cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
Creators: name: Ding, Jun
name: Willer, Cristen J.
name: Scheet, Paul
name: Li, Yun
name: Abecasis, Gonçalo R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Genome-wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility. Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality of these estimates. Our approach is already widely used to facilitate comparison of results across studies as well as meta-analyses of GWAS. Here, we use simulations and experimental genotypes to evaluate its accuracy and utility, considering choices of genotyping panels, reference panel configurations, and designs where genotyping is replaced with shotgun sequencing. Importantly, we show that genotype imputation not only facilitates cross study analyses but also increases power of genetic association studies. We show that genotype imputation of common variants using HapMap haplotypes as a reference is very accurate using either genome-wide SNP data or smaller amounts of data typical in fine-mapping studies. Furthermore, we show the approach is applicable in a variety of populations. Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies.
A Space Industry Ontology Suite
Creators: name: Rovetto, Robert
Publisher: name: Zenodo
Year: 2023
Subjects: ontology
standard
data management
global workshop
ontology commons ecosystem
FAIR

description: This use case develops a set of ontologies (and related systems) for space industry: astronautics and astronomy related, with conceptual, philosophical and formal ontological exploration: spatiality and spatio-temporality, causality, discipline-specific questions. It develops top-level and mid-level space domain reference models.
On the use of shot noise for photon counting
Creators: name: Zmuidzinas, Jonas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Lieu et al. (2015) have recently claimed that it is possible to substantially improve the sensitivity of radio astronomical observations. In essence, their proposal is to make use of the intensity of the photon shot noise as a measure of the photon arrival rate. Lieu et al. (2015) provide a detailed quantum-mechanical calculation of a proposed measurement scheme that uses two detectors and conclude that this scheme avoids the sensitivity degradation that is associated with photon bunching. If correct, this result could have a profound impact on radio astronomy. Here I present a detailed analysis of the sensitivity attainable using shot-noise measurement schemes that use either one or two detectors, and demonstrate that neither scheme can avoid the photon bunching penalty. I perform both semiclassical and fully quantum calculations of the sensitivity, obtaining consistent results, and provide a formal proof of the equivalence of these two approaches. These direct calculations are furthermore shown to be consistent with an indirect argument based on a correlation method that establishes an independent limit to the sensitivity of shot-noise measurement schemes. Collectively, these results conclusively demonstrate that the photon bunching sensitivity penalty applies to shot noise measurement schemes just as it does to ordinary photon counting, in contradiction to the fundamental claim made by Lieu et al. (2015). The source of this contradiction is traced to a logical fallacy in their argument.
description: 34 pages, 9 figures; submitted to ApJ
A Geometric Approach of Gradient Descent Algorithms in Linear Neural Networks
Creators: name: Chitour, Yacine
name: Liao, Zhenyu
name: Couillet, Romain
Publisher: name: arXiv
Year: 2018
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: Primary: 68T07, 37B35, Secondary: 37D10

description: In this paper, we propose a geometric framework to analyze the convergence properties of gradient descent trajectories in the context of linear neural networks. We translate a well-known empirical observation of linear neural nets into a conjecture that we call the \emph{overfitting conjecture} which states that, for almost all training data and initial conditions, the trajectory of the corresponding gradient descent system converges to a global minimum. This would imply that the solution achieved by vanilla gradient descent algorithms is equivalent to that of the least-squares estimation, for linear neural networks of an arbitrary number of hidden layers. Built upon a key invariance property induced by the network structure, we first establish convergence of gradient descent trajectories to critical points of the square loss function in the case of linear networks of arbitrary depth. Our second result is the proof of the \emph{overfitting conjecture} in the case of single-hidden-layer linear networks with an argument based on the notion of normal hyperbolicity and under a generic property on the training data (i.e., holding for almost all training data).
description: 28 pages, 4 figures, to appear in Mathematical Control and Related Fields
Kernel machine SNP-set analysis for censored survival outcomes in genome-wide association studies
Creators: name: Liu, Geoffrey
name: Wu, Michael C.
name: Christiani, David C.
name: Lin, Xinyi
name: Zhou, Qian
name: Cai, Tianxi
name: Lin, Xihong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: In this paper, we develop a powerful test for identifying SNP-sets that are predictive of survival with data from genome-wide association studies (GWAS). We first group typed SNPs into SNP-sets based on genomic features and then apply a score test to assess the overall effect of each SNP-set on the survival outcome through a kernel machine Cox regression framework. This approach uses genetic information from all SNPs in the SNP-set simultaneously and accounts for linkage disequilibrium (LD), leading to a powerful test with reduced degrees of freedom when the typed SNPs are in LD with each other. This type of test also has the advantage of capturing the potentially non-linear effects of the SNPs, SNP-SNP interactions (epistasis), and the joint effects of multiple causal variants. By simulating SNP data based on the LD structure of real genes from the HapMap project, we demonstrate that our proposed test is more powerful than the standard single SNP minimum p-value based test for association studies with censored survival outcomes. We illustrate the proposed test with a real data application.
Locally standard torus actions and sheaves over Buchsbaum posets
Creators: name: Ayzenberg, Anton
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 57N65, 55R20 (Primary), 55R91, 18F20, 55N30, 55U30, 18G40 (Secondary)

description: We consider a sheaf of exterior algebras on a simplicial poset $S$ and introduce a notion of homological characteristic function. Two natural objects are associated with these data: a graded sheaf $\mathcal{I}$ and a graded cosheaf $\widehatΠ$. When $S$ is a homology manifold, we prove the isomorphism $H^{n-1-p}(S;\mathcal{I})\cong H_{p}(S;\widehatΠ)$ which can be considered as an extension of the Poincare duality. In general, there is a spectral sequence $E^2_{p,q}\cong H^{n-1-p}(S;\mathcal{U}_{n-1+q}\otimes \mathcal{I})\Rightarrow H_{p+q}(S;\widehatΠ)$, where $\mathcal{U}_*$ is the local homology stack on $S$. This spectral sequence, in turn, extends Zeeman--McCrory spectral sequence. This sheaf-theoretical result is applied to toric topology. We consider a manifold $X$ with a locally standard action of a compact torus and acyclic proper faces of the orbit space. A principal torus bundle $Y$ is associated with $X$, so that $X\cong Y/\sim$. The orbit type filtration on $X$ is covered by the topological filtration on $Y$. We prove that homological spectral sequences associated with these two filtrations are isomorphic in many nontrivial positions.
description: 23 pages. Several typos were corrected and the numbering of theorems changed
Single-valued hyperlogarithms, correlation functions and closed string amplitudes
Creators: name: Vanhove, Pierre
name: Zerbini, Federico
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Number Theory (math.NT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We give new proofs of a global and a local property of the integrals which compute closed string theory amplitudes at genus zero. Both kinds of properties are related to the newborn theory of single-valued periods, and our proofs provide an intuitive understanding of this relation. The global property, known in physics as the KLT formula, is a factorisation of the closed string integrals into products of pairs of open string integrals. We deduce it by identifying closed string integrals with special values of single-valued correlation functions in two dimensional conformal field theory, and by obtaining their conformal block decomposition. The local property is of number theoretical nature. We write the asymptotic expansion coefficients as multiple integrals over the complex plane of special functions known as single-valued hyperlogarithms. We develop a theory of integration of single-valued hyperlogarithms, and we use it to demonstrate that the asymptotic expansion coefficients belong to the ring of single-valued multiple zeta values.
description: v1. 91 pages. v2: 50 pages. Major revision of the exposition : title and abstract changed, paper shortened with improved proofs and presentation. No changes in the content and the results
Can Kozai-Lidov cycles explain Kepler-78b?
Creators: name: Rice, Ken
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Kepler-78b is one of a growing sample of planets similar, in composition and size, to the Earth. It was first detected with NASA's \emph{Kepler} spacecraft and then characterised in more detail using radial velocity follow-up observations. Not only is its size very similar to that of the Earth ($1.2 R_\oplus$), it also has a very similar density ($5.6$ g cm$^{-2}$). What makes this planet particularly interesting is that it orbits its host star every $8.5$ hours, giving it an orbital distance of only $0.0089$ au. What we investigate here is whether or not such a planet could have been perturbed into this orbit by an outer companion on an inclined orbit. In this scenario, the outer perturber causes the inner orbit to undergo Kozai-Lidov cycles which, if the periapse comes sufficiently close to the host star, can then lead to the planet being tidally circularised into a close orbit. We find that this process can indeed produce such very-close-in planets within the age of the host star ($\sim 600 - 900$ Myr), but it is more likely to find such ultra-short-period planets around slightly older stars ($> 1$ Gyr). However, given the size of the Kepler sample and the likely binarity, our results suggest that Kepler-78b may indeed have been perturbed into its current orbit by an outer stellar companion. The likelihood of this happening, however, is low enough that other processes - such as planet-planet scattering - could also be responsible.
description: 10 pages, 9 figures, accepted for publication in MNRAS
Strominger connection and pluriclosed metrics
Creators: name: Zhao, Quanting
name: Zheng, Fangyang
Publisher: name: arXiv
Year: 2019
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C55

description: In this paper, we prove a conjecture raised by Angella, Otal, Ugarte, and Villacampa recently, which states that if the Strominger connection (also known as Bismut connection) of a compact Hermitian manifold is Kähler-like, in the sense that its curvature tensor obeys all the symmetries of the curvature of a Kähler manifold, then the metric must be pluriclosed. What we actually showed is a bit more: for any given Hermitian manifold, the Strominger Kähler-like condition is equivalent to the pluriclosedness of the metric plus the parallelness of the torsion.
Using Riemannian geometry for SSVEP-based Brain Computer Interface
Creators: name: Kalunga, Emmanuel K.
name: Chevallier, Sylvain
name: Barthelemy, Quentin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Riemannian geometry has been applied to Brain Computer Interface (BCI) for brain signals classification yielding promising results. Studying electroencephalographic (EEG) signals from their associated covariance matrices allows a mitigation of common sources of variability (electronic, electrical, biological) by constructing a representation which is invariant to these perturbations. While working in Euclidean space with covariance matrices is known to be error-prone, one might take advantage of algorithmic advances in information geometry and matrix manifold to implement methods for Symmetric Positive-Definite (SPD) matrices. This paper proposes a comprehensive review of the actual tools of information geometry and how they could be applied on covariance matrices of EEG. In practice, covariance matrices should be estimated, thus a thorough study of all estimators is conducted on real EEG dataset. As a main contribution, this paper proposes an online implementation of a classifier in the Riemannian space and its subsequent assessment in Steady-State Visually Evoked Potential (SSVEP) experimentations.
description: 29 pages, 6 figures, 1 table, research report. Update on the overall text, most of the figure are modified, the algorithm is explained more clearly, updated comparisons with state of the art methods
Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience
Creators: name: Agrawal, Arpana
name: Heiss, Gerardo
name: Monroe, Kristine R.
name: Caporaso, Neil
name: Heit, John A.
name: Kittner, Steven J.
name: Hansel, Nadia N.
name: Udren, Jenna
name: Barnes, Kathleen
name: Bennett, Siiri N.
name: Kang, Jae Hee
name: Marazita, Mary L.
name: Fitzpatrick, Annette L.
name: Boyd, Heather A.
name: Kraft, Peter
name: Williams, Kayleen
name: Pasquale, Louis R.
name: Cornelis, Marilyn C.
name: Ramos, Erin M.
name: van Dam, Rob M.
name: Lowe, William
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Genome-wide association study (GWAS) consortia and collaborations formed to detect genetic loci for common phenotypes or investigate gene-environment (G*E) interactions are increasingly common. While these consortia effectively increase sample size, phenotype heterogeneity across studies represents a major obstacle that limits successful identification of these associations. Investigators are faced with the challenge of how to harmonize previously collected phenotype data obtained using different data collection instruments which cover topics in varying degrees of detail and over diverse time frames. This process has not been described in detail. We describe here some of the strategies and pitfalls associated with combining phenotype data from varying studies. Using the Gene Environment Association Studies (GENEVA) multi-site GWAS consortium as an example, this paper provides an illustration to guide GWAS consortia through the process of phenotype harmonization and describes key issues that arise when sharing data across disparate studies. GENEVA is unusual in the diversity of disease endpoints and so the issues it faces as its participating studies share data will be informative for many collaborations. Phenotype harmonization requires identifying common phenotypes, determining the feasibility of cross-study analysis for each, preparing common definitions, and applying appropriate algorithms. Other issues to be considered include genotyping timeframes, coordination of parallel efforts by other collaborative groups, analytic approaches, and imputation of genotype data. GENEVA's harmonization efforts and policy of promoting data sharing and collaboration, not only within GENEVA but also with outside collaborations, can provide important guidance to ongoing and new consortia.
Objectivisation In Simplified Quantum Brownian Motion Models
Creators: name: Tuziemski, J.
name: Korbicz, J. K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Birth of objective properties from subjective quantum world has been one of the key questions in the quantum-to-classical transition. Basing on recent results in the field, we study it in a quantum mechanical model of a boson-boson interaction-quantum Brownian motion. Using various simplifications we prove a formation for thermal environments of, so called, spectrum broadcast structures, responsible for perceived objectivity. In the quantum measurement limit we prove that this structure is always formed, providing the characteristic timescales. Including self-Hamiltonians of the environment, we show the exponential scaling of the effect with the size of the environment. Finally, in the full model we numerically study the influence of squeezing in the initial state of the environment, showing broader regions of formation than for non-squeezed thermal states.
description: Invited publication for the special issue "Quantum Optics and Quantum Information Processing" of Photonics
An infinite natural sum
Creators: name: Lipparini, Paolo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03E10, 06A05

description: As far as algebraic properties are concerned, the usual addition on the class of ordinal numbers is not really well behaved; for example, it is not commutative, nor left cancellative etc. In a few cases, the natural Hessemberg sum is a better alternative, since it shares most of the usual properties of the addition on the naturals. A countably infinite version of the natural sum has been used in a recent paper by Väänänen and Wang, with applications to infinitary logics. We provide an order theoretical characterization of this operation. We show that this countable natural sum differs from the more usual infinite ordinal sum only for an initial finite "head" and agrees on the remaining infinite "tail". We show how to evaluate the countable natural sum just by computing a finite natural sum. Various kinds of infinite mixed sums of ordinals are discussed.
description: v3 added a remark connected with surreal numbers
The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery
Creators: name: Crawford, D.C.
name: Fesinmeyer, M.D.
name: Pendergrass, S.A.
name: Buyske, S.
name: Cai, C.
name: Moreland, L.
name: Reiner, A.P.
name: Hindorff, L.A.
name: Matise, T.C.
name: Kooperberg, C.
name: Le Marchand, L.
name: Avery, C.L.
name: Lin, Y.
name: Jackson, R.D.
name: Wallace, R.
name: Heiss, G.
name: Haiman, C.
name: Monroe, K.
name: Ambite, J.L.
name: Hsu, C.-N.
name: Ritchie, M.D.
name: Wilkens, L.R.
name: Dudek, S.M.
name: Brown-Gentry, K.
name: Torstenson, E.S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The field of phenomics has been investigating network structure among large arrays of phenotypes, and genome-wide association studies (GWAS) have been used to investigate the relationship between genetic variation and single diseases/outcomes. A novel approach has emerged combining both the exploration of phenotypic structure and genotypic variation, known as the phenome-wide association study (PheWAS). The Population Architecture using Genomics and Epidemiology (PAGE) network is a National Human Genome Research Institute (NHGRI)-supported collaboration of four groups accessing eight extensively characterized epidemiologic studies. The primary focus of PAGE is deep characterization of well-replicated GWAS variants and their relationships to various phenotypes and traits in diverse epidemiologic studies that include European Americans, African Americans, Mexican Americans/Hispanics, Asians/Pacific Islanders, and Native Americans. The rich phenotypic resources of PAGE studies provide a unique opportunity for PheWAS as each genotyped variant can be tested for an association with the wide array of phenotypic measurements available within the studies of PAGE, including prevalent and incident status for multiple common clinical conditions and risk factors, as well as clinical parameters and intermediate biomarkers. The results of PheWAS can be used to discover novel relationships between SNPs, phenotypes, and networks of interrelated phenotypes; identify pleiotropy; provide novel mechanistic insights; and foster hypothesis generation. The PAGE network has developed infrastructure to support and perform PheWAS in a high-throughput manner. As implementing the PheWAS approach has presented several challenges, the infrastructure and methodology, as well as insights gained in this project, are presented herein to benefit the larger scientific community.
K-theoretic crystals for set-valued tableaux of rectangular shapes
Creators: name: Pechenik, Oliver
name: Scrimshaw, Travis
Publisher: name: arXiv
Year: 2019
Subjects: subject: Combinatorics (math.CO)
subject: Algebraic Geometry (math.AG)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 05E05, 05A19, 14M15, 17B37

description: In earlier work with C.~Monical, we introduced the notion of a K-crystal, with applications to K-theoretic Schubert calculus and the study of Lascoux polynomials. We conjectured that such a K-crystal structure existed on the set of semistandard set-valued tableaux of any fixed rectangular shape. Here, we establish this conjecture by explicitly constructing the K-crystal operators. As a consequence, we establish the first combinatorial formula for Lascoux polynomials $L_{wλ}$ when $λ$ is a multiple of a fundamental weight as the sum over flagged set-valued tableaux. Using this result, we then prove corresponding cases of conjectures of Ross--Yong (2015) and Monical (2016) by constructing bijections with the respective combinatorial objects.
description: 23 pages, 2 figures; v2 changed the statement of Conjecture 6.1; v3 corrections to K-crystal operators and other changes from comments
GrandDetAuto: Detecting Malicious Nodes in Large-Scale Autonomous Networks
Creators: name: Abera, Tigist
name: Brasser, Ferdinand
name: Gunn, Lachlan J.
name: Jauernig, Patrick
name: Koisser, David
name: Sadeghi, Ahmad-Reza
Publisher: name: arXiv
Year: 2019
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Autonomous collaborative networks of devices are rapidly emerging in numerous domains, such as self-driving cars, smart factories, critical infrastructure, and Internet of Things in general. Although autonomy and self-organization are highly desired properties, they increase vulnerability to attacks. Hence, autonomous networks need dependable mechanisms to detect malicious devices in order to prevent compromise of the entire network. However, current mechanisms to detect malicious devices either require a trusted central entity or scale poorly. In this paper, we present GrandDetAuto, the first scheme to identify malicious devices efficiently within large autonomous networks of collaborating entities. GrandDetAuto functions without relying on a central trusted entity, works reliably for very large networks of devices, and is adaptable to a wide range of application scenarios thanks to interchangeable components. Our scheme uses random elections to embed integrity validation schemes in distributed consensus, providing a solution supporting tens of thousands of devices. We implemented and evaluated a concrete instance of GrandDetAuto on a network of embedded devices and conducted large-scale network simulations with up to 100000 nodes. Our results show the effectiveness and efficiency of our scheme, revealing logarithmic growth in run-time and message complexity with increasing network size. Moreover, we provide an extensive evaluation of key parameters showing that GrandDetAuto is applicable to many scenarios with diverse requirements.
Privacy-preserving parametric inference: a case for robust statistics
Creators: name: Avella-Medina, Marco
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Cryptography and Security (cs.CR)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Differential privacy is a cryptographically-motivated approach to privacy that has become a very active field of research over the last decade in theoretical computer science and machine learning. In this paradigm one assumes there is a trusted curator who holds the data of individuals in a database and the goal of privacy is to simultaneously protect individual data while allowing the release of global characteristics of the database. In this setting we introduce a general framework for parametric inference with differential privacy guarantees. We first obtain differentially private estimators based on bounded influence M-estimators by leveraging their gross-error sensitivity in the calibration of a noise term added to them in order to ensure privacy. We then show how a similar construction can also be applied to construct differentially private test statistics analogous to the Wald, score and likelihood ratio tests. We provide statistical guarantees for all our proposals via an asymptotic analysis. An interesting consequence of our results is to further clarify the connection between differential privacy and robust statistics. In particular, we demonstrate that differential privacy is a weaker stability requirement than infinitesimal robustness, and show that robust M-estimators can be easily randomized in order to guarantee both differential privacy and robustness towards the presence of contaminated data. We illustrate our results both on simulated and real data.
Kinetic Electron and Ion Instability of the Lunar Wake Simulated at Physical Mass Ratio
Creators: name: Haakonsen, Christian Bernt
name: Hutchinson, Ian H.
name: Zhou, Chuteng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: The solar wind wake behind the moon is studied with 1D electrostatic particle-in-cell (PIC) simulations using a physical ion to electron mass ratio (unlike prior investigations); the simulations also apply more generally to supersonic flow of dense magnetized plasma past non-magnetic objects. A hybrid electrostatic Boltzmann electron treatment is first used to investigate the ion stability in the absence of kinetic electron effects, showing that the ions are two-stream unstable for downstream wake distances (in lunar radii) greater than about three times the solar wind Mach number. Simulations with PIC electrons are then used to show that kinetic electron effects can lead to disruption of the ion beams at least three times closer to the moon than in the hybrid simulations. This disruption occurs as the result of a novel wake phenomenon: the non-linear growth of electron holes spawned from a narrow dimple in the electron velocity distribution. Most of the holes arising from the dimple are small and quickly leave the wake, approximately following the unperturbed electron phase-space trajectories, but some holes originating near the center of the wake remain and grow large enough to trigger disruption of the ion beams. Non-linear kinetic-electron effects are therefore essential to a comprehensive understanding of the 1D electrostatic stability of such wakes, and possible observational signatures in ARTEMIS data from the lunar wake are discussed.
description: 9 pages, 10 figures
Light-shift modulated photon-echo
Creators: name: Chanelière, Thierry
name: Hétet, Gabriel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We show that the AC-Stark shift (light-shift) is a powerful and versatile tool to control the emission of a photon-echo in the context of optical storage. As a proof-of-principle, we demonstrate that the photon-echo efficiency can be fully modulated by applying light-shift control pulses in an erbium doped solid. The control of the echo emission is attributed to the spatial gradient induced by the light-shift beam.
Consumer Perspectives on Genetic Testing for Psychiatric Disorders: The Attitudes of Veterans with Posttraumatic Stress Disorder and Their Families
Creators: name: Calhoun, Patrick S.
name: Kirby, Angela C.
name: Hauser, Michael A.
name: Dennis, Michelle F.
name: Beckham, Jean C.
name: Wilson, Sarah M.
name: Elbogen, Eric B.
name: Dedert, Eric A.
name: Hertzberg, Jeff S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The perspectives of patients with posttraumatic stress disorder (PTSD) on genetic research have not yet been investigated in the genetics research literature. To provide a basis for research on attitudes toward genetic research in PTSD, we surveyed the U.S. Military Afghanistan/Iraq-era veterans with PTSD and their social support companions to investigate the attitudes and knowledge about genetics and genetic testing. One hundred forty-six veterans (76 with PTSD and 70 without PTSD) participated in this study. Each veteran participant had a corresponding companion (primarily spouses, but also relatives and friends) who they identified as a primary member of their social support network. Participants and companions completed self-report measures on knowledge of genetics and attitudes toward genetic testing for PTSD. Results indicated that, relative to veterans without PTSD, veterans with PTSD had similar levels of genetic knowledge, but less-favorable attitudes toward genetic testing. Differences persisted after controlling for age and genetics knowledge. No differences between companions of those with and without PTSD were observed. Results suggest that the perspective of those with PTSD regarding genetic testing is in need of further investigation, especially if potentially beneficial genetic testing for PTSD is to be utilized in the target population.
title: Morning Has Broken: Uncommon Grace in an Ordinary Family
Creators: name: Kent, Charlotte Gail
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2008

description: Morning Has Broken: Uncommon Grace in an Ordinary Family is a memoir about finding personal meaning and peace in spite of family chaos due to a troubled son, marital distress, career problems and serious illness. The chaos almost causes the family — especially the writer — to implode. But in the end, as everything she thought was necessary for a satisfying life is either threatened or stripped away, she finds a place inside herself where nothing is wrong and everything is as it is supposed to be. This becomes her moment of grace, when she realizes that she is "enough" without any improvements and that every imperfect or difficult moment becomes sacred through acceptance. Ultimately, Morning Has Broken: Uncommon Grace in an Ordinary Family is about the miracle of being happy.
Genomics Education for the Public: Perspectives of Genomic Researchers and ELSI Advisors
Creators: name: Markey, Janell M.
name: Roberts, Megan C.
name: Dressler, Lynn G.
name: Jones, Sondra Smolek
name: Byerly, Katherine W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Aims: For more than two decades genomic education of the public has been a significant challenge. As genomic information becomes integrated into daily life and routine clinical care, the need for public education is even more critical. We conducted a pilot study to learn how genomic researchers and ethical, legal, and social implications advisors who were affiliated with large-scale genomic variation studies have approached the issue of educating the public about genomics. Methods/Results: Semi-structured telephone interviews were conducted with researchers and advisors associated with the SNP/HAPMAP studies and the Cancer Genome Atlas Study. Respondents described approach(es) associated with educating the public about their study. Interviews were audio-recorded, transcribed, coded, and analyzed by team review. Although few respondents described formal educational efforts, most provided recommendations for what should/could be done, emphasizing the need for an overarching entity(s) to take responsibility to lead the effort to educate the public. Opposing views were described related to: who this should be; the overall goal of the educational effort; and the educational approach. Four thematic areas emerged: What is the rationale for educating the public about genomics?; Who is the audience?; Who should be responsible for this effort?; and What should the content be? Policy issues associated with these themes included the need to agree on philosophical framework(s) to guide the rationale, content, and target audiences for education programs; coordinate previous/ongoing educational efforts; and develop a centralized knowledge base. Suggestions for next steps are presented. Conclusion: A complex interplay of philosophical, professional, and cultural issues can create impediments to genomic education of the public. Many challenges, however, can be addressed by agreement on a guiding philosophical framework(s) and identification of a responsible entity(s) to provide leadership for developing/overseeing an appropriate infrastructure to support the coordination/integration/sharing and evaluation of educational efforts, benefiting consumers and professionals.
Jordan symmetry reduction for conic optimization over the doubly nonnegative cone: theory and software
Creators: name: Brosch, Daniel
name: de Klerk, Etienne
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 90C22, 20B40

description: A common computational approach for polynomial optimization problems (POPs) is to use (hierarchies of) semidefinite programming (SDP) relaxations. When the variables in the POP are required to be nonnegative, these SDP problems typically involve nonnegative matrices, i.e. they are conic optimization problems over the doubly nonnegative cone. The Jordan reduction, a symmetry reduction method for conic optimization, was recently introduced for symmetric cones by Parrilo and Permenter [Mathematical Programming 181(1), 2020]. We extend this method to the doubly nonnegative cone, and investigate its application to known relaxations of the quadratic assignment and maximum stable set problems. We also introduce new Julia software where the symmetry reduction is implemented.
description: 19 pages, titled change from earlier version. arXiv admin note: text overlap with arXiv:1908.00872
title: Teilen von Wissen im Offboarding in der öffentlichen Verwaltung Deutschlands
title: Knowledge sharing during offboarding in German public administration
Creators: name: Beel, Leon
Publisher: name: Universität Potsdam
Year: 2022
Subjects: subject: 351 Öffentliche Verwaltung

description: Die vorliegende Arbeit untersucht, inwiefern extrapersonale Einflussfaktoren das Verhalten der Wissensteilung im Offboarding in der öffentlichen Verwaltung Deutschlands beeinflussen. Hier besteht eine Forschungslücke, die es insbesondere vor dem Hintergrund einer nahenden Pensionierungswelle und der daraus resultierenden Gefahr eines massiven Wissensverlusts zu schließen gilt. Zu diesem Zweck werden unterschiedliche Analyseebenen verknüpft, Einflussfaktoren aus der Literatur herausgearbeitet und in die Theorie des geplanten Verhaltens eingebunden. Anschließend werden Hypothesen formuliert, wie extrapersonale Einflussfaktoren, die sich aus der Verwaltung als organisationalen Kontext und dem Prozess des Offboarding ergeben, das Verhalten der Wissensteilung fördern oder hemmen. Die Testung der Hypothesen erfolgt durch die Erhebung und Auswertung qualitativer Interviewdaten. Daraus resultierende Erkenntnisse verdeutlichen, dass die anstehende Pensionierungswelle in der deutschen Verwaltung eine stärkere Ausrichtung des organisationalen Wissensmanagements auf den Prozess des Offboarding und dessen Gestaltung erfordert, um Wissensverluste zu reduzieren.
description: This bachelor thesis examines the extent to which extra-personal influencing factors shape the behavior of knowledge sharing in offboarding processes in German public administration. There is a research gap here that needs to be closed urgently, especially given the approaching wave of retirements and the resulting risk of a massive loss of knowledge. For this purpose, different levels of analysis are linked, influencing factors are identified and integrated into the Theory of Planned Behavior. Hypotheses are then formulated as to how extra-personal influencing factors resulting from administration as an organizational context and the process of offboarding promote or inhibit knowledge sharing behavior. The hypotheses are tested by collecting and analyzing qualitative interview data. The findings make it clear that the upcoming wave of retirements in the German public administration requires a stronger orientation of organizational knowledge management towards the process of offboarding and its design in order to reduce knowledge losses.
description: Schriftenreihe für Public und Nonprofit Management; 29
Using scanning lidar data to predict future wind flows
Creators: name: Engels, Wouter
name: Rotteveel, Roel
Publisher: name: Zenodo
Year: 2023

description: Presentation at the Wind Energy Science Conference 2023 as part of the Mini Symposium "IEA Wind Task 52: Lidar-Assisted Control, Turbulence Estimation, and Digitalization Scanning LIDARs can provide detailed data on the wind field in a wind farm. This data may then be post processed to understand what the wind conditions were at each wind turbine, and to identify where the wakes ended up. However, ideally, one would be able to use the scanning lidar data to predict the wind field in the wind farm. Ultimately such predictions could be used in a wind farm controller to yaw and pitch just to the extent that is necessary to achieve the required amount of wake steering.
 In the research presented here, we endeavour to predict the wind conditions around the wind turbine based on a purely data-driven approach based on earlier scanning lidar measurements. Other research on data-driven approaches for wakes have so far involved 2D, simulated data (e.g [2,3]) or have focussed on identifying which bit of the measured data is a wake [4]. In contrast, we will not try to find the wakes as such, but to predict future scans after a series of scans.
 The research is based on the ECN-NORCOWE measurement campaign acquired at the ECN Wind Turbine Test Station Wieringermeer (EWTW). A Windcube® lidar was positioned such that the image covered the wakes of 3 of the Nordex N-80 turbines and, depending on the wind direction, occasionally the wakes of other turbines can be seen.
 The approach used here is a staged approach, as is shown in figure 1. First, a convolutional autoencoder (see, e.g. [5]) is trained to decrease the number of measuring points in a scan to a more manageable latent space, while still being able to reproduce an acceptable reproduction of what happens near the wind turbines. This effectively is a form of data compression.
 The second step is then to train an Long Short-Term Memory [6] with this reduced dataset and use it to predict future latent spaces, that can then be decoded using the auto-encoder.
 The results so far indicate that this approach shows potential: it outperforms static predictions and simpler approaches (figure 2). For instance, a change in wind direction was predicted several steps ahead (figure 3). However, there is still significant room for improvement.
Carbon in Red Giants in Globular Clusters and Dwarf Spheroidal Galaxies
Creators: name: Kirby, Evan N.
name: Guo, Michelle
name: Zhang, Andrew J.
name: Deng, Michelle
name: Cohen, Judith G.
name: Guhathakurta, Puragra
name: Shetrone, Matthew D.
name: Lee, Young Sun
name: Rizzi, Luca
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present carbon abundances of red giants in Milky Way globular clusters and dwarf spheroidal galaxies (dSphs). Our sample includes measurements of carbon abundances for 154 giants in the clusters NGC 2419, M68, and M15 and 398 giants in the dSphs Sculptor, Fornax, Ursa Minor, and Draco. This sample doubles the number of dSph stars with measurements of [C/Fe]. The [C/Fe] ratio in the clusters decreases with increasing luminosity above log(L/L_sun) ~= 1.6, which can be explained by deep mixing in evolved giants. The same decrease is observed in dSphs, but the initial [C/Fe] of the dSph giants is not uniform. Stars in dSphs at lower metallicities have larger [C/Fe] ratios. We hypothesize that [C/Fe] (corrected to the initial carbon abundance) declines with increasing [Fe/H] due to the metallicity dependence of the carbon yield of asymptotic giant branch stars and due to the increasing importance of Type Ia supernovae at higher metallicities. We also identified 11 very carbon-rich giants (8 previously known) in three dSphs. However, our selection biases preclude a detailed comparison to the carbon-enhanced fraction of the Milky Way stellar halo. Nonetheless, the stars with [C/Fe] < +1 in dSphs follow a different [C/Fe] track with [Fe/H] than the halo stars. Specifically, [C/Fe] in dSphs begins to decline at lower [Fe/H] than in the halo. The difference in the metallicity of the [C/Fe] "knee" adds to the evidence from [alpha/Fe] distributions that the progenitors of the halo had a shorter timescale for chemical enrichment than the surviving dSphs.
description: accepted to ApJ; 20 pages, 11 figures, 2 machine-readable tables
Bayesian analyses of multiple epistatic QTL models for body weight and body composition in mice
Creators: name: KIM, KYOUNGMI
name: EISEN, EUGENE J.
name: ALLISON, DAVID B.
name: BARTOLUCCI, ALFRED
name: POMP, DANIEL
name: YI, NENGJUN
name: ZINNIEL, DENISE K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: To comprehensively investigate the genetic architecture of growth and obesity, we performed Bayesian analyses of multiple epistatic quantitative trait locus (QTL) models for body weights at five ages (12 days, 3, 6, 9 and 12 weeks) and body composition traits (weights of two fat pads and five organs) in mice produced from a cross of the F1 between M16i (selected for rapid growth rate) and CAST/Ei (wild-derived strain of small and lean mice) back to M16i. Bayesian model selection revealed a temporally regulated network of multiple QTL for body weight, involving both strong main effects and epistatic effects. No QTL had strong support for both early and late growth, although overlapping combinations of main and epistatic effects were observed at adjacent ages. Most main effects and epistatic interactions had an opposite effect on early and late growth. The contribution of epistasis was more pronounced for body weights at older ages. Body composition traits were also influenced by an interacting network of multiple QTL. Several main and epistatic effects were shared by the body composition and body weight traits, suggesting that pleiotropy plays an important role in growth and obesity.
Hyperbolic Minesweeper is in P
Creators: name: Kopczyński, Eryk
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computational Complexity (cs.CC)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We show that, while Minesweeper is NP-complete, its hyperbolic variant is in P. Our proof does not rely on the rules of Minesweeper, but is valid for any puzzle based on satisfying local constraints on a graph embedded in the hyperbolic plane.
description: fixed an error in Corollary 5.6: planar graph -> (r,d)-hyperbolic graph
Mapping interacting QTL for count phenotypes using hierarchical Poisson and binomial models: an application to reproductive traits in mice
Creators: name: ALLISON, DAVID B.
name: POMP, DANIEL
name: REYNOLDS, RICHARD
name: LI, JUN
name: YI, NENGJUN
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: We proposed hierarchical Poisson and binomial models for mapping multiple interacting quantitative trait loci (QTL) for count traits in experimental crosses. We applied our methods to two counted reproductive traits, live fetuses (LF) and dead fetuses (DF) at 17 days gestation, in a F2 female mouse population. We treated observed number of corpora lutea (ovulation rate) as the baseline and the total trials in our Poisson and binomial models, respectively. We detected more than 10 QTL for LF and DF, most having epistatic and pleiotropic effects. The epistatic effects were larger, involved more QTL, and explained a larger proportion of phenotypic variance than the main effects. Our analyses revealed a complex network of multiple interacting QTL for the reproductive traits, and increase our understanding of the genetic architecture of reproductive characters. The proposed statistical models and methods provide valuable tools for detecting multiple interacting QTL for complex count phenotypes.
Bright but slow - Type II supernovae from OGLE-IV - Implications for magnitude limited surveys
Creators: name: Poznanski, Dovi
name: Kostrzewa-Rutkowska, Zuzanna
name: Wyrzykowski, Lukasz
name: Blagorodnova, Nadejda
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We study a sample of 11 Type II supernovae (SNe) discovered by the OGLE-IV survey. All objects have well sampled I-band light curves, and at least one spectrum. We find that 2 or 3 of the 11 SNe have a declining light curve, and spectra consistent with other SNe II-L, while the rest have plateaus that can be as short as 70d, unlike the 100d typically found in nearby galaxies. The OGLE SNe are also brighter, and show that magnitude limited surveys find SNe that are different than usually found in nearby galaxies. We discuss this sample in the context of understanding Type II SNe as a class and their suggested use as standard candles.
description: Accepted to MNRAS, minor changes