explore the relationship of magnetic parameters with elemental and palaeobiological data of Laguna Potrok Aike to develop a model of lake-level changes and related hydrological and climatic fluctuations. Magnetic measurements were performed on subsamples from 15 500 cal. BP to the present, and associated rock magnetic parameters were calculated to infer magnetic mineralogy, concentration and grain size. According to the model, parameters dependent on magnetic concentration and grain size are directly related to lake-level changes. During dry periods, the remanent coercivity displays high values, whereas the proportion of magnetite is relatively low. Low percentages of greigite are observed, indicating that the water of the lake was stratified at least four times during the studied period, at approximately 10 300, 8900, 8500 and 8300 cal. BP. The preservation of greigite by inhibiting its complete transformation into pyrite is associated with a rapid burial that occurs with high sedimentation rates. Thermal stratification could be caused by a slight cooling in the area triggered by a weakening of the Westerlies and/or low activity of the sun, sum to the effect of a flood of melt water in the North Atlantic.

Description: Measurement of magnetic vector or tensor quantities, namely of field or field gradient, delivers more details of the underlying geological setting in geomagnetic prospection than a scalar measurement of a single component or of the scalar total magnetic intensity. Currently, highest measurement resolutions are achievable with superconducting quantum interference device (SQUID)-based systems. Due to technological limitations, it is necessary to suppress the parasitic magnetic field response from the SQUID gradiometer signals, which are a superposition of one tensor component and all three orthogonal magnetic field components. This in turn requires an accurate estimation of the local magnetic field. Such a measurement can itself be achieved via three additional orthogonal SQUID reference magnetometers. It is the calibration of such a SQUID reference vector magnetometer system that is the subject of this paper. A number of vector magnetometer calibration methods are described in the literature. We present two methods that we have implemented and compared, for their suitability of rapid data processing and integration into a full tensor magnetic gradiometry, SQUID-based, system. We conclude that the calibration routines must necessarily model fabrication misalignments, field offset and scale factors, and include comparison with a reference magnetic field. In order to enable fast processing on site, the software must be able to function as a stand-alone toolbox.

Description: Motional induction in the ocean by tides has long been observed by both land and satellite measurements of magnetic fields. While these signals are weak (~10 nT) when compared to the main magnetic field, their persistent nature makes them important for consideration during geomagnetic field modelling. Previous studies have reported several discrepancies between observations and numerical predictions of the tidal magnetic signals and those studies were inconclusive of the source of the error. We address this issue by (1) analysing magnetometer data from ocean-bottom stations, where the low-noise and high-signal environment is most suitable for detecting the weak tidal magnetic signals, (2) by numerically predicting the magnetic field with a spatial resolution that is 16 times higher than the previous studies and (3) by using four different models of upper-mantle conductivity. We use vector magnetic data from six ocean-bottom electromagnetic (OBEM) stations located in the Northwestern Pacific Ocean. The OBEM tidal amplitudes were derived using an iteratively re-weighted least-squares (IRLS) method and by limiting the analysis of lunar semidiurnal (M2), lunar elliptic semidinurnal (N2) and diurnal (O1) tidal modes to the night-time. Using a 3-D electromagnetic induction solver and the TPX07.2 tidal model, we predict the tidal magnetic signal. We use earth models with non-uniform oceans and four 1-D mantle sections underneath taken from Kuvshinov and Olsen, Shimizu et al. and Baba et al. to compare the effect of upper-mantle conductivity. We find that in general, the predictions and observations match within 10–70 per cent across all the stations for each of the tidal modes. The median normalized percent difference (NPD) between observed and predicted amplitudes for the tidal modes M2, N2 and O1 were 15 per cent, 47 per cent and 98 per cent, respectively, for all the stations and models. At the majority of stations, and for each of the tidal modes, the higher resolution (0.25° 0.25°) modelling gave amplitudes consistently closer to the observations than the lower resolution (1° 1°) modelling. The difference in lithospheric resistance east and west of the Izu–Bonin trench system seems to be affecting the model response and observations in the O1 tidal mode. This response is not seen in the M2 and N2 modes, thereby indicating that the O1 mode is more sensitive to lithospheric resistance.

Description: Magnetotelluric observations over one or 2-D structures that are distorted by 3-D electro-galvanic effects, need to be corrected for their proper conversion into reliable images of the subsurface electrical resistivity distribution. One of the most widely used approaches for correcting the data is the Groom–Bailey decomposition of the impedance tensor in terms of the unknown parameters of strike, twist and shear, along with the also unknown 2-D impedances. The standard approach for recovering the 2-D impedances is to solve numerically for all the unknowns as a non-linear inverse problem. In this work, we pose the recovery of the undistorted impedances in terms of a quadratic equation whose solutions filter out the distortions after a final tune for the appropriate shear parameter. The formula relies on two known invariants of the impedance tensor, the series and parallel invariants that have special immunity to some of the distorting parameters. Compared with the standard numerical recovery, the analytical solution provides more accurate results; they are clear-cut for both amplitudes and phases. The recovered amplitudes of the impedance are independent of strike, twist and shear, and the phases, in addition, of static effects. The recovery formula is transparent to random noise; hence the data preserve the original uncertainties. The applications to individual soundings of the COPROD2S1 data set and to a profile over a seismogenic region in Baja California, illustrate the effectiveness of the approach.

Description: Great progress has been made in the numerical simulation of planetary dynamos, though these numerical experiments still operate in a regime very far from the planets. For example, it seems unlikely that viscous forces are at all significant in planetary interiors, yet some of the simulations display a significant dependence on viscosity, and indeed in some of the simulations the dynamo mechanism is itself viscously driven, taking the form of helical Ekman pumping within columnar convection rolls. Given the similarity of the external magnetic fields observed in the terrestrial planets and gas giants, and the extremely small value of the Ekman number in all such cases, it seems natural to suppose that the underlying dynamo mechanism in these planets is simple, robust, independent of viscosity and insensitive to mechanical boundary conditions. A key step to identifying this mechanism is to determine the source of helicity in planetary cores, which itself should be robust, independent of viscosity and insensitive to boundary conditions. In this paper, we explore the possibility that the helicity in the core of the Earth arises from the spontaneous emission of inertial waves, driven by the equatorial heat flux in the outer core. We also ask if a similar mechanism might operate in other planets, and perhaps act to supplement the helicity driven by Ekman pumping in the (viscous) numerical simulations. We demonstrate that such waves do indeed produce the required helicity distribution outside the tangent cylinder. Moreover, we show that these waves inevitably propagate along the axis of the columnar vortices, and indeed they are the very mechanism by which the columnar vortices form in the first place and the means by which the columns subsequently evolve. We also calculate the emf induced by such axially propagating inertial waves and show that, in principle, this emf is sufficient to support a self-sustaining dynamo of the α 2 type. Finally, we derive the scaling laws for this kind of inertial-wave dynamo. We compare these predictions with the (imperfect) simulations, and also with what little we know about the Earth's core. The numerical experiments fall into two categories; the slowly rotating simulations which cannot sustain inertial waves at the small scales and the rapidly rotating (planet-like) ones which can. Our scaling laws are consistent with the latter class of simulations, and also with what we know about the Earth.

Description: The main sources of magnetic minerals in soils unaffected by anthropogenic pollution are iron oxides and hydroxides derived from parent materials through soil formation processes. Soil magnetic minerals can be used as indicators of environmental factors including soil forming processes, degree of pedogenesis, weathering processes and biological activities. In this study measurements of magnetic susceptibility are used to detect the presence and the concentration of soil magnetic minerals in topsoil and bulk samples in a small cultivated field, which forms a hydrological unit that can be considered to be representative of the rainfed agroecosystems of Mediterranean mountain environments. Additional magnetic studies such as isothermal remanent magnetization (IRM), anhysteretic remanent magnetization (ARM) and thermomagnetic measurements are used to identify and characterize the magnetic mineralogy of soil minerals. The objectives were to analyse the spatial variability of the magnetic parameters to assess whether topographic factors, soil redistribution processes, and soil properties such as soil texture, organic matter and carbonate contents analysed in this study, are related to the spatial distribution pattern of magnetic properties. The medians of mass specific magnetic susceptibility at low frequency ( lf ) were 36.0 and 31.1 10 –8 m 3 kg –1 in bulk and topsoil samples respectively. High correlation coefficients were found between the lf in topsoil and bulk core samples ( r  = 0.951, p  〈 0.01). In addition, volumetric magnetic susceptibility was measured in situ in the field ( is ) and values varied from 13.3 to 64.0 10 –5 SI. High correlation coefficients were found between lf in topsoil measured in the laboratory and volumetric magnetic susceptibility field measurements ( r  = 0.894, p  〈 0.01). The results obtained from magnetic studies such as IRM, ARM and thermomagnetic measurements show the presence of magnetite, which is the predominant magnetic carrier, and hematite. The predominance of superparamagnetic minerals in upper soil layers suggests enrichment in pedogenic minerals. The finer soil particles, the organic matter content and the magnetic susceptibility values are statistically correlated and their spatial variability is related to similar physical processes. Runoff redistributes soil components including magnetic minerals and exports fine particles out the field. This research contributed to further knowledge on the application of soil magnetic properties to derive useful information on soil processes in Mediterranean cultivated soils.

Description: The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (〈10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance.

Description: State of the art numerical models of the Geodynamo are still performed in a parameter regime extremely remote from the values relevant to the physics of the Earth's core. In order to establish a connection between dynamo modelling and the geophysical motivation, it is necessary to use scaling laws. Such scaling laws establish the dependence of essential quantities (such as the magnetic field strength) on measured or controlled quantities. They allow for a direct confrontation of advanced models with geophysical constraints. We combine a numerical approach, based on a multiple linear regression method in the form of power laws, applied to a database of 102 direct numerical simulations (courtesy of U. Christensen), and a physical approach, based on energetics and forces balances. We show that previous empirical scaling laws for the magnetic field strength essentially reflect the statistical balance between energy production and dissipation for saturated dynamos. Such power based scaling laws are thus necessarily valid for any dynamo in statistical equilibrium and applicable to any numerical model, irrespectively of the dynamo mechanism. We show that direct numerical fits can provide contradictory results owing to biases in the parameters space covered in the numerics and to the role of a priori hypothesis on the fraction of ohmic dissipation. We introduce predictive scaling laws, that is relations involving input parameters of the governing equations only. We guide our reasoning on physical considerations. We show that our predictive scaling laws can properly describe the numerical database and reflect the dominant forces balance at work in these numerical simulations. We highlight the dependence of the magnetic field strength on the rotation rate. Finally, our results stress that available numerical models operate in a viscous dynamical regime, which is not relevant to the Earth's core.

Description: High-quality palaeomagnetic data for the early Carboniferous of Central Asia are scarce and the palaeogeographic evolution of this area prior to final amalgamation of the region east of the Ural mountains is still rather obscure. Here, we present palaeomagnetic data for early Carboniferous deposits from two areas in the Kyrgyz North Tianshan (NTS). Detailed rock-magnetic analysis indicates the presence of magnetite and haematite as magnetic carriers in these red sediments. In the Kazakh basin section (KEL), we identify a high-temperature component (HTC) of magnetization during stepwise thermal demagnetization at temperatures of up to ~680 °C yielding a site mean direction of D  = 176.2°, I  = –36.4°, k  = 57.4 and α 95  = 8.9° after tilt correction. Two HTCs of magnetization were identified in samples from the Sonkul Basin (DUN) with maximum blocking temperatures of ~600 °C (magnetite) and ~680 °C (haematite). The magnetite component was also identified with alternating field demagnetization. The resulting site mean directions for these two components identified in 16 and 14 sites, respectively, are D  = 149.3°, I  = –50.3°, k  = 73.6 and α 95  = 4.3° for the magnetite and D  = 139.6°, I  = –35.1°, k  = 71.6 and α 95  = 4.7° for the haematite component. All three mean directions show a significant increase of the precision parameter k after tilt correction indicating acquisition of the high-temperature magnetization prior to the main folding event in the Jurassic. We explain the difference of the two components of DUN by a process of inclination bias due to compaction to which the platy haematite particles are more susceptible. Applying the elongation-inclination (E/I) method to directional data from over 100 individual samples from location DUN results in a negligible correction for the magnetite component (〈5°), whereas the inclination of the haematite component corrects from –35.0° to –50.3° ( f  = 0.6, error interval –41.4° to –57.9°), which is then equal to the uncorrected magnetite inclination. The small number of samples from section KEL does not allow application of the E/I technique and inclination correction based on high field anisotropy of isothermal remanent magnetization was applied, yielding a corrected inclination of –75.2° ± 4°. Assuming comparable degrees of compaction for both study areas and applying the flattening factor obtained in DUN on samples from KEL, however, would result in comparable inclinations. The identification of inclination shallowing at both sections indicates that the age of magnetization is close to the deposition age. Assuming a reversed polarity of the directions from both areas results in palaeolatitudes of ~30°N for section DUN and ~60°N for the anisotropy-based correction of section KEL. The large difference, however, is geologically very unlikely. The inclination of the magnetite component of DUN (unaffected by inclination shallowing) favours a palaeoposition of ~30°N. This is supported by the inclination shallowing corrected haematite component of DUN yielding a comparable inclination. Therefore, our results indicate that the NTS domain was situated at ~30°N in the early Carboniferous. Furthermore, the NTS zone was probably not connected to Baltica or Siberia prior to the late Palaeozoic.

Description: An exploratory 3-D model of the electrical conductivity structure of the Australian continent is presented. The model is derived from the inversion of vertical magnetic-field transfer functions from the Australia-wide Array of Geomagnetic Stations. Crustal conductivity anomalies evident in the model are consistent with those previously mapped by independent magnetometer array studies and new electrical structures are suggested in the upper mantle. The model represents a seamless continent-scale basis for further models likely to be derived from subsequent studies. The model reveals three upper-mantle enhanced-conductivity anomalies beneath Archaean cratonic regions and two upper-mantle anomalies beneath Phanerozoic terranes in eastern Australia. Two of these anomalies have been investigated by recent magnetotelluric (MT) surveys, one in the Yilgarn Craton–Officer Basin–Musgrave Block the other in the Gawler Craton region, and are consistent with the MT results. Across much of central Australia enhanced conductivity at depths of 50–100 km is observed in the model. This region corresponds well with a recognized seismic velocity gradient at 75–100 km. Conductivity differences are also observed beneath Archaean cratons in Western Australia. The Pilbara Craton is represented as an enhanced conductivity anomaly at about 100 km, corresponding well with the lower-velocity anomaly evident in surface wave tomography models. The Yilgarn Craton is imaged as a low-conductivity body, with conductivity two orders of magnitude lower than the Pilbara Craton, continuing to greater depths.

Description: This paper presents new directional archeomagnetic data from nine Meso-/Neolithic fireplaces, sampled in a cave shelter, at Arconciel, in western Switzerland. Rock magnetic measurements indicate a homogenous magnetic mineralogy in all fireplaces, with magnetite as the main magnetic carrier. The remanent magnetization is stable and generally shows one characteristic directional component. Nine new directions, which were obtained from Arconciel, are combined with 356 other archeomagnetic data from a circular area with a radius of 700 km around this site, to obtain a penalized least square spline fit for the past 9000 yr. We found in general good agreement with other local compilations, such as the Balkan curve, the regional SCHA.DIF.8k model and with lake sediments from UK, Fennoscandia and Switzerland. Nevertheless, a time lag of several centuries is observed for a declination maximum between the archeomagnetic spline fit and the other European data records around 5900 BC. This time lag is also observed in the Swiss lake sediment record; therefore we interpret this shift as a local feature of the Earth's magnetic field.

Description: We present a new approach for 2-D magnetotelluric forward numerical modelling in contrast to traditional numerical methods like finite elements or finite differences. The method used for solving the partial differential equations is based on a mesh-free technique which does not need an underlaying mesh or grid. We use the Meshless Local Petrov–Galerkin (MLPG) method in combination with radial basis functions to simulate the response of a given conductivity model to a plane-wave source. We compare the mesh-free solution with known simulation programs and simple analytical solutions. Furthermore, we discuss the new magnetotelluric modelling method in terms of implementation and stability. First, we study the convergence and discretization errors of the new method with a simple half-space conductivity model. Then we compare our mesh-free simulation results with simple 2-D conductivity models with the results of a well-known finite element program. In the end, we provide a smooth conductivity model calculated with the mesh-free approach. The modelling results, even with randomly distributed nodes, are in a good agreement with those obtained by the finite element method.

Description: Determining the taxonomic lineage of DNA sequences is an important step in metagenomic analysis. Short DNA fragments from next-generation sequencing projects and microbes that lack close relatives in reference sequenced genome databases pose significant problems to taxonomic attribution methods. Our new classification algorithm, RITA (Rapid Identification of Taxonomic Assignments), uses the agreement between composition and homology to accurately classify sequences as short as 50 nt in length by assigning them to different classification groups with varying degrees of confidence. RITA is much faster than the hybrid PhymmBL approach when comparable homology search algorithms are used, and achieves slightly better accuracy than PhymmBL on an artificial metagenome. RITA can also incorporate prior knowledge about taxonomic distributions to increase the accuracy of assignments in data sets with varying degrees of taxonomic novelty, and classified sequences with higher precision than the current best rank-flexible classifier. The accuracy on short reads can be increased by exploiting paired-end information, if available, which we demonstrate on a recently published bovine rumen data set. Finally, we develop a variant of RITA that incorporates accelerated homology search techniques, and generate predictions on a set of human gut metagenomes that were previously assigned to different ‘enterotypes’. RITA is freely available in Web server and standalone versions.

Description: The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana , suggesting an ability to discover potential unstable repeats.