Stephens Model Research Articles

Low-frequency electrodynamics in the mixed state of superconducting NbN and a-MoGe films using two-coil mutual inductance technique

We investigate the low-frequency electrodynamics in the vortex state of two type-II superconducting films, namely, a moderate-to-strongly pinned Niobium Nitride (NbN) and a very weakly pinned amorphous Molybdenum Germanium (a-MoGe) film. We employ a two-coil mutual inductance technique to extract the complex penetration depth, λ~ . The sample response is studied through the temperature variation of λ~ in the mixed state, where we employ a model developed by Coffey and Clem (the CC model) to extract different vortex lattice (VL) parameters, such as the restoring pinning force constant (Labusch parameter), VL drag coefficient and pinning potential barrier. We observe that a consistent description of the inductive and dissipative part of the response is only possible when we take the viscous drag on the vortices to be several orders of magnitude larger than the viscous drag estimated from the Bardeen–Stephen model.

Two-stage strategy using denoising autoencoders for robust reference-free genotype imputation with missing input genotypes.

Widely used genotype imputation methods are based on the Li and Stephens model, which assumes that new haplotypes can be represented by modifying existing haplotypes in a reference panel through mutations and recombinations. These methods use genotypes from SNP arrays as inputs to estimate haplotypes that align with the input genotypes by analyzing recombination patterns within a reference panel, and then infer unobserved variants. While these methods require reference panels in an identifiable form, their public use is limited due to privacy and consent concerns. One strategy to overcome these limitations is to use de-identified haplotype information, such as summary statistics or model parameters. Advances in deep learning (DL) offer the potential to develop imputation methods that use haplotype information in a reference-free manner by handling it as model parameters, while maintaining comparable imputation accuracy to methods based on the Li and Stephens model. Here, we provide a brief introduction to DL-based reference-free genotype imputation methods, including RNN-IMP, developed by our research group. We then evaluate the performance of RNN-IMP against widely-used Li and Stephens model-based imputation methods in terms of accuracy (R2), using the 1000 Genomes Project Phase 3 dataset and corresponding simulated Omni2.5 SNP genotype data. Although RNN-IMP is sensitive to missing values in input genotypes, we propose a two-stage imputation strategy: missing genotypes are first imputed using denoising autoencoders; RNN-IMP then processes these imputed genotypes. This approach restores the imputation accuracy that is degraded by missing values, enhancing the practical use of RNN-IMP.

Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model.

The Li and Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel. For small panels, the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics. However, LS becomes inefficient when sample size is large, because of its linear time complexity. Recently the PBWT, an efficient data structure capturing the local haplotype matching among haplotypes, was proposed to offer a fast method for giving some optimal solution (Viterbi) to the LS HMM. Previously, we introduced the minimal positional substring cover (MPSC) problem as an alternative formulation of LS whose objective is to cover a query haplotype by a minimum number of segments from haplotypes in a reference panel. The MPSC formulation allows the generation of a haplotype threading in time constant to sample size (O(N)). This allows haplotype threading on very large biobank-scale panels on which the LS model is infeasible. Here, we present new results on the solution space of the MPSC. In addition, we derived a number of optimal algorithms for MPSC, including solution enumerations, the length maximal MPSC, and h-MPSC solutions. In doing so, our algorithms reveal the solution space of LS for large panels. We show that our method is informative in terms of revealing the characteristics of biobank-scale data sets and can improve genotype imputation.

Fast, accurate local ancestry inference with FLARE

Local ancestry is the source ancestry at each point in the genome of an admixed individual. Inferred local ancestry is used for admixture mapping and population genetic analyses. We present FLARE (fast local ancestry estimation), a method for local ancestry inference. FLARE achieves high accuracy through the use of an extended Li and Stephens model, and it achieves exceptional computational performance through incorporation of computational techniques developed for genotype imputation. Memory requirements are reduced through on-the-fly compression of reference haplotypes and stored checkpoints. Computation time is reduced through the use of composite reference haplotypes. These techniques allow FLARE to scale to datasets with hundreds of thousands of sequenced individuals and to provide superior accuracy on large-scale data. FLARE is open source and available at https://github.com/browning-lab/flare.

Achieving improved accuracy for imputation of ancientDNA.

Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data. We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU. The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser. Supplementary information is available at Bioinformatics online.

An average-case sublinear forward algorithm for the haploid Li and Stephens model

BackgroundHidden Markov models of haplotype inheritance such as the Li and Stephens model allow for computationally tractable probability calculations using the forward algorithm as long as the representative reference panel used in the model is sufficiently small. Specifically, the monoploid Li and Stephens model and its variants are linear in reference panel size unless heuristic approximations are used. However, sequencing projects numbering in the thousands to hundreds of thousands of individuals are underway, and others numbering in the millions are anticipated.ResultsTo make the forward algorithm for the haploid Li and Stephens model computationally tractable for these datasets, we have created a numerically exact version of the algorithm with observed average case sublinear runtime with respect to reference panel size k when tested against the 1000 Genomes dataset.ConclusionsWe show a forward algorithm which avoids any tradeoff between runtime and model complexity. Our algorithm makes use of two general strategies which might be applicable to improving the time complexity of other future sequence analysis algorithms: sparse dynamic programming matrices and lazy evaluation.

Positive and negative monoclinic deformation of corundum-type trigonal crystal structures of M 2O3 metal oxides

The crystal structures of several transition metal oxides, Ti2O3, V2O3, Cr2O3, Al2O3 and α-Fe2O3, are studied using synchrotron radiation X-ray powder diffraction. The observed angular dependence of the integral breadths is described by two models: (i) the distorted corundum-type structure model described by the space group C2/c and (ii) the Stephens model of anisotropic Bragg peak broadening. These two models are shown to be equivalent. Ti2O3, V2O3 and Cr2O3 show a `positive' distortion which is related to the possible metal–metal bond suggested by Goodenough in the literature (the deformation leads to shorter metal–metal distances) whereas Al2O3 and α-Fe2O3 show a `negative' distortion which leads to relatively longer metal–metal distances.

Haplotype matching in large cohorts using the Li and Stephens model.

MotivationThe Li and Stephens model, which approximates the coalescent describing the pattern of variation in a population, underpins a range of key tools and results in genetics. Although highly efficient compared to the coalescent, standard implementations of this model still cannot deal with the very large reference cohorts that are starting to become available, and practical implementations use heuristics to achieve reasonable runtimes.ResultsHere I describe a new, exact algorithm (‘fastLS’) that implements the Li and Stephens model and achieves runtimes independent of the size of the reference cohort. Key to achieving this runtime is the use of the Burrows-Wheeler transform, allowing the algorithm to efficiently identify partial haplotype matches across a cohort. I show that the proposed data structure is very similar to, and generalizes, Durbin’s positional Burrows-Wheeler transform.

High pressure x-ray diffraction studies of the nanostructured Ge34Sb66 solid solution produced by mechanical alloying

A nanostructured solid solution of Ge34Sb66 produced by mechanical alloying was investigated by the angle-dispersive X-ray diffraction method from synchrotron radiation by using a diamond anvil cell technique. Pressure induced phase transitions were observed. Starting from A7 symmetry at ambient conditions, Ge34Sb66 was transformed to a high pressure host-guest structure at 12.0 GPa. The compressibility and bond distances of A7 phase were determined by the Rietveld refinement of the x-ray diffraction data. The lattice parameters and cell volume were described by Birch–Murnaghan equation-of-state. The Bragg peaks of the A7 structure show a strong reflection-indices-dependent line-broadening due to the applied pressure. Hence, they were simulated by Stephens's model. The host-guest X-ray pattern was simulated by the Pseudo-two-phase Rietveld method.

Promoting Resilience in New Perioperative Nurses

New nursing graduates experience many challenges when transitioning from the academic environment to the practice setting. For many, the period of transition from student to employee is less than optimal, with many still experiencing reality shock, cognitive dissonance, and theory-practice gaps. The Stephens Model of Nursing Student Resilience addresses the unique issues faced by new graduate nurses to assist them in developing healthy coping strategies and to promote resilience. This model forms the basis of the RN Personal Resilience Enhancement Plan, a supplemental onboarding program created to assist new nurses in confidently facing challenges encountered during orientation and successfully moving forward as nursing professionals. This article describes the concept of resilience and explains how to link the RN Personal Resilience Enhancement Plan to the onboarding process in the perioperative setting.

Genotype Imputation with Millions of Reference Samples

We present a genotype imputation method that scales to millions of reference samples. The imputation method, based on the Li and Stephens model and implemented in Beagle v.4.1, is parallelized and memory efficient, making it well suited to multi-core computer processors. It achieves fast, accurate, and memory-efficient genotype imputation by restricting the probability model to markers that are genotyped in the target samples and by performing linear interpolation to impute ungenotyped variants. We compare Beagle v.4.1 with Impute2 and Minimac3 by using 1000 Genomes Project data, UK10K Project data, and simulated data. All three methods have similar accuracy but different memory requirements and different computation times. When imputing 10 Mb of sequence data from 50,000 reference samples, Beagle's throughput was more than 100× greater than Impute2's throughput on our computer servers. When imputing 10 Mb of sequence data from 200,000 reference samples in VCF format, Minimac3 consumed 26× more memory per computational thread and 15× more CPU time than Beagle. We demonstrate that Beagle v.4.1 scales to much larger reference panels by performing imputation from a simulated reference panel having 5 million samples and a mean marker density of one marker per four base pairs.

End FGM from the ground up

British Journal of Midwifery • August 2014 • Vol 22, No 8 On 22 July, the Government and UNICEF, held the first Girl Summit aimed at mobilising efforts at home and abroad to end female genital mutilation (FGM) and child, early and forced marriage (CEFM) within a generation. The effects of FGM in the UK are wider reaching than we previously thought. Following a report by City University London and human rights organisation Equality Now (2014), it is now believed that more than 135 000 women and girls in the UK are FGM survivors—more than twice the previous estimate (NHS Choices, 2013). Furthermore, it is estimated that about 60 000 girls aged 0–14 years old were born in England and Wales to mothers who had undergone FGM. Prime Minister, David Cameron called on the global community to help. He said that ‘Britain doesn’t have any special magic’ to stop these practices alone— so global action is needed. During the summit, the Government announced new action and funding to protect millions of girls from these atrocities. £1.4 million is to be spent on an FGM Prevention Programme, in partnership with NHS England, to help care for survivors and safeguard those at risk. Theresa May, Home Secretary, announced that a special unit will be set up in England to tackle FGM as part of a wide-ranging package of reforms to stop the practice in the UK (Topping, 2014). The laws around FGM will become strengthened; parents will be held responsible if their child is a victim of the practice and new legislation was announced that will mean they can be prosecuted if they fail to prevent their daughter being cut. May also announced that there will be a consultation to make it mandatory for professionals to report FGM. It is amazing that this is not already the case. Much of the battle to end these practices lies in increasing cultural understanding and knowledge of FGM and CEFM; that is why the Girl Summit has taken to social media to help raise the profile and ask people to pledge support. So far, over 10 000 people have pledged via Twitter and Facebook, including celebrities such as actor and writer Stephen Fry and model Christy Turlington, and the message has reached more than 950 million people through these networks—such is the power and reach of social media. Despite all the focus from high-profile celebrities and politicians, FGM won’t be eradicated unless resources are put into the professionals on the ground. Midwives are often the first health professional that women who have undergone FGM see, they therefore have an important role in its detection and prevention. It’s all well and good having a summit, but it won’t mean a thing if midwives aren’t supported with the time, resources and training to help end these abhorent practices in this generation. BJM

Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads.

Hidden Markov model, based on Li and Stephens model that takes into account chromosome sharing of multiple individuals, results in mainstream haplotype phasing algorithms for genotyping arrays and next-generation sequencing (NGS) data. However, existing methods based on this model assume that the allele count data are independently observed at individual sites and do not consider haplotype informative reads, i.e. reads that cover multiple heterozygous sites, which carry useful haplotype information. In our previous work, we developed a new hidden Markov model to incorporate a two-site joint emission term that captures the haplotype information across two adjacent sites. Although our model improves the accuracy of genotype calling and haplotype phasing, haplotype information in reads covering non-adjacent sites and/or more than two adjacent sites is not used because of the severe computational burden. We develop a new probabilistic model for genotype calling and haplotype phasing from NGS data that incorporates haplotype information of multiple adjacent and/or non-adjacent sites covered by a read over an arbitrary distance. We develop a new hybrid Markov Chain Monte Carlo algorithm that combines the Gibbs sampling algorithm of HapSeq and Metropolis-Hastings algorithm and is computationally feasible. We show by simulation and real data from the 1000 Genomes Project that our model offers superior performance for haplotype phasing and genotype calling for population NGS data over existing methods. HapSeq2 is available at www.ssg.uab.edu/hapseq/.

Structural and vibrational investigations on Ge34Sb66 solid solutions produced by mechanical alloying

A nanostructured solid solution Ge34Sb66 was produced from Ge and Sb by mechanical alloying and its structural and vibrational properties were investigated by X-ray diffraction (XRD) and micro-Raman spectroscopy. The Rietveld refinement of the XRD measurements allowed the investigation of the evolution of the solid solution with the milling time. The Bragg peaks of the Sb solvent phase showed a strongly reflection-indices-dependent line broadening due to the spatial variation of the Sb/Ge ratio. The asymmetric broadening in the deformed peaks was analyzed considering the Stephens model. Volume fractions of crystalline and interfacial components of the milled powder were estimated from the XRD patterns. Although XRD measurements indicated the formation of a solid solution, Raman measurements revealed the presence of nanocrystalline Ge, and its crystallite size was estimated from the Raman analysis.

The effect of data quality on model performance with application to daily evaporation estimation

The model performance is usually influenced by the quality of the data used in model construction. If the model performance is less affected by data quality, the resulting estimates will be more reliable. In this paper, the variation in model performance due to different data quality is explored in a field-scale application. Hence, two models, the proposed support vector machine (SVM) based model and the Stephen and Stewart (SS) model, are employed for daily estimation of evaporation at an experiment station. Five scenarios corresponding to different data qualities are designed to evaluate the effect of data quality on model performance. Additionally, the most effective meteorological variables influencing evaporation are obtained by a systematic input determination process. These most effective meteorological variables are used as inputs to the SVM-based model. The results show that the model performance decreases as the data quality decreases (i.e. the percentage of missing data increases). However, the estimation accuracy of SVM-based models is still better than that of the SS model. Moreover, the variation of model performance of the SVM-based model is smaller than that of the SS model. That is, the negative impact of different data quality is effectively decreased by using the SVM-based model instead of the SS model.

Vortex motion in Nb/PdNi/Nb trilayers: New aspects in the flux flow state

We study the dynamics of vortex lines in Supercondutor/Ferromagnet/Superconductor (SFS) heterostructures at microwave frequencies. We have employed swept-frequency, Corbino-disk and resonant, dielectric-resonator techniques to obtain the field and temperature dependence of the vortex-state parameters. We concentrate here on the genuine flux-flow resistivity ρff, that we access at subcritical currents using a sufficiently high driving frequency. We find that ρff does not follow the well-known Bardeen–Stephen model. Instead, it is well described by a full time-dependent Ginzburg–Landau expression at very thin F layer thickness, but changes to a previously unreported field-dependence when the F layer exceeds a few nm.

Relativistic Four-Component DFT Calculations of 1H NMR Chemical Shifts in Transition-Metal Hydride Complexes: Unusual High-Field Shifts Beyond the Buckingham–Stephens Model

State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

X-ray diffraction studies on asymmetrically broadened peaks of heavily deformed zirconium-based alloys

The diffraction peaks of Zircaloy-2 and Zr–2.5% Nb alloys at various deformations are found to be asymmetric in nature. In order to characterize the microstructure from these asymmetric peaks of these deformed alloys, X-ray diffraction line profile analysis like Williamson–Hall technique, Variance method based on second- and fourth-order restricted moments and Stephens model based on anisotropic strain distribution have been adopted. The domain size and dislocation density have been evaluated as a function of deformation for both these alloys. These techniques are useful where the dislocation structure is highly inhomogeneous inside the matrix causing asymmetry in the line profile, particularly for deformed polycrystalline materials.

The viscous flux flow and flux creep induced by pulsed magnetic field in YBCO disk

We have investigated the magnetic flux motion in a high quality YBCO disk induced by a pulsed magnetic field. The effect of static bias fields was also studied in the temperature range of 30–95 K. The flux flow resistivity ρ f increased with increasing the pulsed magnetic field approximately according to the Bardeen–Stephen model, that is ρ f/ ρ n≈ B/ B c2. The viscosity coefficient η decreased with increasing temperature and static bias field.

Anisotropy of the flux creep in the motion of vortices along twin-boundary planes in YBa2Cu3O7−x single crystals

The anisotropy of the magnetic flux creep in vortex motion parallel to the planes of twin boundaries is investigated experimentally. It is shown that at relatively low magnetic fields the creep velocity is independent of the magnetic field and of the angle α≡∠H,ab. It is found that the differential resistivity ρd≡dE/dJ tends to saturation at large transport currents, where its value is approximately equal to the viscous drag on vortices in the Bardeen–Stephen model. In low magnetic fields oriented near the ab plane of the crystal the trapping of flux lines between CuO superconducting planes is observed.