cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
"Spin-Disentangled" Exact Diagonalization of Repulsive Hubbard Systems: Superconducting Pair Propagation
Creators: name: Cini, Michele
name: Stefanucci, Gianluca
name: Perfetto, Enrico
name: Callegari, Agnese
Publisher: name: arXiv
Year: 2002
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: By a novel exact diagonalization technique we show that bound pairs propagate between repulsive Hubbard clusters in a superconducting fashion. The size of the matrices that must be handled depends on the number of fermion configurations {\em per spin}, which is of the order of the square root of the overall size of the Hilbert space. We use CuO$_{4}$ units connected by weak O-O links to model interplanar coupling and c-axis superconductivity in Cuprates. The numerical evidence on Cu$_{2}$O$_{8}$ and Cu$_{3}$O$_{12}$ prompts a new analytic scheme describing the propagation of bound pairs and also the superconducting flux quantization in a 3-d geometry.
description: 5 pages, 3 figures
Atmospheric Electricity at the Ice Giants
Creators: name: Aplin, K. L.
name: Fischer, G.
name: Nordheim, T. A.
name: Konovalenko, A.
name: Zakharenko, V.
name: Zarka, P.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Space Physics (physics.space-ph)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: FOS: Physical sciences

description: Lightning was detected by Voyager 2 at Uranus and Neptune, and weaker electrical processes also occur throughout planetary atmospheres from galactic cosmic ray (GCR) ionisation. Lightning is an indicator of convection, whereas electrical processes away from storms modulate cloud formation and chemistry, particularly if there is little insolation to drive other mechanisms. The ice giants appear to be unique in the Solar System in that they are distant enough from the Sun for GCR-related mechanisms to be significant for clouds and climate, yet also convective enough for lightning to occur. This paper reviews observations (both from Voyager 2 and Earth), data analysis and modelling, and considers options for future missions. Radio, energetic particle and magnetic instruments are recommended for future orbiters, and Huygens-like atmospheric electricity sensors for in situ observations. Uranian lightning is also expected to be detectable from terrestrial radio telescopes.
description: Revised version for Space Science Reviews
Modeling interest rate dynamics: an infinite-dimensional approach
Creators: name: Cont, Rama
Publisher: name: arXiv
Year: 1999
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Probability (math.PR)
subject: Pricing of Securities (q-fin.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: FOS: Economics and business

description: We present a family of models for the term structure of interest rates which describe the interest rate curve as a stochastic process in a Hilbert space. We start by decomposing the deformations of the term structure into the variations of the short rate, the long rate and the fluctuations of the curve around its average shape. This fluctuation is then described as a solution of a stochastic evolution equation in an infinite dimensional space. In the case where deformations are local in maturity, this equation reduces to a stochastic PDE, of which we give the simplest example. We discuss the properties of the solutions and show that they capture in a parsimonious manner the essential features of yield curve dynamics: imperfect correlation between maturities, mean reversion of interest rates and the structure of principal components of term structure deformations. Finally, we discuss calibration issues and show that the model parameters have a natural interpretation in terms of empirically observed quantities.
description: Keywords: interest rates, stochastic PDE, term structure models, stochastic processes in Hilbert space. Other related works may be retrieved on http://www.eleves.ens.fr:8080/home/cont/papers.html
Analytical Query Execution Optimized for all Layers of Modern Hardware
Creators: Polychroniou, Orestis
Publisher: name: Columbia University
Year: 2018
Subjects: Computer science
Databases
Querying (Computer science)
Hardware

description: Analytical database queries are at the core of business intelligence and decision support. To analyze the vast amounts of data available today, query execution needs to be orders of magnitude faster. Hardware advances have made a profound impact on database design and implementation. The large main memory capacity allows queries to execute exclusively in memory and shifts the bottleneck from disk access to memory bandwidth. In the new setting, to optimize query performance, databases must be aware of an unprecedented multitude of complicated hardware features. This thesis focuses on the design and implementation of highly efficient database systems by optimizing analytical query execution for all layers of modern hardware. The hardware layers include the network across multiple machines, main memory and the NUMA interconnection across multiple processors, the multiple levels of caches across multiple processor cores, and the execution pipeline within each core. For the network layer, we introduce a distributed join algorithm that minimizes the network traffic. For the memory hierarchy, we describe partitioning variants aware to the dynamics of the CPU caches and the NUMA interconnection. To improve the memory access rate of linear scans, we optimize lightweight compression variants and evaluate their trade-offs. To accelerate query execution within the core pipeline, we introduce advanced SIMD vectorization techniques generalizable across multiple operators. We evaluate our algorithms and techniques on both mainstream hardware and on many-integrated-core platforms, and combine our techniques in a new query engine design that can better utilize the features of many-core CPUs. In the era of hardware becoming increasingly parallel and datasets consistently growing in size, this thesis can serve as a compass for developing hardware-conscious databases with truly high-performance analytical query execution.
Rapthius peruvianus Lord & Ivie 2016, new combination
Creators: name: Lord, Nathan P.
name: Ivie, Michael A.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Zopheridae
Rapthius
Rapthius peruvianus

description: Rapthius peruvianus (Franz, 1969), new combination
(Figs. 19, 21)
 Tarphius peruvianus Franz 1969: 144. New combination.
 Description. Rapthius peruvianus is the only known member of this genus and is diagnosed and characterized by the features given in the generic description above. Likely species level diagnostic features may include the number and placement of pronotal and elytral tubercles (Fig. 19).
 Distribution. Peru (Fig. 21).
 Biology. Specimens were collected by sifting forest litter.
 Type Material. 2 specimens. Holotype (carded, NHMW): Umg. Tarapoto; Peru, lg. Franz / Tarphius; peruanus; m.; det. H. Franz / [red label, in Franz’ s hand] Typus. Paratype (carded, NHMW): [tip of genitalia partially extruded, appears broken] Umg. Tarapoto; Peru,lg. Franz / [light yellow label, in Franz’ s hand] Tarphius; peruanus; m.; [typed] PARATYPUS.
 Comments. Franz (1969) elected to place the species in an unrelated Old World genus known primarily from the Canary Islands. This species does not belong in Tarphius.
description: Published as part of Lord, Nathan P. & Ivie, Michael A., 2016, Several New Genera and Species of New World Synchitini (Coleoptera: Zopheridae: Colydiinae), pp. 715-753 in The Coleopterists Bulletin 70 (4) on pages 715-753, DOI: 10.1649/0010-065X-70.4.715, http://zenodo.org/record/5340179
Additional file 1: of Stock identification of minor carp, Cirrhinus reba, Hamilton 1822 through landmark-based morphometric and meristic variations
Creators: name: Rokhsana Ethin
name: Md Hossain
name: Animesh Roy
name: Rutegwa, Marcellin
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Inorganic Chemistry
subject: 60506 Virology

description: Table S1. List of eight meristic characters used for the analysis of C. reba stock variations.Â (DOCX 15 kb)
Additional file 5 of The effect of a novel glycolysis-related gene signature on progression, prognosis and immune microenvironment of renal cell carcinoma
Creators: name: Xu, Fangshi
name: Guan, Yibing
name: Xue, Li
name: Huang, Shanlong
name: Gao, Ke
name: Yang, Zhen
name: Chong, Tie
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Supplementary Table 1. The description of glycolysis-related gene sets.
On metric-connection compatibility and the signature change of space-time
Creators: name: Iliev, Bozhidar Z.
Publisher: name: arXiv
Year: 1998
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: Differential Geometry (math.DG)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We discuss and investigate the problem of existence of metric-compatible linear connections for a given space-time metric which is, generally, assumed to be semi-pseudo-Riemannian. We prove that under sufficiently general conditions such connections exist iff the rank and signature of the metric are constant. On this base we analyze possible changes of the space-time signature.
description: 18 standard LaTeX 2e pages. The packages AMS-LaTeX and amsfonts are required
Generalized Hermite Polynomials and the Heat Equation for Dunkl Operators
Creators: name: Rösler, Margit
Publisher: name: arXiv
Year: 1997
Subjects: subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics
subject: 33C80, 35K05

description: Based on the theory of Dunkl operators, this paper presents a general concept of multivariable Hermite polynomials and Hermite functions which are associated with finite reflection groups on $\b R^N$. The definition and properties of these generalized Hermite systems extend naturally those of their classical counterparts; partial derivatives and the usual exponential kernel are here replaced by Dunkl operators and the generalized exponential kernel K of the Dunkl transform. In case of the symmetric group $S_N$, our setting includes the polynomial eigenfunctions of certain Calogero-Sutherland type operators. The second part of this paper is devoted to the heat equation associated with Dunkl's Laplacian. As in the classical case, the corresponding Cauchy problem is governed by a positive one-parameter semigroup; this is assured by a maximum principle for the generalized Laplacian. The explicit solution to the Cauchy problem involves again the kernel K, which is, on the way, proven to be nonnegative for real arguments.
description: 24 pages, AMS-LaTeX
A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis
Creators: name: Hoffmann, Max J.
name: Engelmann, Felix
name: Matera, Sebastian
Publisher: name: Freie Universität Berlin
Year: 2017
Subjects: subject: Adsorption
subject: Reaction rate constants
subject: Desorption
subject: Carbon dioxide
subject: Oxidation
subject: 500 Naturwissenschaften und Mathematik

description: Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for the atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past, the application of sensitivity analysis, such as degree of rate control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study, we present an efficient and robust three-stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using the CO oxidation on RuO2(110) as a prototypical reaction. In the first step, we utilize the Fisher information matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on the linear response theory for calculating the sensitivity measure for non- critical conditions which covers the majority of cases. Finally, we adapt a method for sampling coupled finite differences for evaluating the sensitivity measure for lattice based models. This allows for an efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano-scale design of heterogeneous catalysts.
Slipinskius Lord and Ivie 2016, new genus
Creators: name: Lord, Nathan P.
name: Ivie, Michael A.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Zopheridae
Slipinskius

description: Slipinskius Lord and Ivie, new genus  (Figs. 4, 20, 22)
 Norix sensu Ślipiński and Lawrence 1997: 403, figs. 313–320, 472. Not Norix Broun. Misidentification.
description: Published as part of Lord, Nathan P. & Ivie, Michael A., 2016, Several New Genera and Species of New World Synchitini (Coleoptera: Zopheridae: Colydiinae), pp. 715-753 in The Coleopterists Bulletin 70 (4) on pages 715-753, DOI: 10.1649/0010-065X-70.4.715, http://zenodo.org/record/5340179
Lower bounds on the non-Clifford resources for quantum computations
Creators: name: Beverland, Michael
name: Campbell, Earl
name: Howard, Mark
name: Kliuchnikov, Vadym
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We establish lower-bounds on the number of resource states, also known as magic states, needed to perform various quantum computing tasks, treating stabilizer operations as free. Our bounds apply to adaptive computations using measurements and an arbitrary number of stabilizer ancillas. We consider (1) resource state conversion, (2) single-qubit unitary synthesis, and (3) computational tasks. To prove our resource conversion bounds we introduce two new monotones, the stabilizer nullity and the dyadic monotone, and make use of the already-known stabilizer extent. We consider conversions that borrow resource states, known as catalyst states, and return them at the end of the algorithm. We show that catalysis is necessary for many conversions and introduce new catalytic conversions, some of which are close to optimal. By finding a canonical form for post-selected stabilizer computations, we show that approximating a single-qubit unitary to within diamond-norm precision $\varepsilon$ requires at least $1/7\cdot\log_2(1/\varepsilon) - 4/3$ $T$-states on average. This is the first lower bound that applies to synthesis protocols using fall-back, mixing techniques, and where the number of ancillas used can depend on $\varepsilon$. Up to multiplicative factors, we optimally lower bound the number of $T$ or $CCZ$ states needed to implement the ubiquitous modular adder and multiply-controlled-$Z$ operations. When the probability of Pauli measurement outcomes is 1/2, some of our bounds become tight to within a small additive constant.
description: 62 pages
MOESM2 of An automated homology-based approach for identifying transposable elements
Creators: name: Kennedy, Ryan
name: Unger, Maria
name: Christley, Scott
name: Collins, Frank
name: Madey, Gregory
Publisher: name: figshare
Year: 2011
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology
subject: Computational Biology

description: Additional file 2:ClustalX alignments of selected A. gambiae PEST non-LTR elements from TEfam and the TESeeker -produced full-length elements. (PDF 911 KB)
Emerging edge states on the surface of the epitaxial semimetal CuMnAs thin film
Creators: name: Nguyen, Giang D.
name: Pitike, Krishna
name: Wadley, Peter
name: Cooper, Valentino R
name: Yoon, Mina
name: Berlijn, Tom
name: Li, An-Ping
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Epitaxial thin films of CuMnAs have recently attracted attention due to their potential to host relativistic antiferromagnetic spintronics and exotic topological physics. Here we report on the structural and electronic properties of a tetragonal CuMnAs thin film studied using scanning tunneling microscopy (STM) and density functional theory (DFT). STM reveals a surface terminated by As atoms, with the expected semi-metallic behavior. An unexpected zigzag step edge surface reconstruction is observed with emerging electronic states below the Fermi energy. DFT calculations indicate that the step edge reconstruction can be attributed to an As deficiency that results in changes in the density of states of the remaining As atoms at the step edge. This understanding of the surface structure and step edges on the CuMnAs thin film will enable in-depth studies of its topological properties and magnetism.
Non-negative Curvature and Conullity of the Curvature Tensor
Creators: name: Brooks, Thomas G.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C20 (Primary)

description: The conullity of a curvature tensor is the codimension of its kernel. We consider the cases of conullity two in any dimension and conullity three in dimension four. We show that these conditions are compatible with non-negative sectional curvature only if either the manifold is diffeomorphic to $\mathbb{R}^n$ or the universal cover is an isometric product with a Euclidean factor. Moreover, we show that finite volume manifolds with conullity 3 are locally products.
description: 12 pages, 1 figure
Interface Motion in Disordered Ferromagnets
Creators: name: Roters, L.
name: Lubeck, S.
name: Usadel, K. D.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider numerically the depinning transition in the random-field Ising model. Our analysis reveals that the three and four dimensional model displays a simple scaling behavior whereas the five dimensional scaling behavior is affected by logarithmic corrections. This suggests that d=5 is the upper critical dimension of the depinning transition in the random-field Ising model. Furthermore, we investigate the so-called creep regime (small driving fields and temperatures) where the interface velocity is given by an Arrhenius law.
description: some misprints corrected
Proof of the symmetry of the off-diagonal heat-kernel and Hadamard's expansion coefficients in general $C^{\infty}$ Riemannian manifolds
Creators: name: Moretti, Valter
Publisher: name: arXiv
Year: 1999
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We consider the problem of the symmetry of the off-diagonal heat-kernel coefficients as well as the coefficients corresponding to the short-distance-divergent part of the Hadamard expansion in general smooth (analytic or not) manifolds. The requirement of such a symmetry played a central rôle in the theory of the point-splitting one-loop renormalization of the stress tensor in either Riemannian or Lorentzian manifolds. Actually, the symmetry of these coefficients has been assumed as a hypothesis in several papers concerning these issues without an explicit proof. The difficulty of a direct proof is related to the fact that the considered off-diagonal heat-kernel expansion, also in the Riemannian case, in principle, may be not a proper asymptotic expansion. On the other hand, direct computations of the off-diagonal heat-kernel coefficients are impossibly difficult in nontrivial cases and thus no case is known in the literature where the symmetry does not hold. By approximating $C^\infty$ metrics with analytic metrics in common (totally normal) geodesically convex neighborhoods, it is rigorously proven that, in general $C^\infty$ Riemannian manifolds, any point admits a geodesically convex neighborhood where the off-diagonal heat-kernel coefficients, as well as the relevant Hadamard's expansion coefficients, are symmetric functions of the two arguments.
description: 30 pages, latex, no figures, minor errors corrected, English improved, shortened version accepted for publication in Commun. Math. Phys
Prospects for CP & P violation in $Λ_{c}^+$ decay at STCF
Creators: name: Shi, Xiao-Dong
name: Kang, Xian-Wei
name: Bigi, Ikaros
name: Wang, Wei-Ping
name: Peng, Hai-Ping
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: CP violation is an excellent tool for probing flavor dynamics as we learnt first with $K_L \to 2 π$ and later also with the weak decays of beauty mesons. LHCb 2019 data have shown CP violation for the first time in $D^0\to K^-K^+$ vs. $D^0\toπ^-π^+$. Searching for CP asymmetries is of great interest in charm quark sector in the Standard Model (SM) or even more beyond it. In charm hadron decays, lots of work had focused on two-body final states, and the measurements of CP asymmetries in three- or four-body final states are rare. Dalitz plots have shown an excellent record for three-body final states, and more results are desired for four-body ones. In this work we study CP asymmetries in the decays $Λ^+_c \to p K^-π^+π^0$/$Λπ^+π^+π^-$/$pK_Sπ^+π^-$, where the SM gives zero values for the first two channels, while $3.3 \times 10^{-3}$ for the last one due to $K^0 - \bar K^0$ oscillation. We performed a fast Monte Carlo simulation study by using electron-positron annihilation data of 1~$\textrm{ab}^{-1}$ at center-of-mass energy $\sqrt{s}\, =\, 4.64$ GeV. The data is expected to be available by the next generation Super Tau Charm Facility proposed by China and Russia with one year (or even less) data taking operation. The results indicate that a sensitivity at the level of 0.2$\sim$0.5% is accessible for these processes, which would be enough to measure nonzero CP-violating asymmetries as large as 1%.
description: final version, to appear in PRD
Shear localization in a model glass
Creators: name: Varnik, F.
name: Bocquet, L.
name: Barrat, J. -L.
name: Berthier, L.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Using molecular dynamics simulations, we show that a simple model of a glassy material exhibits the shear localization phenomenon observed in many complex fluids. At low shear rates, the system separates into a fluidized shear-band and an unsheared part. The two bands are characterized by a very different dynamics probed by a local intermediate scattering function. Furthermore, a stick-slip motion is observed at very small shear rates. Our results, which open the possibility of exploring complex rheological behavior using simulations, are compared to recent experiments on various soft glasses.
description: 4 pages, 4 figures (5 figure files)
Additional file 6 of The effect of a novel glycolysis-related gene signature on progression, prognosis and immune microenvironment of renal cell carcinoma
Creators: name: Xu, Fangshi
name: Guan, Yibing
name: Xue, Li
name: Huang, Shanlong
name: Gao, Ke
name: Yang, Zhen
name: Chong, Tie
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6: Supplementary Table 2. The detailed parameter settings of GSEA. GSEA, Gene-set enrichment analysis; MSigDB, The Molecular Signatures Database; NA, not applicable; Meandiv, Mean deviation.
MOESM1 of An automated homology-based approach for identifying transposable elements
Creators: name: Kennedy, Ryan
name: Unger, Maria
name: Christley, Scott
name: Collins, Frank
name: Madey, Gregory
Publisher: name: figshare
Year: 2011
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Additional file 1:ClustalX alignment of the manually annotated mariner and the TESeeker -produced mariner , both from P. humanus humanus . (PDF 61 KB)
Analyzing Genomic Studies and a Screen for Genes that Suppress Information Loss During DNA Damage Repair
Creators: Pierce, Steven
Publisher: name: Columbia University
Year: 2013
Subjects: subject: Biology
subject: Cytology
subject: Bioinformatics
subject: FOS: Computer and information sciences

description: This thesis is concerned with the means by which cells preserve genetic information and, in particular, with the competition between different DNA damage responses. DNA is continuously damaged and imperfect repair can have extremely detrimental effects. Double strand breaks are the most severe form of damage and can be repaired in several different ways or countered by other cellular responses. DNA context is important; cell cycle, chromosomal structure, and sequence all can make DSBs more likely or more problematic to repair. Saccharomyces cerevisiae is very resilient to DSBs and primarily uses a process called homologous recombination to repair DNA damage. To further our understanding of how S. cerevisiae efficiently uses homologous recombination, and thereby minimizes genetic degradation, I performed a screen for genes affecting this process. >In devising this study, I set out to quickly quantify the contribution of every non-essential yeast gene to suppressing genetic rearrangements and deletions at a single locus. Before I began I did not fully appreciate how variable and contingent this type of recombination phenotype could be. Accounting for the complex and changing recombination baseline across many tests became a significant effort unto itself. The requirements of the experimental protocols precluded the use of traditional recombination rate calculation methods. Searching for the means to compare the utility of normalizations and to validate my results, I sought general approaches for analyzing genome wide screen data and coordinating interpretation with existing knowledge. It was advantageous during this study to develop novel analysis tools. The second chapter describes one of these tools we developed, a technique called CLIK (Cutoff Linked to Interaction Knowledge). CLIK uses preexisting biological information to evaluate screen performance and to empirically define a significance threshold. This technique was used to analyze the screen results described in chapter three. The screen in chapter three represents the primary work of this dissertation. Its purpose was to identify genes and biological processes important for the suppression of recombination between DNA tandem repeats in yeast. By searching for gene deletion strains that show an increase in non-conservative single strand annealing, I found that many genetic backgrounds could induce altered recombination frequencies, with genes involved in DNA repair, mitochondria structural and ribosomal, and chromatin remodeling genes being most important for minimizing the loss of genetic information by HR. In addition, I found that the remodeling complex INO80 subunits, ARP8 and IES5 are significant in suppressing SSA.
On the Hitchin morphism for higher dimensional varieties
Creators: name: Chen, Tsao-Hsien
name: Chau, Ngo Bao
Publisher: name: arXiv
Year: 2019
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: In this paper, we explore the structure of the Hitchin morphism for higher dimensional varieties. We show that the Hitchin morphism factors through a closed subscheme of the Hitchin base, which is in general a non-linear subspace of lower dimension. We conjecture that the resulting morphism, which we call the spectral data morphism, is surjective. In the course of the proof, we establish connections between the Hitchin morphisms for higher dimensional varieties, the invariant theory of the commuting schemes, and Weyl's polarization theorem. We use the factorization of the Hitchin morphism to construct the spectral and cameral covers. In the case of general linear groups and algebraic surfaces, we show that spectral surfaces admit canonical finite Cohen-Macaulayfications, which we call the Cohen-Macaulay spectral surfaces, and we use them to obtain a description of the generic fibers of the Hitchin morphism similar to the case of curves. Finally, we study the Hitchin morphism for some class of algebraic surfaces.
description: This paper supersedes the preprint arXiv:1711.02592
Analyzing Hierarchical Data with the DINA-HC Approach
Creators: Zhang, Jianzhou
Publisher: name: Columbia University
Year: 2015
Subjects: subject: Educational tests and measurements
subject: Statistics
subject: FOS: Mathematics

description: Cognitive Diagnostic Models (CDMs) are a class of models developed in order to diagnose the cognitive attributes of examinees. They have received increasing attention in recent years because of the need of more specific attribute and item related information. A particular cognitive diagnostic model, namely, the hierarchical deterministic, input, noisy ‘and’ gate model with convergent attribute hierarchy (DINA-HC) is proposed to handle situations when the attributes have a convergent hierarchy. Su (2013) first introduced the model as the deterministic, input, noisy ‘and’ gate with hierarchy (DINA-H) and retrofitted The Trends in International Mathematics and Science Study (TIMSS) data utilizing this model with linear and unstructured hierarchies. Leighton, Girl, and Hunka (1999) and Kuhn (2001) introduced four forms of hierarchical structures (Linear, Convergent, Divergent, and Unstructured) by assuming the interrelated competencies of the cognitive skills. Specifically, the convergent hierarchy is one of the four hierarchies (Leighton, Gierl & Hunka, 2004) and it was used to describe the attributes that have a convergent structure. One of the features of this model is that it can incorporate the hierarchical structures of the cognitive skills in the model estimation process (Su, 2013). The advantage of the DINA-HC over the Deterministic, input, noisy ‘and’ gate (DINA) model (Junker & Sijtsma, 2001) is that it will reduce the number of parameters as well as the latent classes by imposing the particular attribute hierarchy. This model follows the specification of the DINA except that it will pre-specify the attribute profiles by utilizing the convergent attribute hierarchies. Only certain possible attribute pattern will be allowed depending on the particular convergent hierarchy. Properties regarding the DINA-HC and DINA are examined and compared through the simulation and empirical study. Specifically, the attribute profile pattern classification accuracy, the model and item fit are compared between the DINA-HC and DINA under different conditions when the attributes have convergent hierarchies. This study indicates that the DINA-HC provides better model fit, less biased parameter estimates and higher attribute profile classification accuracy than the DINA when the attributes have a convergent hierarchy. The sample size, the number of attributes, and the test length have been shown to have an effect on the parameter estimates. The DINA model has better model fit than the DINA-HC when the attributes are not dependent on each other.
Slipinskius chilensis Lord & Ivie 2016, new combination
Creators: name: Lord, Nathan P.
name: Ivie, Michael A.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Zopheridae
Slipinskius
Slipinskius chilensis

description: Slipinskius chilensis (Franz, 1969), new combination
(Figs. 4, 20, 22)
description: Published as part of Lord, Nathan P. & Ivie, Michael A., 2016, Several New Genera and Species of New World Synchitini (Coleoptera: Zopheridae: Colydiinae), pp. 715-753 in The Coleopterists Bulletin 70 (4) on pages 715-753, DOI: 10.1649/0010-065X-70.4.715, http://zenodo.org/record/5340179
Cross sections for 2-to-3 meson-meson scattering
Creators: name: Li, Wan-Xia
name: Xu, Xiao-Ming
name: Weber, H. J.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study 2-to-3 meson-meson scattering based on the process that a gluon is created from a constituent quark or antiquark and subsequently the gluon creates a quark-antiquark pair. The transition potential for the process is derived in QCD. Eight Feynman diagrams at tree level are involved in the 2-to-3 meson-meson scattering. Starting from the $S$-matrix element, we derive the unpolarized cross section from the eight transition amplitudes corresponding to the eight Feynman diagrams. The transition amplitudes contain color, spin, and flavor matrix elements. The 2-to-3 meson-meson scattering includes $ππ\to πK\bar{K}$, $πK \to ππK$, $πK \to KK\bar{K}$, $KK \to πKK$, and $K\bar{K} \to πK\bar{K}$. Cross sections for the reactions are calculated. The cross sections depend on temperature obviously, and the cross section for $πK \to ππK$ for total isospin $I=3/2$ at zero temperature is compared to experimental data. By comparison with inelastic 2-to-2 meson-meson scattering, we find that 2-to-3 meson-meson scattering may be as important as inelastic 2-to-2 meson-meson scattering.
description: 43 pages, 11 figures, 4 tables, LaTeX; more discussions added
$C_λ$-extended harmonic oscillator and (para)supersymmetric quantum mechanics
Creators: name: Quesne, C.
name: Vansteenkiste, N.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Quantum Algebra (math.QA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: $C_λ$-extended oscillator algebras are realized as generalized deformed oscillator algebras. For $λ= 3$, the spectrum of the corresponding bosonic oscillator Hamiltonian is shown to strongly depend on the algebra parameters. A connection with cyclic shape invariant potentials is noted. A bosonization of PSSQM of order two is obtained.
description: 18 pages, LaTeX 2e
Towards constructing one-particle representations of the deformed Poincaré algebra
Creators: name: Yakushin, I.
Publisher: name: arXiv
Year: 1997
Subjects: subject: Quantum Algebra (math.QA)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We give a method for obtaining states of massive particle representations of the two-parameter deformation of the Poincaré algebra proposed in q-alg/9601010, q-alg/9505030 and q-alg/9501026. We discuss four procedures to generate eigenstates of a complete set of commuting operators starting from the rest state. One result of this work is the fact that upon deforming to the quantum Poincaré algebra the rest state is split into an infinite number of states. Another result is that the energy spectrum of these states is discrete. Some curious residual degeneracy remains: there are states constructed by applying different operators to the rest state which nevertheless are indistinguishable by eigenvalues of all the observables in the algebra.
description: 23 pages. New interpretation of the results is given: upon the deformation the rest state of Poincar\'e algebra is split into an infinite number of states with discrete energy spectrum. Title, abstract and conclusion are changed
Defending Against Universal Attacks Through Selective Feature Regeneration
Creators: name: Borkar, Tejas
name: Heide, Felix
name: Karam, Lina
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Deep neural network (DNN) predictions have been shown to be vulnerable to carefully crafted adversarial perturbations. Specifically, image-agnostic (universal adversarial) perturbations added to any image can fool a target network into making erroneous predictions. Departing from existing defense strategies that work mostly in the image domain, we present a novel defense which operates in the DNN feature domain and effectively defends against such universal perturbations. Our approach identifies pre-trained convolutional features that are most vulnerable to adversarial noise and deploys trainable feature regeneration units which transform these DNN filter activations into resilient features that are robust to universal perturbations. Regenerating only the top 50% adversarially susceptible activations in at most 6 DNN layers and leaving all remaining DNN activations unchanged, we outperform existing defense strategies across different network architectures by more than 10% in restored accuracy. We show that without any additional modification, our defense trained on ImageNet with one type of universal attack examples effectively defends against other types of unseen universal attacks.
description: CVPR 2020. Code: https://github.com/tsborkar/Selective-feature-regeneration Webpage: https://www.cs.princeton.edu/~fheide/SelectiveFeatureRegeneration/
Self-Similar Factor Approximants
Creators: name: Gluzman, S.
name: Yukalov, V. I.
name: Sornette, D.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving a novel type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are named the self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of the self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions which include a variety of transcendental functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties.
description: 22 pages + 11 ps figures
Aphthona pusilla Laboissiere 1942
Creators: name: Döberl, Manfred
Publisher: name: Zenodo
Year: 2012
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Chrysomelidae
Aphthona
Aphthona pusilla

description: Aphthona pusilla Laboissière, 1942
(Figs. 1, 15, 26)
 Material examined (40 spec.). YEMEN: SOCOTRA ISLAND: Zemhon area, 10°30′58′′N 54°6′39′′E, 270-350 m, 3.-4.ii.2010, 5 spec. unsexed, L. Purchart & J. Vybíral leg. (3 in JBCB, 2 in MDCA); Al Haghier Mts., Scant Mt. env., 12°34.6′N 54°01.5′E, 1450 m, 12.-13.xi.2010, 2 spec. unsexed, J. Bezděk leg. (JBCB); Al Haghier Mts., Wadi Madar, 12°33.2′N 54°00.4′E, 1180-1230 m, 12.-14.xi.2010, 2 spec. unsexed, J. Bezděk leg. (JBCB); Aloove area, Hassan vill. env., 12°31.2′N 54°07.4′E, 221 m, 9.-10.xi.2010, 1 spec. unsexed, J. Bezděk leg. (JBCB); Sirhin area, Dixam plateau, 12°31.8′N 53°59.9′E, 812 m, 1.-2.xii.2003, 2 spec. unsexed, P. Kabátek leg. (NMPC); Hadiboh env., 12°65′02′′N 54°02′04′′E, 10-100 m, 21.xi.-12.xii.2003, 23 spec. unsexed, D. Král leg. (NMPC); Noged plain, Qaareh (waterfall), 12°20′10′′N 53°37′56′′E, 57 m, 5.-6.xii.2003, 2 spec. unsexed, D. Král leg. (NMPC); Dixam plateau, Wadi Zeeriq, 12°31′08′′N 53°59′09′′E, 750 m, 3.xii.2003, 2 spec. unsexed, D. Král leg. (NMPC); Shibhon plateau, Eserhe, 12°25.5´N 53°56.6´E, 547 m, 13.vi.2012, 1 spec. unsexed, J. Bezděk, J. Hájek, V. Hula, P. Kment, I. Malenovský, J. Niedobová & L. Purchart leg. (NMPC).
 Distribution. Aphthona pusilla is an African species described from Democratic Republic of Congo (LABOISSÈRE 1942), known also from Eritrea, Ethiopia, Guinea, Nigeria, Rwanda, Burundi and Sierra Leone (SCHERER 1972, BIONDI 1994). Possibly it occurs also in Oman – reported as ‘ Aphthona sp. 1 ’ by DOGUET (1984a) (this record was repeated by MEDVEDEV 1996, but erroneously attributed to Saudi Arabia). First record from Socotra Island.
description: Published as part of Döberl, Manfred, 2012, Alticinae (Coleoptera: Chrysomelidae) of Socotra Island, pp. 429-447 in Acta Entomologica Musei Nationalis Pragae 52 on page 430, DOI: 10.5281/zenodo.5339756
On Group Averaging for SO(n,1)
Creators: name: Gomberoff, Andres
name: Marolf, Donald
Publisher: name: arXiv
Year: 1999
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Algebra (math.QA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The technique known as group averaging provides powerful machinery for the study of constrained systems. However, it is likely to be well defined only in a limited set of cases. Here, we investigate the possibility of using a `renormalized' group averaging in certain models. The results of our study may indicate a general connection between superselection sectors and the rate of divergence of the group averaging integral.
description: Minor corrections, 17 pages,RevTex
Gravitational Baryogenesis in Non-Minimal Coupled $f(R,T)$ Gravity
Creators: name: Sahoo, P. K.
name: Bhattacharjee, Snehasish
Publisher: name: arXiv
Year: 2019
Subjects: subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: Baryogenesis refers to the theoretical process that occurred in the early history of the universe producing excess of matter over antimatter. Hitherto, fundamental physics which can give rise to such events is unknown. Many theories have emerged which may be able to suffice this conundrum, although concrete understanding is obscure. Gravitational baryogenesis is one such theory introduced by H. Davoudiasl, et al., Phys. Rev. Lett. \textbf{93} (2004) 201301. In this theory, for a CP violating interaction proportional to $\partial_μR$, where R denote Ricci scalar, gravitational baryogenesis is inevitable. In this paper, we have investigated the consequences of CP violating interactions proportional to $\partial_μR$, $\partial_μT$ and $\partial_μf(R,T)$ in the framework of non-minimal f(R,T) gravity. We found that for interactions proportional to $\partial_μR$ and $\partial_μf(R,T)$, baryogenesis can be realized with suitable parameter spaces producing a net baryon asymmetry factor consistent with observations, whereas for interaction proportional to $\partial_μT$, results in a baryon asymmetry incompatible with observations.rther, we obtained baryon to entropy ratio in each case and put constraints on parameters spaces of our model.
description: 7 pages, 2 figures, published version in IJTP
Deep Unsupervised Learning of 3D Point Clouds via Graph Topology Inference and Filtering
Creators: name: Chen, Siheng
name: Duan, Chaojing
name: Yang, Yaoqing
name: Li, Duanshun
name: Feng, Chen
name: Tian, Dong
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: We propose a deep autoencoder with graph topology inference and filtering to achieve compact representations of unorganized 3D point clouds in an unsupervised manner. Many previous works discretize 3D points to voxels and then use lattice-based methods to process and learn 3D spatial information; however, this leads to inevitable discretization errors. In this work, we handle raw 3D points without such compromise. The proposed networks follow the autoencoder framework with a focus on designing the decoder. The encoder adopts similar architectures as in PointNet. The decoder involves three novel modules. The folding module folds a canonical 2D lattice to the underlying surface of a 3D point cloud, achieving coarse reconstruction; the graph-topology-inference module learns a graph topology to represent pairwise relationships between 3D points, pushing the latent code to preserve both coordinates and pairwise relationships of points in 3D point clouds; and the graph-filtering module couples the above two modules, refining the coarse reconstruction through a learnt graph topology to obtain the final reconstruction. The proposed decoder leverages a learnable graph topology to push the codeword to preserve representative features and further improve the unsupervised-learning performance. We further provide theoretical analyses of the proposed architecture. In the experiments, we validate the proposed networks in three tasks, including 3D point cloud reconstruction, visualization, and transfer classification. The experimental results show that (1) the proposed networks outperform the state-of-the-art methods in various tasks; (2) a graph topology can be inferred as auxiliary information without specific supervision on graph topology inference; and (3) graph filtering refines the reconstruction, leading to better performances.
description: To appear in IEEE Transactions on Image Processing