Local Deconvolution Research Articles

Genetic determinants of serum bilirubin using inferred native American gene variants in Chilean adolescents.

Gene variants in the UGT1A1 gene are strongly associated with circulating bilirubin levels in several populations, as well as other variants of modest effect across the genome. However, the effects of such variants are unknown regarding the Native American ancestry of the admixed Latino population. Our objective was to assess the Native American genetic determinants of serum bilirubin in Chilean admixed adolescents using the local ancestry deconvolution approach. We measured total serum bilirubin levels in 707 adolescents of the Chilean Growth and Obesity Cohort Study (GOCS) and performed high-density genotyping using the Illumina-MEGA array (>1.7 million genotypes). We constructed a local ancestry reference panel with participants from the 1000 Genomes Project, the Human Genome Diversity Project, and our GOCS cohort. Then, we inferred and isolated haplotype tracts of Native American, European, or African origin to perform genome-wide association studies. In the whole cohort, the rs887829 variant and others near UGT1A1 were the unique signals achieving genome-wide statistical significance (b = 0.30; p = 3.34 × 10-57). After applying deconvolution methods, we found that significance is also maintained in Native American (b = 0.35; p = 3.29 × 10-17) and European (b = 0.28; p = 1.14 × 10-23) ancestry components. The rs887829 variant explained a higher percentage of the variance of bilirubin in the Native American (37.6%) compared to European ancestry (28.4%). In Native American ancestry, carriers of the TT genotype of this variant averaged 4-fold higher bilirubinemia compared to the CC genotype (p = 2.82 × 10-12). We showed for the first time that UGT1A1 variants are the primary determinant of bilirubin levels in Native American ancestry, confirming its pan-ethnic relevance. Our study illustrates the general value of the local ancestry deconvolution approach to assessing isolated ancestry effects in admixed populations.

A Centroiding Method for Targets in Star Images Based on Local PSF Estimation and Iterative Deconvolution

A Centroiding Method for Targets in Star Images Based on Local PSF Estimation and Iterative Deconvolution

Influence of wall shear stress on the secondary flow in square ducts

We investigate turbulent duct flows with a square cross section using well-resolved large-eddy simulations (LES). A physically consistent subgrid-scale turbulence model based on the Adaptive Local Deconvolution Method (ALDM) for implicit LES is used. The wall shear stress is artificially modified at one of the four walls to analyse the influence on the secondary flow. A direct numerical simulation (DNS) of a symmetrical duct flow is used as reference to assess the influence of a modified wall shear stress. The modification results in an asymmetrical distribution of the secondary flow source terms, affecting the momentum distribution. Further, the anisotropy of the Reynolds stress tensor, which induces the secondary flow vortices is considerably affected by the wall shear stress modulation.

Momentum boundary layers in transcritical channel flows

We present well-resolved large-eddy simulations (LES) of a channel flow solving the fully compressible Navier–Stokes equations in conservative form. An adaptive look-up table method is used for thermodynamic and transport properties. We apply a physically consistent subgrid-scale turbulence model, that is based on the Adaptive Local Deconvolution Method (ALDM) for implicit LES. The wall temperatures are set to enclose the pseudo-boiling temperature at a supercritical pressure, leading to strong property variations within the channel geometry. In total seven cases are computed covering different Reynolds numbers, pseudo-boiling positions and pressure values. The hot wall at the top and the cold wall at the bottom produce asymmetric mean velocity and temperature profiles which result in different momentum layer thicknesses. All cases feature a turbulent mass flux which is essential in turbulence modelling. Furthermore, we analyse the turbulent kinetic energy budgets, perform a quadrant and octant analysis of the Reynolds shear stress and employ an invariant map to study the anisotropy in transcritical turbulent channel flows.

A comparative study of deconvolution techniques for quantum-gas microscope images

Quantum-gas microscopes are used to study ultracold atoms in optical lattices at the single-particle level. In these systems atoms are localised on lattice sites with separations close to or below the diffraction limit. To determine the lattice occupation with high fidelity, a deconvolution of the images is often required. We compare three different techniques, a local iterative deconvolution algorithm, Wiener deconvolution and the Lucy–Richardson algorithm, using simulated microscope images. We investigate how the reconstruction fidelity scales with varying signal-to-noise ratio, lattice filling fraction, varying fluorescence levels per atom, and imaging resolution. The results of this study identify the limits of singe-atom detection and provide quantitative fidelities which are applicable for different atomic species and quantum-gas microscope setups.

Localized adaptive waveform inversion: theory and numerical verification

SUMMARYCorrectly interpreting phase events thanks to data processing techniques based on correlation or deconvolution has been the focus of numerous studies in the field of high-resolution seismic imaging using full-waveform inversion. To mitigate the non-convexity of the misfit function and the risk to converge towards non-informative local minima, correlation and deconvolution techniques make it possible to focus on phase information instead of amplitude information and to design more convex misfit function, alleviating the dependency of the full-waveform inversion process on the accuracy of initial models. Such techniques however rely on the assumption that phase events can be compared one by one, or that all the phase events are shifted in time in a similar way. This assumption is not satisfied in practice, which limits the effectiveness of these correlation/deconvolution-based methods. To overcome this issue, we propose to account for the non-stationary relation between observed and predicted data through a local in-time deconvolution technique, based on time–frequency analysis of the signal using a Gabor transform. This makes it possible to estimate instantaneous time-shift between locally coherent phase events. This strategy generalizes the conventional normalized deconvolution technique, which has been popularized under the name of adaptive waveform inversion. To support the introduction of our novel method, we compare it with four misfit functions based respectively on classical cross-correlation, penalized cross-correlation, penalized deconvolution, and adaptive waveform inversion. We analyse the behaviour of these methods on specific scenarios, and then propose a comparison on 2-D synthetic benchmarks. We show how our ‘localized’ adaptive waveform inversion applies in these realistic tests and overcomes some of the limitations of the aforementioned techniques.

Large eddy simulations of reacting and non-reacting transcritical fuel sprays using multiphase thermodynamics

We present a novel framework for high-fidelity simulations of inert and reacting sprays at transcritical conditions with highly accurate and computationally efficient models for complex real-gas effects in high-pressure environments, especially for the hybrid subcritical/supercritical mode of evaporation during the mixing of fuel and oxidizer. The high-pressure jet disintegration is modeled using a diffuse interface method with multiphase thermodynamics, which combines multi-component real-fluid volumetric and caloric state equations with vapor–liquid equilibrium calculations for the computation of thermodynamic properties of mixtures at transcritical pressures. Combustion source terms are evaluated using a finite-rate chemistry model, including real-gas effects based on the fugacity of the species in the mixture. The adaptive local deconvolution method is used as a physically consistent turbulence model for large eddy simulation (LES). The proposed method represents multiphase turbulent fluid flows at transcritical pressures without relying on any semi-empirical breakup and evaporation models. All multiphase thermodynamic model equations are presented for general cubic state equations coupled with a rapid phase-equilibrium calculation method that is formulated in a reduced space based on the molar specific volume function. LES results show a very good agreement with available experimental data for the reacting and non-reacting engine combustion network benchmark spray A at transcritical operating conditions.

Fast Reconstruction of Three-Quarter Sampling Measurements Using Recurrent Local Joint Sparse Deconvolution and Extrapolation

Recently, non-regular three-quarter sampling has shown to deliver an increased image quality of image sensors by using differently oriented L-shaped pixels compared to the same number of square pixels. A three-quarter sampling sensor can be understood as a conventional low-resolution sensor where one quadrant of each square pixel is opaque. Subsequent to the measurement, the data can be reconstructed on a regular grid with twice the resolution in both spatial dimensions using an appropriate reconstruction algorithm. For this reconstruction, local joint sparse deconvolution and extrapolation (L-JSDE) has shown to perform very well. As a disadvantage, L-JSDE requires long computation times of several dozen minutes per megapixel. In this paper, we propose a faster version of L-JSDE called recurrent L-JSDE (RL-JSDE) which is a reformulation of L-JSDE. For reasonable recurrent measurement patterns, RL-JSDE provides significant speedups on both CPU and GPU without sacrificing image quality. Compared to L-JSDE, 20-fold and 733-fold speedups are achieved on CPU and GPU, respectively.

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

Skeletal muscle repair is driven by the coordinated self-renewal and fusion of myogenic stem and progenitor cells. Single-cell gene expression analyses of myogenesis have been hampered by the poor sampling of rare and transient cell states that are critical for muscle repair, and do not inform the spatial context that is important for myogenic differentiation. Here, we demonstrate how large-scale integration of single-cell and spatial transcriptomic data can overcome these limitations. We created a single-cell transcriptomic dataset of mouse skeletal muscle by integration, consensus annotation, and analysis of 23 newly collected scRNAseq datasets and 88 publicly available single-cell (scRNAseq) and single-nucleus (snRNAseq) RNA-sequencing datasets. The resulting dataset includes more than 365,000 cells and spans a wide range of ages, injury, and repair conditions. Together, these data enabled identification of the predominant cell types in skeletal muscle, and resolved cell subtypes, including endothelial subtypes distinguished by vessel-type of origin, fibro-adipogenic progenitors defined by functional roles, and many distinct immune populations. The representation of different experimental conditions and the depth of transcriptome coverage enabled robust profiling of sparsely expressed genes. We built a densely sampled transcriptomic model of myogenesis, from stem cell quiescence to myofiber maturation, and identified rare, transitional states of progenitor commitment and fusion that are poorly represented in individual datasets. We performed spatial RNA sequencing of mouse muscle at three time points after injury and used the integrated dataset as a reference to achieve a high-resolution, local deconvolution of cell subtypes. We also used the integrated dataset to explore ligand-receptor co-expression patterns and identify dynamic cell-cell interactions in muscle injury response. We provide a public web tool to enable interactive exploration and visualization of the data. Our work supports the utility of large-scale integration of single-cell transcriptomic data as a tool for biological discovery.

Systematic Review on Local Ancestor Inference From a Mathematical and Algorithmic Perspective.

Genotypic data provide deep insights into the population history and medical genetics. The local ancestry inference (LAI) (also termed local ancestry deconvolution) method uses the hidden Markov model (HMM) to solve the mathematical problem of ancestry reconstruction based on genomic data. HMM is combined with other statistical models and machine learning techniques for particular genetic tasks in a series of computer tools. In this article, we surveyed the mathematical structure, application characteristics, historical development, and benchmark analysis of the LAI method in detail, which will help researchers better understand and further develop LAI methods. Firstly, we extensively explore the mathematical structure of each model and its characteristic applications. Next, we use bibliometrics to show detailed model application fields and list articles to elaborate on the historical development. LAI publications had experienced a peak period during 2006–2016 and had kept on moving in the following years. The efficiency, accuracy, and stability of the existing models were evaluated by the benchmark. We find that phased data had higher accuracy in comparison with unphased data. We summarize these models with their distinct advantages and disadvantages. The Loter model uses dynamic programming to obtain a globally optimal solution with its parameter-free advantage. Aligned bases can be used directly in the Seqmix model if the genotype is hard to call. This research may help model developers to realize current challenges, develop more advanced models, and enable scholars to select appropriate models according to given populations and datasets.

Large-eddy simulation of turbulent channel flow at transcritical states

We present well-resolved large-eddy simulations (LES) of a channel flow solving the fully compressible Navier–Stokes equations in conservative form. An adaptive look-up table method is used for thermodynamic and transport properties. A physically consistent subgrid-scale turbulence model is incorporated, that is based on the Adaptive Local Deconvolution Method (ALDM) for implicit LES. The wall temperatures are set to enclose the pseudo-boiling temperature at a supercritical pressure, leading to strong property variations within the channel geometry. The hot wall at the top and the cold wall at the bottom produce asymmetric mean velocity and temperature profiles which result in different momentum and thermal boundary layer thicknesses. Different turbulent Prandtl number formulations and their components are discussed in context of strong property variations.

Improving Selection Detection with Population Branch Statistic on Admixed Populations.

Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.

Heterogeneous Idealization of Ion Channel Recordings - Open Channel Noise.

We propose a new model-free segmentation method for idealizing ion channel recordings. This method is designed to deal with heterogeneity of measurement errors. This in particular applies to open channel noise which, in general, is particularly difficult to cope with for model-free approaches. Our methodology is able to deal with lowpass filtered data which provides a further computational challenge. To this end we propose a multiresolution testing approach, combined with local deconvolution to resolve the lowpass filter. Simulations and statistical theory confirm that the proposed idealization recovers the underlying signal very accurately at presence of heterogeneous noise, even when events are shorter than the filter length. The method is compared to existing approaches in computer experiments and on real data. We find that it is the only one which allows to identify openings of the PorB porine at two different temporal scales. An implementation is available as an R package.

Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals

Polygenic Scores (PSs) describe the genetic component of an individual’s quantitative phenotype or their susceptibility to diseases with a genetic basis. Currently, PSs rely on population-dependent contributions of many associated alleles, with limited applicability to understudied populations and recently admixed individuals. Here we introduce a combination of local ancestry deconvolution and partial PS computation to account for the population-specific nature of the association signals in individuals with admixed ancestry. We demonstrate partial PS to be a proxy for the total PS and that a portion of the genome is enough to improve susceptibility predictions for the traits we test. By combining partial PSs from different populations, we are able to improve trait predictability in admixed individuals with some European ancestry. These results may extend the applicability of PSs to subjects with a complex history of admixture, where current methods cannot be applied.

Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes.

Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (i.e., unbalanced representation of source populations); and iii) the reproduction mode (e.g., selfing, vegetative propagation). If a source population was not represented in the data set, no bias was observed in inference accuracy for regions originating from represented sources and regions from the missing source were assigned differently depending on the methods. Overall, the selected ancestry inference methods may be used for crop plant analysis if all ancestral sources are known.

Boosting Compressed Sensing Using Local Measurements and Sliding Window Reconstruction

In the framework of compressed sensing, image data is measured using less measurements than the total number of pixels. Each measurement consists of a (random) linear combination of all pixels. Since image data is approximately sparse in an appropriate transform domain, a reasonable reconstruction is possible for many measurement matrices, especially for i.i.d. Gaussian measurement matrices. In a seemingly different field, non-regular sampling techniques such as three-quarter sampling have shown promising results to enhance the resolution of an imaging sensor by effectively sub-sampling a higher resolution image. Here, the measurements can be described as linear combinations of only three pixels, which can also be seen as a (spectral) compressed sensing measurement. Since each measurement is spatially localized, the reconstruction can be performed in overlapping sliding windows. In this work, we show that compressed sensing reconstruction algorithms can greatly benefit from such an overlapping sliding window reconstruction. Compared to conventional block-wise compressed sensing with i.i.d. Gaussian measurement matrices, the reconstruction quality in terms of the PSNR increases up to +5dB using small, local i.d.d. Gaussian measurement blocks. Additionally, we propose a local joint sparse deconvolution and extrapolation (L-JSDE) to reconstruct images from arbitrary local measurements. For several applications with local measurements we show that L-JSDE increases the PSNR by +2.2dB relative to conventional block-wise i.i.d. Gaussian measurements reconstructed with the state-of-the-art reconstruction algorithm D-AMP using the same overall sampling density.

FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data

Abstract Several thousand genomes have been completed with millions of variants identified in the human deoxyribonucleic acid sequences. These genomic variations, especially those introduced by admixture, significantly contribute to a remarkable phenotypic variability with medical and/or evolutionary implications. Elucidating local ancestry estimates is necessary for a better understanding of genomic variation patterns throughout modern human evolution and adaptive processes, and consequences in human heredity and health. However, existing local ancestry deconvolution tools are accessible as individual scripts, each requiring input and producing output in its own complex format. This limits the user’s ability to retrieve local ancestry estimates. We introduce a unified framework for multi-way local ancestry inference, FRANC, integrating eight existing state-of-the-art local ancestry deconvolution tools. FRANC is an adaptable, expandable and portable tool that manipulates tool-specific inputs, deconvolutes ancestry and standardizes tool-specific results. To facilitate both medical and population genetics studies, FRANC requires convenient and easy to manipulate input files and allows users to choose output formats to ease their use in further potential local ancestry deconvolution applications.

Research on Bearing Fault Diagnosis Method Based on Filter Features of MOMLMEDA and LSTM

As the supporting unit of rotating machinery, bearing can ensure efficient operation of the equipment. Therefore, it is very important to monitor the status of bearings accurately. A bearing fault diagnosis mothed based on Multipoint Optimal Minimum Local Mean Entropy Deconvolution Adjusted (MOMLMEDA) and Long Short-Term Memory (LSTM) is proposed. MOMLMEDA is an improved algorithm based on Multipoint Optimal Minimum Entropy Deconvolution Adjusted (MOMEDA). By setting the local kurtosis mean as a new selection criterion, it can effectively avoid the interference of false kurtosis caused by noise and improve the accuracy of optimal kurtosis position. The optimal filter designed by optimal kurtosis position has periodic and amplitude characteristics, which are used as the fault feature in this paper. However, this feature has temporal characteristics and cannot be used as input of general neural network directly. LSTM is selected as the classification network in this paper. It can effectively avoid the influence of the temporal problem existing in feature vectors. Accurate diagnosis of bearing faults is realized by training classification neural network with samples. The overall recognition rate is up to 93.50%.

Numerical Investigations of Turbulent Flows around Hydrofoil by Using Implicit Large Eddy Simulation

Based on Implicit Large Eddy Simulation (ILES), the Adaptive Local Deconvolution Method (ALDM) was proposed to develop an implicit Sub-Grid Scale (SGS) model for three-dimensional (3D) turbulent unsteady flow around the NACA0012 Hydrofoil at a high Reynolds number of 2400,000. With the help of User Define Function (UDF) of the Fluent CFD software, the 3D turbulent unsteady flows were carried out by using ILES and LES respectively. The lift coefficients predicted by both models were in good agreement with the experimental data and the relative error of lift coefficient predicted by both models decreases firstly and then increases with the increase of the incident angle, but the numerical results by ILES were more close to the experimental, which verified the feasibility and accuracy of the ILES model. In addition, the predicted pressure contour and streamline distributions by ILES and LES at different incident angles in a wide range were also investigated further. The larger of the incident angle, the production and shedding of the vortex are stronger. The predicted results by both the models have the similar tendency, and the ILES could more finely capture the flow patterns. For a large incident angle of 20°, the internal flow analyses by ILES could well reproduce the whole process of the vortex from generation to development and shedding around the hydrofoil.

A comprehensive survey of models for dissecting local ancestry deconvolution in human genome.

Over the past decade, studies of admixed populations have increasingly gained interest in both medical and population genetics. These studies have so far shed light on the patterns of genetic variation throughout modern human evolution and have improved our understanding of the demographics and adaptive processes of human populations. To date, there exist about 20 methods or tools to deconvolve local ancestry. These methods have merits and drawbacks in estimating local ancestry in multiway admixed populations. In this article, we survey existing ancestry deconvolution methods, with special emphasis on multiway admixture, and compare these methods based on simulation results reported by different studies, computational approaches used, including mathematical and statistical models, and biological challenges related to each method. This should orient users on the choice of an appropriate method or tool for given population admixture characteristics and update researchers on current advances, challenges and opportunities behind existing ancestry deconvolution methods.