Predicting Genetic Values: A Kernel-Based Best Linear Unbiased Prediction With Genomic Data

Genomic data provide a valuable source of information for modeling covariance structures, allowing a more accurate prediction of total genetic values (GVs). We apply the kriging concept, originally developed in the geostatistical context for predictions in the low-dimensional space, to the high-dimensional space spanned by genomic single nucleotide polymorphism (SNP) vectors and study its properties in different gene-action scenarios. Two different kriging methods [“universal kriging” (UK) and “simple kriging” (SK)] are presented. As a novelty, we suggest use of the family of Matérn covariance functions to model the covariance structure of SNP vectors. A genomic best linear unbiased prediction (GBLUP) is applied as a reference method. The three approaches are compared in a whole-genome simulation study considering additive, additive-dominance, and epistatic gene-action models. Predictive performance is measured in terms of correlation between true and predicted GVs and average true GVs of the individuals ranked best by prediction. We show that UK outperforms GBLUP in the presence of dominance and epistatic effects. In a limiting case, it is shown that the genomic covariance structure proposed by VanRaden (2008) can be considered as a covariance function with corresponding quadratic variogram. We also prove theoretically that if a specific linear relationship exists between covariance matrices for two linear mixed models, the GVs resulting from BLUP are linked by a scaling factor. Finally, the relation of kriging to other models is discussed and further options for modeling the covariance structure, which might be more appropriate in the genomic context, are suggested

Диффузия водорода в палладии: рас-четы из первых принципов

Целью данной работы является теоретическое исследование профилей диффузионных барьеров и температурной зависимости коэффициентов диффузии водорода в палладии. По результатам расчетов наиболее вероятным механизмом диффузии атома Н в Pd являются диффузионные скачки через октаэдрические – тетраэдрические – октаэдрическе междоузлия (величина барьеров в этих случаях составляет ~ 0,39 и 0,16 эВ, соответственно). Для большинства диффузионных скачков, высота барьеров в твердом растворе Pd16H2 ниже, чем высота барьеров в твердом растворе Pd16H. При температурах 600-900 K, значения коэффициентов диффузии водорода вдоль направлений [110] и [001] решетки Pd хорошо согласуются с результатами других работ.The purpose of this study is theoretically study of the diffusion barrier profiles and the temperature dependence of the hydrogen diffusion coefficients in palladium. According to the results of our calculations, diffusion jumps through octahedral-tetrahedral-octahedral interstitial sites are the most probable mechanism of diffusion of the H atom in Pd (the barrier in these cases amounts to ~ 0.39 and 0.16 eV, respectively). For most diffusion jumps, the value of the barriers in a solid solution of Pd16H2 is lower than the value of the barriers in a solid solution of Pd16H. At temperatures of 600-900 K, the values of the hydrogen diffusion coefficients along the [110] and [001] directions of the Pd lattice agree well with the results of other studies

Autocorrected off-axis holography of two-dimensional materials

The reduced dimensionality in two-dimensional materials leads to a wealth of unusual properties, which are currently explored for both fundamental and applied sciences. In order to study the crystal structure, edge states, the formation of defects and grain boundaries, or the impact of adsorbates, high-resolution microscopy techniques are indispensable. Here we report on the development of an electron holography (EH) transmission electron microscopy (TEM) technique, which facilitates high spatial resolution by an automatic correction of geometric aberrations. Distinguished features of EH beyond conventional TEM imaging are gap-free spatial information signal transfer and higher dose efficiency for certain spatial frequency bands as well as direct access to the projected electrostatic potential of the two-dimensional material. We demonstrate these features with the example of h-BN, for which we measure the electrostatic potential as a function of layer number down to the monolayer limit and obtain evidence for a systematic increase of the potential at the zig-zag edges

KKbar photoproduction from protons

We study the contribution of the Drell mechanism driven by K^+ and K^- exchange to the reaction gamma N -> KKbar N. Our calculation implements the full KN and KbarN reaction amplitudes in the form of partial wave amplitudes taken from a meson-exchange model (KN) and a partial wave analysis (KbarN), respectively. Comparing our results to data of the LAMP2 collaboration we observe that the Drell mechanism alone cannot describe the large Lambda(1520) photoproduction rate observed experimentally. We argue that the discrepancy could be due to significant contributions from K*-meson exchange with subsequent excitation of the Lambda(1520) resonance. After adding such contributions to our model a good agreement of the LAMP2 experiment is achieved. When applying the same model to the recent SAPHIR data we find an excellent description of the K^+p spectrum and can determine the parameters of the Lambda(1600) P01 resonance, M_R = 1617 +/- 2 MeV and Gamma_R = 117 +/- 4 MeV, from the K^-p mass distribution.Comment: updated version, analysis of new CLAS data included, 11 pages, 11 figure

A scale-corrected comparison of linkage disequilibrium levels between genic and non-genic regions

The understanding of non-random association between loci, termed linkage disequilibrium (LD), plays a central role in genomic research. Since causal mutations are generally not included in genomic marker data, LD between those and available markers is essential for capturing the effects of causal loci on localizing genes responsible for traits. Thus, the interpretation of association studies requires a detailed knowledge of LD patterns. It is well known that most LD measures depend on minor allele frequencies (MAF) of the considered loci and the magnitude of LD is influenced by the physical distances between loci. In the present study, a procedure to compare the LD structure between genomic regions comprising several markers each is suggested. The approach accounts for different scaling factors, namely the distribution of MAF, the distribution of pair-wise differences in MAF, and the physical extent of compared regions, reflected by the distribution of pair-wise physical distances. In the first step, genomic regions are matched based on similarity in these scaling factors. In the second step, chromosome- and genome-wide significance tests for differences in medians of LD measures in each pair are performed. The proposed framework was applied to test the hypothesis that the average LD is different in genic and non-genic regions. This was tested with a genome-wide approach with data sets for humans (Homo sapiens), a highly selected chicken line (Gallus gallus domesticus) and the model plant Arabidopsis thaliana. In all three data sets we found a significantly higher level of LD in genic regions compared to non-genic regions. About 31% more LD was detected genome-wide in genic compared to non-genic regions in Arabidopsis thaliana, followed by 13.6% in human and 6% chicken. Chromosome-wide comparison discovered significant differences on all 5 chromosomes in Arabidopsis thaliana and on one third of the human and of the chicken chromosomes

The Kaon-Photoproduction Of Nucleons In The Quark Model

In this paper, we develop a general framework to study the meson-photoproductions of nucleons in the chiral quark model. The S and U channel resonance contributions are expressed in terms of the Chew-Goldberger-Low-Nambu (CGLN) amplitudes. The kaon-photoproduction processes, $\gamma p\to K^+ \Lambda$, $\gamma p\to K^+ \Sigma^0$, and $\gamma p\to K^0\Sigma^+$, are calculated. The initial results show that the quark model provides a much improved description of the reaction mechanism for the kaon-photoproductions of the nucleon with less parameters than the traditional phenomenological approaches.Comment: 25 pages, 9 postscript figures can be obtained from the author

Observation of ultrafast solid-density plasma dynamics using femtosecond X-ray pulses from a free-electron laser

The complex physics of the interaction between short pulse high intensity lasers and solids is so far hardly accessible by experiments. As a result of missing experimental capabilities to probe the complex electron dynamics and competing instabilities, this impedes the development of compact laser-based next generation secondary radiation sources, e.g. for tumor therapy [Bulanov2002,ledingham2007], laboratory-astrophysics [Remington1999,Bulanov2015], and fusion [Tabak2014]. At present, the fundamental plasma dynamics that occur at the nanometer and femtosecond scales during the laser-solid interaction can only be elucidated by simulations. Here we show experimentally that small angle X-ray scattering of femtosecond X-ray free-electron laser pulses facilitates new capabilities for direct in-situ characterization of intense short-pulse laser plasma interaction at solid density that allows simultaneous nanometer spatial and femtosecond temporal resolution, directly verifying numerical simulations of the electron density dynamics during the short pulse high intensity laser irradiation of a solid density target. For laser-driven grating targets, we measure the solid density plasma expansion and observe the generation of a transient grating structure in front of the pre-inscribed grating, due to plasma expansion, which is an hitherto unknown effect. We expect that our results will pave the way for novel time-resolved studies, guiding the development of future laser-driven particle and photon sources from solid targets

Observation of Ultrafast Solid-Density Plasma Dynamics Using Femtosecond X-Ray Pulses from a Free-Electron Laser

The complex physics of the interaction between short-pulse ultrahigh-intensity lasers and solids is so far difficult to access experimentally, and the development of compact laser-based next-generation secondary radiation sources, e.g., for tumor therapy, laboratory astrophysics, and fusion, is hindered by the lack of diagnostic capabilities to probe the complex electron dynamics and competing instabilities. At present, the fundamental plasma dynamics that occur at the nanometer and femtosecond scales during the laser-solid interaction can only be elucidated by simulations. Here we show experimentally that small-angle x-ray scattering of femtosecond x-ray free-electron laser pulses facilitates new capabilities for direct in situ characterization of intense short-pulse laser-plasma interactions at solid density that allows simultaneous nanometer spatial and femtosecond temporal resolution, directly verifying numerical simulations of the electron density dynamics during the short-pulse high-intensity laser irradiation of a solid density target. For laser-driven grating targets, we measure the solid density plasma expansion and observe the generation of a transient grating structure in front of the preinscribed grating, due to plasma expansion. The density maxima are interleaved, forming a double frequency grating in x-ray free-electron laser projection for a short time, which is a hitherto unknown effect. We expect that our results will pave the way for novel time-resolved studies, guiding the development of future laser-driven particle and photon sources from solid targets

A children’s health perspective on nano- and microplastics

BACKGROUND : Pregnancy, infancy, and childhood are sensitive windows for environmental exposures. Yet the health effects of exposure to nano- and microplastics (NMPs) remain largely uninvestigated or unknown. Although plastic chemicals are a well-established research topic, the impacts of plastic particles are unexplored, especially with regard to early life exposures. OBJECTIVES : This commentary aims to summarize the knowns and unknowns around child- and pregnancy-relevant exposures to NMPs via inhalation, placental transfer, ingestion and breastmilk, and dermal absorption. METHODS : A comprehensive literature search to map the state of the science on NMPs found 37 primary research articles on the health relevance of NMPs during early life and revealed major knowledge gaps in the field. We discuss opportunities and challenges for quantifying child-specific exposures (e.g., NMPs in breastmilk or infant formula) and health effects, in light of global inequalities in baby bottle use, consumption of packaged foods, air pollution, hazardous plastic disposal, and regulatory safeguards. We also summarize research needs for linking child health and NMP exposures and address the unknowns in the context of public health action. DISCUSSION : Few studies have addressed child-specific sources of exposure, and exposure estimates currently rely on generic assumptions rather than empirical measurements. Furthermore, toxicological research on NMPs has not specifically focused on child health, yet children’s immature defense mechanisms make them particularly vulnerable. Apart from few studies investigating the placental transfer of NMPs, the physicochemical properties (e.g., polymer, size, shape, charge) driving the absorption, biodistribution, and elimination in early life have yet to be benchmarked. Accordingly, the evidence base regarding the potential health impacts of NMPs in early life remains sparse. Based on the evidence to date, we provide recommendations to fill research gaps, stimulate policymakers and industry to address the safety of NMPs, and point to opportunities for families to reduce early life exposures to plastic.The European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant.https://ehp.niehs.nih.govdm2022School of Health Systems and Public Health (SHSPH