A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

Protein-coding genes in eukaryotes are interrupted by introns, but intron densities widely differ between eukaryotic lineages. Vertebrates, some invertebrates and green plants have intron-rich genes, with 6–7 introns per kilobase of coding sequence, whereas most of the other eukaryotes have intron-poor genes. We reconstructed the history of intron gain and loss using a probabilistic Markov model (Markov Chain Monte Carlo, MCMC) on 245 orthologous genes from 99 genomes representing the three of the five supergroups of eukaryotes for which multiple genome sequences are available. Intron-rich ancestors are confidently reconstructed for each major group, with 53 to 74% of the human intron density inferred with 95% confidence for the Last Eukaryotic Common Ancestor (LECA). The results of the MCMC reconstruction are compared with the reconstructions obtained using Maximum Likelihood (ML) and Dollo parsimony methods. An excellent agreement between the MCMC and ML inferences is demonstrated whereas Dollo parsimony introduces a noticeable bias in the estimations, typically yielding lower ancestral intron densities than MCMC and ML. Evolution of eukaryotic genes was dominated by intron loss, with substantial gain only at the bases of several major branches including plants and animals. The highest intron density, 120 to 130% of the human value, is inferred for the last common ancestor of animals. The reconstruction shows that the entire line of descent from LECA to mammals was intron-rich, a state conducive to the evolution of alternative splicing

The neutron and its role in cosmology and particle physics

Experiments with cold and ultracold neutrons have reached a level of precision such that problems far beyond the scale of the present Standard Model of particle physics become accessible to experimental investigation. Due to the close links between particle physics and cosmology, these studies also permit a deep look into the very first instances of our universe. First addressed in this article, both in theory and experiment, is the problem of baryogenesis ... The question how baryogenesis could have happened is open to experimental tests, and it turns out that this problem can be curbed by the very stringent limits on an electric dipole moment of the neutron, a quantity that also has deep implications for particle physics. Then we discuss the recent spectacular observation of neutron quantization in the earth's gravitational field and of resonance transitions between such gravitational energy states. These measurements, together with new evaluations of neutron scattering data, set new constraints on deviations from Newton's gravitational law at the picometer scale. Such deviations are predicted in modern theories with extra-dimensions that propose unification of the Planck scale with the scale of the Standard Model ... Another main topic is the weak-interaction parameters in various fields of physics and astrophysics that must all be derived from measured neutron decay data. Up to now, about 10 different neutron decay observables have been measured, much more than needed in the electroweak Standard Model. This allows various precise tests for new physics beyond the Standard Model, competing with or surpassing similar tests at high-energy. The review ends with a discussion of neutron and nuclear data required in the synthesis of the elements during the "first three minutes" and later on in stellar nucleosynthesis.Comment: 91 pages, 30 figures, accepted by Reviews of Modern Physic

Progress towards a public chemogenomic set for protein kinases and a call for contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases

Development of Technique for Face Detection in Image Based on Binarization, Scaling and Segmentation Methods

A technique for face detection in the image is proposed, which is based on binarization, scaling, and segmentation of the image, followed by the determination of the largest connected component that matches the image of the face.Modern methods of binarization, scaling, and taxonomic image segmentation have one or more of the following disadvantages: they have a high computational complexity; require the determination of parameter values. Taxonomic image segmentation methods may have additional disadvantages: they do not allow noise and outliers selection; clusters can't have different shapes and sizes, and their number is fixed.Due to this, to improve the efficiency of face detection techniques, the methods of binarization, scaling and taxonomic segmentation needs to be improved.A binarization method is proposed, the distinction of which is the use of the image background. This allows to simplify the process of scaling and segmentation (since all the pixels in the background are represented by the same color), non-uniform brightness of the face, and not to use the threshold settings and additional parameters.A binary image scaling method is proposed, the distinction of which is the use of an arithmetic mean filter with threshold processing and Fast wavelet transform. This allows to speed up the image segmentation process by about P2 times, where P is the scaling parameter, and not to use the time-consuming procedure for determining.A binary scaled image segmentation method is proposed, the distinction of which is the use of density clustering. This allows to separate areas of the face of non-uniform brightness from the image background, noise and outliers. It also allows clusters to have different shapes and sizes, to not require setting the number of clusters and additional parameters.To determine the scaling parameter, numerous studies were conducted in this work, which concluded that the dependence of the segmentation time on the scaling parameter is close to exponential. It was also found that for small P, where P is the scaling parameter, the quality of face detection deteriorates slightly.The proposed technique for face detection in image based on binarization, scaling and segmentation can be used in intelligent computer systems for biometric identification of a person by the face imag

Probe-dependent Dirac-point gap in the gadolinium-doped thallium-based topological insulator TlBi0.9Gd0.1Se2

A tunable gap in the topological surface state is of great interest for novel spintronic devices and applications in quantum computing. Here, we study the surface electronic structure and magnetic properties of the Gd-doped topological insulator TlBi0.9Gd0.1Se2. Utilizing superconducting quantum interference device magnetometry, we show paramagnetic behavior down to 2 K. Combining spin- and angle-resolved photoemission spectroscopy with different polarizations of light, we demonstrate that the topological surface state is characterized by the Dirac cone with a helical spin structure and confirm its localization within the bulk band gap. By using different light sources in photoemission spectroscopy, various Dirac-point gap values were observed: 50 meV for hν=18eV and 20 meV for hν=6.3eV. Here, we discuss the gap observation by the angle-resolved photoemission spectroscopy method as a consequence of the scattering processes. Simulating the corresponding spectral function, we demonstrate that the asymmetric energy-distribution curve of the surface state leads to an overestimation of the corresponding gap value. We speculate that 20 meV in our case is a trustworthy value and attribute this gap to be originated by scattering both on magnetic and charge impurities provided by Gd atoms and surface defects. Given the complexity and importance of scattering processes in the topological surface state together with our observations of distinctive photoemission asymmetry, we believe our results are important for research of the massive Dirac fermions in novel quantum materials.This work was supported by St. Petersburg State University Project (ID No. 51126254), by the Russian Science Foundation (Grant No. 18-12-00062), by the Ministry of Science and Higher Education of the Russian Federation (Grant No 2020-1902-01-058), and by the Science Development Foundation under the President of the Republic of Azerbaijan (Grant No. EIF-BGM-4-RFTF-1/2017-1/04/1-M-02). The studies were also carried out at the resource centers of St. Petersburg State University “Physical Methods for Surface Investigation” and “Diagnosis of Functional Materials for Medicine, Pharmacology, and Nanoelectronics.” In addition, the work was supported by the German-Russian Interdisciplinary Science Center (G-RISC) funded by the German Federal Foreign Office via the German Academic Exchange Service (DAAD) and Russian-German Laboratory at BESSY II (Helmholtz Zentrum, Berlin). We thank the Hiroshima Synchrotron Radiation Center (Proposal No. 18BG026), Helmholtz-Zentrum Berlin für Materialien und Energie for the allocation of synchrotron radiation beam times, and the N-BARD, Hiroshima University for supplying liquid helium. A.K. was financially supported by KAKENHI (Grants No. 17H06138, No. 17H06152, and No. 18H03683).Peer reviewe