cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Supplementary text and figures from Population differentiation of polygenic score predictions under stabilizing selection
Creators: name: Yair, Sivan
name: Coop, Graham
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Given the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to genomic medicine, and have found application in diverse settings including evolutionary studies of adaptation. Despite their promise, polygenic scores have been found to suffer from limited portability across human populations. This at first seems in conflict with the observation that most common genetic variation is shared among populations. We investigate one potential cause of this discrepancy: stabilizing selection on complex traits. Counterintuitively, while stabilizing selection constrains phenotypic evolution, it accelerates the loss and fixation of alleles underlying trait variation within populations (GWAS loci). Thus even when populations share an optimum phenotype, stabilizing selection erodes the variance contributed by their shared GWAS loci, such that predictions from GWAS in one population explain less of the phenotypic variation in another. We develop theory to quantify how stabilizing selection is expected to reduce the prediction accuracy of polygenic scores in populations not represented in GWAS samples. In addition, we find that polygenic scores can substantially overstate average genetic differences of phenotypes among populations. We emphasize stabilizing selection around a common optimum as a useful null model to connect patterns of allele frequency and polygenic score differentiation.This article is part of the theme issue ‘Fifty years since Lewontins apportionment of human diversity’.
A full relativistic thin disc -- the physics of the plunging region and the value of the stress at the ISCO
Creators: name: Potter, William J.
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The widely used Novikov-Thorne relativistic thin disc equations are only valid down to the radius of the innermost stable circular orbit (ISCO). This leads to an undetermined boundary condition at the ISCO, known as the inner stress of the disc, which sets the luminosity of the disc at the ISCO and introduces considerable ambiguity in accurately determining the mass, spin and accretion rate of black holes from observed spectra. We resolve this ambiguity by self-consistently extending the relativistic disc solution through the ISCO to the black hole horizon by calculating the inspiral of an average disc particle subject to turbulent disc forces, using a new particle-in-disc technique. Traditionally it has been assumed that the stress at the ISCO is zero, with material plunging approximately radially into the black hole at close to the speed of light. We demonstrate that in fact the inspiral is less severe, with several (~4-17) orbits completed before the horizon. This leads to a small non-zero stress and luminosity at and inside the ISCO, with a local surface temperature at the ISCO between ~0.15 and 0.3 times the maximum surface temperature of the disc, in the case where no dynamically important net magnetic field is present. For a range of disc parameters we calculate the value of the inner stress/surface temperature, which is required when fitting relativistic thin disc models to observations. We resolve a problem in relativistic slim disc models in which turbulent heating becomes inaccurate and falls to zero inside the plunging region.
description: 27 pages, 8 figures, accepted for publication in MNRAS
Embedding GitHub Repositories: A Comparative Study of the Python and Java Communities
Creators: name: Yutao, Chen
Publisher: name: University of Chicago
Year: 2021
Subjects: subject: GitHub
subject: Social Coding
subject: Representation Learning
subject: Heterogeneity in Programming Languages

description: GitHub, the largest platform for open-source software, which allows code contributors to collaboratively develop software in a variety of programming languages, has motivated extensive research on social coding. However, the heterogeneity of GitHub communities in different programming languages has not been explored in previous studies. Inspired by the linguistic relativity hypothesis, I deduce that different programming languages might result in distinct patterns in social coding. This research identifies such discrepancies between the Python and Java communities based on repository representations (embeddings) from a unique, newly constructed dataset. By describing the representation learning process as a pipeline, this thesis first demonstrates how to generate high-quality repository embeddings from content and contextual data, including source code (import), readme text, and co-contributor networks. The evaluation results suggest that models derived from Word2Vec, including Doc2Vec, Import2Vec, and Node2Vec, are the most competitive for representing the GitHub data. I then used the best performing embeddings to explore language-specific patterns via questions regarding GitHub activities and success. By investigating the consistency between different embedding spaces, I identified how social (contributor) and functional (import, readme) embedding spaces diverge in the Python community but align in the Java community, implying the difference in their socio-functional mapping. Furthermore, the results indicate that functionally similar Python repositories experience more competition and that Python programmers contribute more to functionally diverse repositories when compared with their Java counterparts. Afterward, by analyzing the correlations between the functional diversity and the average popularity among contributed repositories, I found evidence that Python programmers who commit to dissimilar repositories are more likely to be the contributors of popular repositories, while Java programmers do not exhibit this pattern. Finally, by comparing embeddings with baseline features, I verified their potency to predict repository popularity and discovered that functional embeddings are beneficial for predicting Python repositories, while social embeddings contribute more to Java repositories. These language-related heterogeneities can be attributed to the inherent difference in philosophy between Python and Java: As a language highlighting flexibility and reusability, Python treasures contributors’ ability to produce code for other coders with various functional needs, whereas Java focuses on the independence and thoroughness in programming, prioritizing specialized coding for passive end-users who value only the performance of final products.
Eulerian formulation for the triboelectric charging of polydisperse powder flows
Creators: name: Zeybek, Metin
name: Grosshans, Holger
Publisher: name: arXiv
Year: 2021
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We propose an Eulerian formulation for the triboelectric charging of powder flows. Recently, continuum descriptions of the charging of monodisperse and bidisperse powder appeared. Now, we propose the first Eulerian formulation for this type of flows that can fully account for polydisperse particle size distributions. To this end, the joint particle size, velocity, and charge distribution function is solved through the direct quadrature method of moments. The newly established approach includes the uptake of electrostatic charge by the particles when contacting a solid wall and the exchange of charge in-between particles during collisions. The electrostatic field induced by the charge of the particles and the drag forces of the surrounding gas affect the particle dynamics. Test cases of two-dimensional steady channel flows demonstrate the charging of the flow from the walls towards the center and in downstream direction. Further, the method predicts the effect of variations of the particle size and initial velocity distribution and the charge diffusion coefficient. The ability to handle polydispersity is a step towards the simulation of the electric charge build-up of real powder flows in full-scale technical applications.
Photometry of selected outer main belt asteroids
Creators: name: Shevchenko, V.
name: Mikhalchenko, O.
name: Belskaya, I.
name: Slyusarev, I.
name: Chiorny, V.
name: Krugly, Yu.
name: Hromakina, T.
name: Dovgopol, A.
name: Kiselev, N.
name: Rublevsky, A.
name: Antonyuk, K.
name: Novichonok, A.
name: Kusakin, A.
name: Reva, I.
name: Inasaridze, R.
name: Ayvazian, V.
name: Kapanadze, G.
name: Molotov, I.
name: Oszkiewicz, D.
name: Kwiatkowski, T.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present new photometric observations for twelve asteroids ((122) Gerda, (152) Atala, (260) Huberta, (665) Sabine, (692) Hippodamia, (723) Hammonia, (745) Mauritia, (768) Struveana, (863) Benkoela, (1113) Katja, (1175) Margo, (2057) Rosemary) from the outer part of the main belt aimed to obtain the magnitude-phase curves and to verify geometric albedo and taxonomic class based on their magnitude-phase behaviors. The measured magnitude-phase relations confirm previously determined composition types of (260) Huberta (C-type), (692) Hippodamia (S-type) and (1175) Margo (S-type). Asteroids (665) Sabine and (768) Struveana previously classified as X-type show phase-curve behavior typical for moderate-albedo asteroids and may belong to the M-type. The phase-curve of (723) Hammonia is typical for the S-type which contradicts the previously determined C-type. We confirmed the moderate-albedo of asteroids (122) Gerda and (152) Atala, but their phase-curves are different from typical for the S-type and may indicate more rare compositional types. Based on magnitude-phase behaviors and V-R colors, (2057) Rosemary most probably belongs to M-type, while asteroids (745) Mauritia and (1113) Katja belong to S-complex. The phase curve of the A-type asteroid (863) Benkoela does not cover the opposition effect range and further observations are needed to understand typical features of the phase-curves of A-type asteroids in comparison with other types. We have also determined lightcurve amplitudes of the observed asteroids and obtained new or improved values of the rotation periods for most of them.
description: 16 pages
Editorial
Creators: name: Lopes, J. Bernardino
name: Cravino, J. Paulo
Publisher: name: Indagatio Didactica
Year: 2021

description: O VPCT2020 foi organizado pela Universidade de Trás-os-Montes e Alto Douro (UTAD, Vila Real, Portugal) entre 5 e 7 de novembro de 2020, e decorreu integralmente em modo virtual, devido à pandemia de COVID-19. O VPCT2020 constituiu-se como um fórum multidisciplinar de apresentação, partilha e discussão de relatos de práticas de ensino e de investigação sobre práticas de ensino de Ciências e Tecnologia (C&T), em todos os níveis de ensino. Acolheu professores e investigadores em ensino de Matemática, de Ciências da Natureza, de Física e Química, de Engenharia e de Tecnologia, vindos de Angola, Brasil, Argentina, Espanha e Portugal. Os textos selecionados e agora publicados na Indagatio Didactica são artigos sobre investigações centradas nas práticas de ensino de C&T. Este número especial da Indagatio Didactica é um contributo para divulgar a investigação, feita por professores e investigadores em vários setores de atividade, sobre práticas de ensino formal e informal em C&T.
description: Indagatio Didactica, vol. 13 n.º 1 (2021)
The Galactic Disk-Halo transition - Evidence from Stellar Abundances
Creators: name: Nissen, Poul E.
name: Schuster, William J.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: New information on the relations between the Galactic disks, the halo, and satellite galaxies is being obtained from elemental abundances of stars having metallicities in the range -1.5 < [Fe/H] < -0.5. The first results for a sample of 26 halo stars and 13 thick-disk stars observed with the ESO VLT/UVES spectrograph are presented. The halo stars fall in two distinct groups: One group (9 stars) has [alpha/Fe]= 0.30 +-0.03 like the thick-disk stars. The other group (17 stars) shows a clearly deviating trend ranging from [alpha/Fe]= 0.20 at [Fe/H]= -1.3 to [alpha/Fe]= 0.08 at [Fe/H]= -0.8. The kinematics of the stars are discussed and the abundance ratios Na/Fe, Ni/Fe, Cu/Fe and Ba/Y are applied to see if the low-alpha stars are connected to the thin disk or to Milky Way satellite galaxies. Furthermore, we compare our data with simulations of chemical abundance distributions in hierarchically formed stellar halos in a LambdaCDM Universe.
description: 6 pages, 6 figures. To appear in proceedings of the IAU Symposium No. 254 "The Galaxy Disk in Cosmological Context", Copenhagen 9-13 June 2008, Eds. J. Andersen, J.Bland-Hawthorn & B. Nordstrom, Cambridge University Press
Structural Twinning-induced Insulating Phase in CrN (111) Films
Creators: name: Jin, Qiao
name: Wang, Zhiwen
name: Zhang, Qinghua
name: Zhao, Jiali
name: Cheng, Hu
name: Lin, Shan
name: Chen, Shengru
name: Chen, Shuang
name: Guo, Haizhong
name: He, Meng
name: Ge, Chen
name: Wang, Can
name: Wang, Jia-Ou
name: Gu, Lin
name: Wang, Shanmin
name: Yang, Hongxin
name: Jin, Kui-juan
name: Guo, Er-Jia
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Electronic states of a correlated material can be effectively modified by structural variations delivered from a single-crystal substrate. In this letter, we show that the CrN films grown on MgO (001) substrates have a (001) orientation, whereas the CrN films on α-Al2O3 (0001) substrates are oriented along (111) direction parallel to the surface normal. Transport properties of CrN films are remarkably different depending on crystallographic orientations. The critical thickness for the metal-insulator transition (MIT) in CrN 111 films is significantly larger than that of CrN 001 films. In contrast to CrN 001 films without apparent defects, scanning transmission electron microscopy results reveal that CrN 111 films exhibit strain-induced structural defects, e. g. the periodic horizontal twinning domains, resulting in an increased electron scattering facilitating an insulating state. Understanding the key parameters that determine the electronic properties of ultrathin conductive layers is highly desirable for future technological applications.
description: 19 pages, 4 figures
Kondo lattice model at half-filling
Creators: name: Nourafkan, R.
name: Nafari, N.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The single- and two-channel Kondo lattice model consisting of localized spins interacting antiferromagnetically with the itinerent electrons, are studied using dynamical mean field theory. As an impurity solver for the effective single impurity Anderson model we used the exact diagonalization (ED) method. Using ED allowed us to perform calculations for low temperatures and couplings of arbitrary large strength. Our results for the single-channel case confirm and extend the recent investigations. In the two-channel case we find a symmetry breaking phase transition with increasing coupling strength.
description: 11 pages, 5 figures
Readout of solid-state charge qubits using a single-electron pump
Creators: name: Hines, C.
name: Jacobs, K.
name: Wang, J. B.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A major difficulty in realizing a solid-state quantum computer is the reliable measurement of the states of the quantum registers. In this paper, we propose an efficient readout scheme making use of the resonant tunneling of a ballistic electron produced by a single electron pump. We treat the measurement interaction in detail by modeling the full spatial configuration, and show that for pumped electrons with suitably chosen energy the transmission coefficient is very sensitive to the qubit state. We further show that by using a short sequence of pumping events, coupled with a simple feedback control procedure, the qubit can be measured with high accuracy.
description: 5 pages, revtex4, 4 eps figures. v2: published version
Studies toward a total synthesis of digitoxigenin from thujone
Creators: name: Somerville, John Wallace
Publisher: name: University of British Columbia
Year: 2010

description: This thesis concerns studies directed towards a total synthesis of digitoxigenin 3c from thujone 1. The steroidal analog 85 had previously⁵ been synthesized from thujone and the strategy envisaged for the completion of the synthesis involved alkylation of 85 to produce 86a which, after deoxygenation of the Cl6-ketone followed by reduction of the nitrile, would produce the aldehyde 86b. Aldol condensation of the aldehyde 86b and glyoxylic acid (or an ester thereof) would result in the butenolide 87 which could be converted to the known digitoxigenin synthon 43 by hydrolysis of the C3-ethylene ketal. The steroid analog 85 was synthesized from the commercially available androst-4-ene-3,17-dione 6 by catalytic hydrogenation of the C4,5-double bond, to produce a mixture of the C5α-H and C5β-H diastereomers 88a and 88b, respectively. Separation by preparative liquid chromatography and protection of the C3-ketone of 88b as the ethylene ketal derivative resulted in the Cl7-ketone 89. Wittig reaction of 89 with methyltriphenylphosphonium bromide produced the C17-methylene derivative 91 which was oxidized with selenium dioxide to produce the allylic alcohol 92 and small amounts of the α,β-unsaturated ketone 93. Oxidation of 92 to the required α,β -unsaturated ketone 93 was achieved via the Swern methodology or, alternatively, by treatment with pyridinium dichlorochromate. Oxidation of the trimethylsilylenolether of 93 with DDQ resulted in the cross-conjugated dienone 85. A model study was conducted at this time utilizing the α,β -unsaturated ketone 93 in order to develop the necessary chemistry for elaboration of the butenolide ring. Thus akylation of 93 produced the nitrile 94, the C16-ketone of which was subsequently protected as the corresponding ethylene ketal derivative to provide the required C17β-nitrile 95a. Nuclear Overhauser difference experiments on both 94 and 95a confirmed that both compounds had the required 17β-configuration. Reduction of the nitrile with diisobutylaluminum hydride resulted in the aldehyde 95b which was alkylated with mentholglyoxylate, followed by reduction to produce the butenolide 98 and the trans ester 99. The approach to the synthesis of digitoxigenin was pursued by alkylation of the cross-conjugated diene 85 with diethylaluminum cyanide to produce 86a as a mixture of Cl7-epimers (ratio 2:1, on the basis of NMR). Separation of these isomers proved to be impractical and NOE-difference experiments on this mixture are consistent with the major isomer having the C17β-configuration.
Human-agent coordination in a group formation game
Creators: name: Takko, Tuomas
name: Bhattacharya, Kunal
name: Monsivais, Daniel
name: Kaski, Kimmo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Computer Science and Game Theory (cs.GT)
subject: Multiagent Systems (cs.MA)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: I.6.0; G.3; J.4

description: Coordination and cooperation between humans and autonomous agents in cooperative games raises interesting questions of human decision making and behaviour changes. Here we report our findings from a group formation game in a small-world network of different mixes of human and agent players, aiming to achieve connected clusters of the same colour by swapping places with neighbouring players using non-overlapping information. In the experiments the human players are incentivized by rewarding to prioritize their own cluster while the model of agents' decision making is derived from our previous experiment of purely cooperative game between human players. The experiments were performed by grouping the players in three different setups to investigate the overall effect of having cooperative autonomous agents within teams. We observe that the change in the behavior of human subjects adjusts to playing with autonomous agents by being less risk averse, while keeping the overall performance efficient by splitting the behaviour into selfish and cooperative in the two actions performed during the rounds of the game. Moreover, results from two hybrid human-agent setups suggest that the group composition affects the evolution of clusters. Our findings indicate that in purely or lesser cooperative settings, providing more control to humans could help in maximizing the overall performance of hybrid systems.
description: Chosen to be published in Scientific Reports on 24.05.2021 with DOI: 10.1038/s41598-021-90123-8
The role of the unstable equilibrium points in the transfer of matter in galactic potentials
Creators: name: Romero-Gomez, M.
name: Masdemont, J. J.
name: Garcia-Gomez, C.
name: Athanassoula, E.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Dynamical Systems (math.DS)
subject: Astrophysics (astro-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study the role of the unstable equilibrium points in the transfer of matter in a galaxy using the potential of a rotating triaxial system. In particular, we study the neighbourhood of these points for energy levels and for main model parameters where the zero velocity curves just open and form a bottleneck in the region. For these energies, the transfer of matter from the inner to the outer parts and vice versa starts being possible. We study how the dynamics around the unstable equilibrium points is driven, by performing a partial normal form scheme and by computing the invariant manifolds of periodic orbits and quasi-periodic orbits using the reduced Hamiltonian. In particular, we compute some homoclinic and heteroclinic orbits playing a crucial role. Our results also show that in slow rotating and/or axisymmetric systems the hyperbolic character of the equilibrium points is cancelled, so that no transfer of matter is possible through the bottleneck.
description: 26 pages, 13 Figs, to appear in Communications of Nonlinear Science and Numerical Simulations (Accepted 21st July 2008)
Lackadaisical quantum walks on 2D grids with multiple marked vertices
Creators: name: Nahimovs, Nikolajs
name: Santos, Raqueline A. M.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Lackadaisical quantum walk (LQW) is a quantum analog of a classical lazy walk, where each vertex has a self-loop of weight $l$. For a regular $\sqrt{N}\times\sqrt{N}$ 2D grid LQW can find a single marked vertex with $O(1)$ probability in $O(\sqrt{N\log N})$ steps using $l = d/N$, where $d$ is the degree of the vertices of the grid. For multiple marked vertices, however, $l = d/N$ is not optimal as the success probability decreases with the increase of the number of marked vertices. In this paper, we numerically study search by LQW for different types of 2D grids -- triangular, rectangular and honeycomb -- with multiple marked vertices. We show that in all cases the weight $l = m\cdot d/N$, where $m$ is the number of marked vertices, still leads to $O(1)$ success probability.
description: 14 pages, 8 figures. arXiv admin note: text overlap with arXiv:2007.13564
Effective temperatures from the fluctuation-dissipation measurements in soft glassy materials
Creators: name: Jabbari-Farouji, S.
name: Mizuno, D.
name: Derks, D.
name: Wegdam, G. H.
name: MacKintosh, F. C.
name: Schmidt, C. F.
name: Bonn, D.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We have investigated the validity of the fluctuation-dissipation theorem (FDT) and the applicability of the concept of effective temperature in a number of non-equilibrium soft glassy materials. Using a combination of passive and active microrheology to measure displacement fluctuations and the mechanical response function of probe particles embedded in the materials, we have directly tested the validity of the FDT. Our results show no violation of the FDT over several decades in frequency (1-10$^4$ Hz) for hard sphere colloidal glasses and colloidal glasses and gels of Laponite. We further extended the bandwidth of our measurements to lower frequencies (down to 0.1 Hz) using video microscopy to measure the displacement fluctuations, again without finding any deviations from the FDT.
description: 6 pages, 4 Figures
Genome sequencing of high land plant Corydalis edulis
Creators: name: 杨婷(TING YANG)
Publisher: name: CNGB
Year: 2023
Subjects: Genome sequencing and assembly
Raw sequence reads
Genome sequencing
Multispecies
Evolution

description: In this project, we have sequenced the whole genome sequencing of Corydalis edulis with nanopore technology. Try to dissect the defensive mechanism through camouflage, we collected nine populations that including 67 samples for re-sequencing.
Spectral Analysis of Dirac Operators with delta interactions supported on the boundaries of rough domains
Creators: name: Benhellal, Badreddine
Publisher: name: arXiv
Year: 2021
Subjects: subject: Spectral Theory (math.SP)
subject: FOS: Mathematics
subject: 81Q10, 81V05, 35P15, 58C40

description: Given an open set $Ω\subset\mathbb{R}^3$. We deal with the spectral study of Dirac operators of the form $H_{a,τ}=H+A_{a,τ}δ_{\partialΩ}$, where $H$ is the free Dirac operator in $\mathbb{R}^3$, $A_{a,τ}$ is a bounded invertible, self-adjoint operator in $\mathit{L}^{2}(\partialΩ)^4$, depending on parameters $(a,τ)\in\mathbb{R}\times\mathbb{R}^n$, $n\geqslant1$. We investigate the self-adjointness and the related spectral properties of $H_{a,τ}$, such as the phenomenon of confinement and the Sobolev regularity of the domain in different situations. Our set of techniques, which is based on fundamental solutions and layer potentials, allows us to tackle the above problems under mild geometric measure theoretic assumptions on $Ω$.
description: 35 pages. arXiv admin note: substantial text overlap with arXiv:2102.10207
Near-Room Temperature Ferromagnetic Insulating State in Highly Distorted LaCoO2.5 with CoO5 Square Pyramids
Creators: name: Zhang, Qinghua
name: Gao, Ang
name: Meng, Fanqi
name: Jin, Qiao
name: Lin, Shan
name: Wang, Xuefeng
name: Xiao, Dongdong
name: Wang, Can
name: Jin, Kui-juan
name: Su, Dong
name: Guo, Er-Jia
name: Gu, Lin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Dedicated control of oxygen vacancies is an important route to functionalizing complex oxide films. It is well-known that tensile strain significantly lowers the oxygen vacancy formation energy, whereas compressive strain plays a minor role. Thus, atomically reconstruction by extracting oxygen from a compressive-strained film is challenging. Here we report an unexpected LaCoO2.5 phase with a zigzag-like oxygen vacancy ordering through annealing a compressive-strained LaCoO3 in vacuum. The synergetic tilt and distortion of CoO5 square pyramids with large La and Co shifts are quantified using scanning transmission electron microscopy. The large in-plane expansion of CoO5 square pyramids weaken the crystal-field splitting and facilitated the ordered high-spin state of Co2+, which produces an insulating ferromagnetic state with a Curie temperature of ~284 K and a saturation magnetization of ~0.25 μB/Co. These results demonstrate that extracting targeted oxygen from a compressive-strained oxide provides an opportunity for creating unexpected crystal structures and novel functionalities.
When do stepwise algorithms meet subset selection criteria?
Creators: name: Huo, Xiaoming
name: Xuelei
name: Ni
Publisher: name: arXiv
Year: 2007
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62J07 (Primary)

description: Recent results in homotopy and solution paths demonstrate that certain well-designed greedy algorithms, with a range of values of the algorithmic parameter, can provide solution paths to a sequence of convex optimization problems. On the other hand, in regression many existing criteria in subset selection (including $C_p$, AIC, BIC, MDL, RIC, etc.) involve optimizing an objective function that contains a counting measure. The two optimization problems are formulated as (P1) and (P0) in the present paper. The latter is generally combinatoric and has been proven to be NP-hard. We study the conditions under which the two optimization problems have common solutions. Hence, in these situations a stepwise algorithm can be used to solve the seemingly unsolvable problem. Our main result is motivated by recent work in sparse representation, while two others emerge from different angles: a direct analysis of sufficiency and necessity and a condition on the mostly correlated covariates. An extreme example connected with least angle regression is of independent interest.
description: Published at http://dx.doi.org/10.1214/009053606000001334 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Similarity solutions for two-phase fluids models
Creators: name: Paliathanasis, Andronikos
Publisher: name: arXiv
Year: 2021
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Mathematical Physics (math-ph)
subject: Analysis of PDEs (math.AP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The algebraic properties of drift-flux two-phase fluids models without gravitational and wall friction forces are studied. More precisely, for the two fluids we consider equation of states of polytropic gases. We perform a classification scheme of the unknown parameters of the model such that to determine all the possible admitted Lie symmetries. We find that in the most general case the dynamical system of hyperbolic equations is invariant under the action of a four dimensional Lie algebra, while the larger number of admitted Lie symmetries is six. For each admitted Lie algebra the one-dimensional optimal system is derived which is applied for the determination of all the unique similarity transformations which lead to similarity solutions. Our results are compared with that of previous studies from where we see that most of the solutions presented in this study have not found before in the literature.
description: 25 pages, 4 tables; to appear in Mathematical Methods in the Applied Sciences
Integrated Extrachromosomal Circular DNA Landscape of Clear Cell Renal Cell Carcinoma
Creators: name: 喆 许
Publisher: name: CNGB
Year: 2023
Subjects: Raw sequence reads
Multiisolate

description: Clear cell renal cell carcinoma (ccRCC) ranks the most prevalent urinary tumors. Molecular studies of genomics, transcriptomics, and epigenomics have greatly advanced the diagnosis and treatment. However, the hallmarks of extrachromosomal circular DNA are still unclear in ccRCC. In this study, we thoroughly explored the landscape of eccDNA in paired samples from nighty-nine ccRCC and compare with twenty-three other subtypes of RCCs. A strong correlation of eccDNA and oncogene transcription was identified. Meanwhile, multiple oncogenes carrying eccDNAs were detected from tumor samples. Of note, we also proposed an eccDNA driven immunology effects in late stage ccRCCs.
Syntheses and magnetic studies of manganese(II) monophenylphosphinates and some cadmium(II) doped compounds
Creators: name: Du, Jing-Long
Publisher: name: University of British Columbia
Year: 2010

description: Anhydrous monophenylphosphinates of manganese(II), Mn[H(C₆H₅)PO₂]₂ (Form I, Form II and Form 1(B)) and cadmium(II), Cd[H(C₆H₅)PO₂]₂ (Form I and Form II) were synthesized and characterized by solubility tests, Differential Scanning Calorimetry (DSC), Infrared Spectroscopy, X-ray Powder Diffractometry, Electron Spin Resonance (ESR) spectroscopy, magnetic susceptibility measurements and Electron Spectroscopy for Chemical Analysis (ESCA). These materials are considered to be polymeric with metal ions connected in chains by double bridging phosphinate groups with cross-linkage forming sheets and octahedral metal centers. Magnetic susceptibility studies showed that Mn[H(C₆H₅)PO₂]₂ (Form I) exhibits relatively strong antiferromagnetic exchange interactions (J is about -4.50 cm⁻¹) and the effects on this magnetic exchange of doping diamagnetic cadmium ions into the material have been investigated. A series of mixed metal phosphinates of the form Mn₁₋x Cdx [H(C₆H₅)PO₂]₂ (Form I) where x=0 to 1.00 were prepared and investigated. The effect of doping with cadmium is to break the infinite manganese(II) monophenylphosphinate chain into finite segments and to generate monomer impurities in odd numbered segments. As the extent of doping is increased the average chain length decreases and the fraction of monomer increases. In addition, the exchange coupling constant, J, was found to decrease (from -4.50 to -2.70 cm⁻¹) as the average chain length decreases. Mn[H(C₆H₅)PO₂]₂ (Form 1(B)), which is precipitated from concentrated solutions, contains much shorter chain fragments than the pure Form I material. Mn[H(C₆H₅)PO₂]₂ (Form II) has a distinct infrared spectrum and X-ray powder diffraction pattern and shows much weaker antiferromagnetic behavior (J is about -2.40 cm⁻¹) than the Form I compound. Magnetic studies suggest that in this compound the average chain length is significantly smaller than in Mn[H(C₆H₅)PO₂]₂ (Form I). The hydrated monophenylphosphinates of manganese(II), Mn[H(C₆H₅)PO₂]₂•H₂0 and Mn[H(C₆H₅)PO₂]₂•2H₂0, were synthesized and characterized in this work. The structures of these compounds are considered to be similar to those of the anhydrous materials except in the hydrated compounds one or two of the metal coordination sites are occupied by water molecules. The dihydrate shows only very weak antiferromagnetic properties (J is about -0.50 cm⁻¹). The diphenylphosphinates of manganese(II) and cadmium(II) were also prepared and characterized. The infrared spectra and X-ray powder diffraction patterns for these materials are distinct from each other,which indicates the compounds are not isomorphous. Only rather weak magnetic exchange was observed in the manganese compound. Zn[H(C₆H₅)PO₂]₂ has also been synthesized and partially characterized in this work. The infrared spectrum and X-ray powder diffraction pattern obtained for this compound are unique among all the metal phosphinates studied in this work.
Normal-state transport properties of PrFeAsO$_{1-x}$F$_y$ superconductor
Creators: name: Bhoi, D.
name: Mandal, P.
name: Choudhury, P.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We have synthesized oxygen-deficient fluorine-doped samples of nominal composition PrFeAsO$_{1-x}$F$_y$ to study the normal and superconducting state properties. Resistivity of undoped PrFeAsO exhibits a strong anomaly at around 155 K due to the spin-density-wave instability. Fluorine doping ($x$=0.4, $y$=0.12) suppresses this magnetic instability and drives the system to the superconducting ground state with superconducting onset temperature 50 K. The behavior of normal-state resistivity changes from $T^2$-like to $T$-linear to sublinear in $T$ with increasing temperature indicating that both electron-electron interaction and electron-phonon interaction are strong. From the analysis of $T$ dependence of $ρ$, we have estimated the electron-phonon coupling strength ($λ$) to be quite large (1.3).
description: 14pages,4 Figures
Local partial likelihood estimation in proportional hazards regression
Creators: name: Chen, Songnian
name: Zhou, Lingzhi
Publisher: name: arXiv
Year: 2007
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62G05 (Primary); 62G08, 62G20, 62E02, 60G44 (Secondary)

description: Fan, Gijbels and King [Ann. Statist. 25 (1997) 1661--1690] considered the estimation of the risk function $ψ(x)$ in the proportional hazards model. Their proposed estimator is based on integrating the estimated derivative function obtained through a local version of the partial likelihood. They proved the large sample properties of the derivative function, but the large sample properties of the estimator for the risk function itself were not established. In this paper, we consider direct estimation of the relative risk function $ψ(x_2)-ψ(x_1)$ for any location normalization point $x_1$. The main novelty in our approach is that we select observations in shrinking neighborhoods of both $x_1$ and $x_2$ when constructing a local version of the partial likelihood, whereas Fan, Gijbels and King [Ann. Statist. 25 (1997) 1661--1690] only concentrated on a single neighborhood, resulting in the cancellation of the risk function in the local likelihood function. The asymptotic properties of our estimator are rigorously established and the variance of the estimator is easily estimated. The idea behind our approach is extended to estimate the differences between groups. A simulation study is carried out.
description: Published at http://dx.doi.org/10.1214/009053606000001299 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
New Physics with Tagged Forward Protons at the LHC
Creators: name: Khoze, V. A.
name: Martin, A. D.
name: Ryskin, M. G.
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The addition of forward proton detectors to LHC experiments will significantly enlarge the potential for studying New Physics. A topical example is Higgs production by the central exclusive diffractive process, pp -> p+H+p. We discuss the exclusive production of Higgs bosons in both the SM and MSSM. Special attention is paid to the backgrounds to the H -> bbbar signal.
description: 12 pages, 4 figures, presented by V.A. Khoze at the 21st Workshop Les Rencontres de Physique de la Vallee d'Aoste, La Thuile, 4-10 March, 2007
Mapping the distribution of luminous and dark matter in strong lensing galaxies
Creators: name: Ferreras, I.
name: Saha, P.
name: Williams, L. L. R.
name: Burles, S.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present the distribution of luminous and dark matter in a set of strong lensing (early-type) galaxies. By combining two independent techniques - stellar population synthesis and gravitational lensing - we can compare the baryonic and dark matter content in these galaxies within the regions that can be probed using the images of the lensed background source. Two samples were studied, extracted from the CASTLES and SLACS surveys. The former probes a wider range of redshifts and allows us to explore the mass distribution out to ~5Re. The high resolution optical images of the latter (using HST/ACS) are used to show a pixellated map of the ratio between total and baryonic matter. We find dark matter to be absent in the cores of these galaxies, with an increasing contribution at projected radii R>Re. The slopes are roughly compatible with an isothermal slope (better interpreted as an adiabatically contracted NFW profile), but a large scatter in the slope exists among galaxies. There is a trend suggesting most massive galaxies have a higher content of dark matter in the regions probed by this analysis.
description: 10 pages, 6 figures. To appear in "Dark Galaxies and Lost Baryons", IAU244 conference proceedings
Exclusive $ρ^0$ electroproduction on the proton at CLAS
Creators: name: CLAS Collaboration
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The $e p\to e^\prime p ρ^0$ reaction has been measured, using the 5.754 GeV electron beam of Jefferson Lab and the CLAS detector. This represents the largest ever set of data for this reaction in the valence region. Integrated and differential cross sections are presented. The $W$, $Q^2$ and $t$ dependences of the cross section are compared to theoretical calculations based on $t$-channel meson-exchange Regge theory on the one hand and on quark handbag diagrams related to Generalized Parton Distributions (GPDs) on the other hand. The Regge approach can describe at the $\approx$ 30% level most of the features of the present data while the two GPD calculations that are presented in this article which succesfully reproduce the high energy data strongly underestimate the present data. The question is then raised whether this discrepancy originates from an incomplete or inexact way of modelling the GPDs or the associated hard scattering amplitude or whether the GPD formalism is simply inapplicable in this region due to higher-twists contributions, incalculable at present.
description: 29 pages, 29 figures
Dimensional Control of Octahedral Tilt in SrRuO3 via Infinite-layered Oxides
Creators: name: Lin, Shan
name: Zhang, Qinghua
name: Sang, Xiahan
name: Zhao, Jiali
name: Cheng, Sheng
name: Huon, Amanda
name: Jin, Qiao
name: Chen, Shuang
name: Chen, Shengru
name: Guo, Haizhong
name: He, Meng
name: Ge, Chen
name: Wang, Can
name: Wang, Jia-Ou
name: Fitzsimmons, Michael R.
name: Gu, Lin
name: Zhu, Tao
name: Jin, Kui-juan
name: Guo, Er-Jia
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Manipulation of octahedral distortion at atomic length scale is an effective means to tune the physical ground states of functional oxides. Previous work demonstrates that epitaxial strain and film thickness are variable parameters to modify the octahedral rotation and tilt. However, selective control of bonding geometry by structural propagation from adjacent layers is rarely studied. Here we propose a new route to tune the ferromagnetic response in SrRuO3 (SRO) ultrathin layers by oxygen coordination of adjacent SrCuO2 (SCO) layers. The infinite-layered CuO2 in SCO exhibits a structural transformation from "planar-type" to "chain-type" as reducing film thickness. These two orientations dramatically modify the polyhedral connectivity at the interface, thus altering the octahedral distortion of SRO. The local structural variation changes the spin state of Ru and hybridization strength between Ru 4d and O 2p orbitals, leading to a significant change in the magnetoresistance and anomalous Hall resistivity of SRO layers. These findings could launch further investigations into adaptive control of magnetoelectric properties in quantum oxide heterostructures using oxygen coordination.
Estimating the number of classes
Creators: name: Mao, Chang Xuan
name: Lindsay, Bruce G.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62G15, 62G15 (Primary); 62G05 (Secondary)

description: Estimating the unknown number of classes in a population has numerous important applications. In a Poisson mixture model, the problem is reduced to estimating the odds that a class is undetected in a sample. The discontinuity of the odds prevents the existence of locally unbiased and informative estimators and restricts confidence intervals to be one-sided. Confidence intervals for the number of classes are also necessarily one-sided. A sequence of lower bounds to the odds is developed and used to define pseudo maximum likelihood estimators for the number of classes.
description: Published at http://dx.doi.org/10.1214/009053606000001280 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Synthesis and reactivity of terminal phosphido complexes of iridium(III)
Creators: name: Bhangu, Kiran
Publisher: name: University of British Columbia
Year: 2010

description: The iridium(III) methyl dlarylphosphido complexes, Ir(CH₃)(PR₂)-[N(SiMe₂CH₂PPh₂)₂] (2a: R = phenyl, 2b: R = meta-tolyl), have been successfully prepared by transmetalation of the iridium(III) methyl iodide complex, Ir(CH₃)(I)[N(SiMe₂CH₂PPh₂)₂], with the corresponding lithium diarylphosphide. Based primarily on a nuclear Overhauser effect difference experiment, these complexes are assigned a stereochemistry intermediate between square pyramidal and trigonal bipyramidal forms. The pyramidal geometry at the phosphido ligand is evident from the ³¹P{¹H} NMR spectral data. The complex 2a affords a mixture of at least three, as yet uncharacterized complexes when heated to 60°C for 5 hours in benzene solution; however, clean formation of the planar iridium(I) methyl-diphenylphosphine complex, Ir(PCH₃Ph₂)[N(SiMe₂CH₂PPh₂)₂], 3a, takes place when 2a is exposed to light for 24 hours in benzene solution. A crossover experiment indicates that the latter reaction involves an intramolecular mechanism. The nucleophilicity of the phosphido ligand is evident from the reaction of 2a with CH₃I; the product afforded in this reaction is Ir(CH₃)(PCH₃Ph₂)(I)[N(SiMe₂CH₂PPh₂)₂], 4. A labelling experiment with CD₃I shows that the reaction is intermolecular as the product observed is Ir(CH₃)(PCD₃Ph₂)(I)[N(SiMe₂CH₂PPh₂)₂]. Exposure of 2a at room temperature to one atmosphere of H₂ produces a mixture of the iridium(III) dihydride Ir(H)₂(PHPh₂)[N(SiMe₂CH₂-PPh₂)₂], 5, and methyl hydride Ir(CH₃)(H)(PHPh₂)[N(SiMe₂CH₂PPh₂)2], 6, in 70 and 30% yields, respectively. The analogous reaction with one atmosphere of D₂ reveals that the formation of the methyl hydride complex involves an intramolecular proton abstraction by the phosphide ligand from the bound methyl group, as the minor product observed in this reaction is Ir(CH₂D)(D)(PHPh₂)[N(SiMe₂CH₂PPh₂)₂]. A mechanism is proposed involving the formation of Ir(=CH₂)(PHPh₂)[N(SiMe₂CH₂PPh₂)₂] followed by trapping with D₂ to give the methyl hydride product. The dihydride complex observed in these reactions is apparently produced by heterolytic cleavage of dihydrogen. Under excess CO, complex 2a is converted to an octahedral carbonyl complex Ir(CH3)(CO)(PPh2)[N(SiMe2CH2PPh2)2], 9; the carbonyl and the phosphide ligands in this complex are in cis arrangement. Upon removing the excess CO from the reaction mixture, another stereoisomer, 10, is produced In which the carbonyl and the phosphide ligands are trans to one another. It is suggested that the carbonyl complex 9 observed under excess CO is the kinetically favoured isomer which rearranges to the more thermodynamically stable isomer, 10, upon removal of the excess CO. Both of the carbonyl Isomers are unstable In solution at room temperature as they convert to the planar iridium(I) complex Ir(CO)[N(SiMe₂CH₂PPh₂)₂] and methyldiphenylphosphine.
On The Recently Discovered Pulsations From RX J1856.5-3754
Creators: name: Chkheidze, N.
name: Lomiashvili, D.
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: An explanation of the recently discovered 7 s pulsations from the isolated neutron star RX J1856.5-3754 is presented. It is assumed that the real spin period of this source is $\approx1$ s, whereas the observed spin-modulation is caused by the presence of a nearly transverse, very low frequency drift waves in the pulsar magnetosphere. It is supposed that the period of the drift wave is equal to a recently observed one. The simulated lightcurve is plotted, the angular parameters are defined and the value of the pulsed fraction of only $\sim 1.2%$ is explained.
description: 7 pages, 2 figures