cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Theory of magnetic vortex crystals induced by electric dipole interactions
Creators: name: Muto, Tatsuki
name: Mochizuki, Masahito
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Recent Lorentz transmission electron microscopy experiments have revealed a variety of noncollinear spin textures including topological magnetisms such as skyrmions, biskyrmions and multiple skyrmions in thin-plate magnetic samples of e.g., perovskite manganites and hexaferrites whose crystal structures originally have spatial inversion symmety. Motivated by these experiments, we investigate a spin-lattice coupled model involving both magnetic and electric dipole interactions by the Monte Carlo technique based on the stochastic cut-off method and propose a physical mechanism for realizing topological spin textures in which the electric dipole interaction plays a key role. This mechanism is ubiquitous that stabilizes noncollinear and topological spin textures in thin-plate samples of magnetic materials.
description: 8 pages, 7 figures
Domestic Reactions to China's Presence in Three Latin American Countries: Brazil, Nicaragua and Venezuela
Creators: name: Flores, Fidel Pérez
name: Jatobá, Daniel
Publisher: name: Journal of China and International Relations
Year: 2016

description: China's increasing presence in several Latin American countries is having different effects on national political arenas, probably making room for new specific cleavages. This article is an exploratory study with the purpose of identifying political reactions to China's growing economic presence in three differently sized Latin American countries (Brazil, Venezuela and Nicaragua). Our analytical perspective considers China-related issues as part of the foreign policy agenda in Latin American countries and, in turn, foreign policy issues as a phenomenon that can be observed like any other public policy issue. That is, a realm where actors inside or outside the state use political resources and energy to advance their own preferences. In analyzing the diverse circumstances generated by China’s economic presence in each of the selected cases, we hope to contribute to studies on the politicization of foreign policy in Latin American countries.
description: Journal of China and International Relations, Special Issue 2016
Testing quantum physics in space using high-mass matter-wave interferometry
Creators: name: Kaltenbaek, Rainer
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum superposition is central to quantum theory but challenges our concepts of reality and spacetime when applied to macroscopic objects like Schrödinger's cat. For that reason, it has been a long-standing question whether quantum physics remains valid unmodified even for truly macroscopic objects. By now, the predictions of quantum theory have been confirmed via matter-wave interferometry for massive objects up to $10^4\,$ atomic mass units (amu). The rapid development of new technologies promises to soon allow tests of quantum theory for significantly higher test masses by using novel techniques of quantum optomechanics and high-mass matter-wave interferometry. Such experiments may yield novel insights into the foundations of quantum theory, pose stringent limits on alternative theoretical models or even uncover deviations from quantum physics. However, performing experiments of this type on Earth may soon face principal limitations due to requirements of long times of flight, ultra-low vibrations, and extremely high vacuum. Here, we present a short overview of recent developments towards the implementation of the proposed space-mission MAQRO, which promises to overcome those limitations and to perform matter-wave interferometry in a parameter regime orders of magnitude beyond state-of-the-art.
description: 4 pages, conference proceedings to appear in Proceedings of 50th Rencontres de Moriond (March 2015), Gravitation: 100 Years after GR
A quality control algorithm for filtering SNPs in genome-wide association studies
Creators: name: Pongpanich, Monnat
name: Sullivan, Patrick F.
name: Tzeng, Jung Ying
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: The quality control (QC) filtering of single nucleotide polymorphisms (SNPs) is an important step in genome-wide association studies to minimize potential false findings. SNP QC commonly uses expert-guided filters based on QC variables [e.g. Hardy–Weinberg equilibrium, missing proportion (MSP) and minor allele frequency (MAF)] to remove SNPs with insufficient genotyping quality. The rationale of the expert filters is sensible and concrete, but its implementation requires arbitrary thresholds and does not jointly consider all QC features.
Sci-GaIA Deliverable D4.3 - Second Year Events Report
Creators: name: Rohrer, Chris
Publisher: name: Sci-GaIA Open Access Repository
Year: 2017

description: This deliverable presents the status of the activities of WP4 (Training, dissemination, communication and outreach), Task 4.3 (Sci-GaIA workshops) and Task 4.4 (Final conference)
A statistical framework for Illumina DNA methylation arrays
Creators: name: Wang, Sijian
name: Kuan, Pei Fen
name: Zhou, Xin
name: Chu, Haitao
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: The Illumina BeadArray is a popular platform for profiling DNA methylation, an important epigenetic event associated with gene silencing and chromosomal instability. However, current approaches rely on an arbitrary detection P-value cutoff for excluding probes and samples from subsequent analysis as a quality control step, which results in missing observations and information loss. It is desirable to have an approach that incorporates the whole data, but accounts for the different quality of individual observations.
Supplementary document for Quasi-lossless common-mode plasmon sensing scheme as a high sensitivity compact SPR sensor - 6398516.pdf
Creators: name: Bruhier, Hugo
name: Dutems, Julie
name: Laffont, Emilie
name: crespo-monteiro, nicolas
name: VERRIER, Isabelle
name: Parriaux, Olivier
name: Berini, Pierre
name: JOURLIN, Yves
Publisher: name: Optica Publishing Group
Year: 2023
Subjects: Photonics, Optoelectronics and Optical Communications

description: supplement
Hydro & Thermo Dynamics at Causal Boundaries, Examples in 3d Gravity
Creators: name: Adami, H.
name: Parvizi, A.
name: Sheikh-Jabbari, M. M.
name: Taghiloo, V.
name: Yavartanoo, H.
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study 3-dimensional gravity on a spacetime bounded by a generic 2-dimensional causal surface. We review the solution phase space specified by 4 generic functions over the causal boundary, construct the symplectic form over the solution space and the 4 boundary charges and their algebra. The boundary charges label boundary degrees of freedom. Three of these charges extend and generalize the Brown-York charges to the generic causal boundary, are canonical conjugates of boundary metric components and naturally give rise to a fluid description at the causal boundary. Moreover, we show that the boundary charges besides the causal boundary hydrodynamic description, also admit a thermodynamic description with a natural (geometric) causal boundary temperature and angular velocity. When the causal boundary is the asymptotic boundary of the 3d AdS or flat space, the hydrodynamic description respectively recovers an extension of the known conformal or conformal-Carrollian asymptotic hydrodynamics. When the causal boundary is a generic null surface, we recover the null surface thermodynamics of [1] which is an extension of the usual black hole thermodynamics description.
description: 35 pages, 5 figures
Chembench: a cheminformatics workbench
Creators: name: Pozefsky, Diane
name: Grulke, Christopher M.
name: Tropsha, Alexander
name: Walker, Theo
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: Advances in the field of cheminformatics have been hindered by a lack of freely available tools. We have created Chembench, a publicly available cheminformatics portal for analyzing experimental chemical structure–activity data. Chembench provides a broad range of tools for data visualization and embeds a rigorous workflow for creating and validating predictive Quantitative Structure–Activity Relationship models and using them for virtual screening of chemical libraries to prioritize the compound selection for drug discovery and/or chemical safety assessment.
Invoking forbidden modes in SnO_2 nanoparticles using tip enhanced Raman spectroscopy
Creators: name: Bonu, Venkataramana
name: Das, A.
name: Sivadasan, A. K.
name: Tyagi, A. K.
name: Dhara, Sandip
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Raman forbidden modes and surface defect related Raman features in SnO_2 nanostructures carry information about disorder and surface defects which strongly influence important technological applications like catalysis and sensing. Due to the weak intensities of these peaks, it is difficult to identify these features by using conventional Raman spectroscopy. Tip enhanced Raman spectroscopy (TERS) studies conducted on SnO_2 nanoparticles (NPs) of size 4 and 25 nm have offered significant insights of prevalent defects and disorders. Along with one order enhancement in symmetry allowed Raman modes, new peaks related to disorder and surface defects of SnO_2 NPs were found with significant intensity. Temperature dependent Raman studies were also carried out for these NPs and correlated with the TERS spectra. For quasi-quantum dot sized 4 nm NPs, the TERS study was found to be the best technique to probe the finite size related Raman forbidden modes.
description: 11 pages, 6 figures, journal. J. Raman Spectrosc (Rapid Communication) 2015
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
Creators: name: Hayes, D. Neil
name: Wilkerson, Matthew D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Summary: Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery.Availability: ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/).Contact: mwilkers@med.unc.eduSupplementary Information: Supplementary data are available at Bioinformatics online.
Two fast X-ray transients in archival Chandra data
Creators: name: Glennie, A.
name: Jonker, P. G.
name: Fender, R. P.
name: Nagayama, T.
name: Pretorius, M. L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present the discovery of two new X-ray transients in archival Chandra data. The first transient, XRT 110103, occurred in January 2011 and shows a sharp rise of at least three orders of magnitude in count rate in less than 10 s, a flat peak for about 20 s and decays by two orders of magnitude in the next 60 s. We find no optical or infrared counterpart to this event in preexisting survey data or in an observation taken by the SIRIUS instrument at the Infrared Survey Facility 2.1 yr after the transient, providing limiting magnitudes of J>18.1, H>17.6 and Ks>16.3. This event shows similarities to the transient previously reported in Jonker et al. which was interpreted as the possible tidal disruption of a white dwarf by an intermediate mass black hole. We discuss the possibility that these transients originate from the same type of event. If we assume these events are related a rough estimate of the rates gives 1.4*10^5 per year over the whole sky with a peak 0.3-7 keV X-ray flux greater than 2*10^-10 erg cm^-2 s^-1 . The second transient, XRT 120830, occurred in August 2012 and shows a rise of at least three orders of magnitude in count rate and a subsequent decay of around one order of magnitude all within 10 s, followed by a slower quasi-exponential decay over the remaining 30 ks of the observation. We detect a likely infrared counterpart with magnitudes J=16.70+/-0.06, H=15.92+/-0.04 and Ks=15.37+/-0.06 which shows an average proper motion of 74+/-19 milliarcsec per year compared to archival 2MASS observations. The JHKs magnitudes, proper motion and X-ray flux of XRT 120830 are consistent with a bright flare from a nearby late M or early L dwarf.
description: Accepted for publication in MNRAS, 6 pages, 5 figures
Activity-driven phase transition causes coherent flows of chromatin
Creators: name: Eshghi, Iraj
name: Zidovska, Alexanda
name: Grosberg, Alexander Y.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular motors tethered to chromatin. Cooperation occurs if each motor acts simultaneously on the polymer and the surrounding solvent, exerting on them equal and opposite forces. This drives the flow of solvent past the polymer, which in turn affects the orientation of nearby motors and, if the drive is strong enough, an active polar (``ferromagnetic'') phase of motors can spontaneously form. Depending on boundary conditions, either transverse flows, or sustained longitudinal oscillations and waves are possible. Predicted time and length scales are consistent with experiments. We now have in hand a coarse-grained description of chromatin dynamics which reproduces the directed coherent flows of chromatin seen in experiments. This field-theoretic description can be analytically coupled to other features of the nuclear environment such as fluctuating or porous boundaries, local heterogeneities in the distribution of chromatin or its activity, leading to insights on the effects of activity on the cell nucleus and its contents.
New measurements of $Ω_m$ from gamma-ray bursts
Creators: name: Izzo, Luca
name: Muccino, Marco
name: Zaninoni, Elena
name: Amati, Lorenzo
name: Della Valle, Massimo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Context: Data from cosmic microwave background radiation (CMB), baryon acoustic oscillations (BAO), and supernovae Ia (SNe-Ia) support a constant dark energy equation of state with $w_0 \sim -1$. Measuring the evolution of $w$ along the redshift is one of the most demanding challenges for observational cosmology. Aims: We discuss the existence of a close relation for GRBs, named Combo-relation, based on characteristic parameters of GRB phenomenology such as the prompt intrinsic peak energy $E_{p,i}$, the X-ray afterglow, the initial luminosity of the shallow phase $L_0$, the rest-frame duration $τ$ of the shallow phase, and the index of the late power-law decay $α_X$. We use it to measure $Ω_m$ and the evolution of the dark energy equation of state. We also propose a new calibration method for the same relation, which reduces the dependence on SNe Ia systematics. Methods: We have selected a sample of GRBs with 1) a measured redshift $z$; 2) a determined intrinsic prompt peak energy $E_{p,i}$, and 3) a good coverage (0.3-10) keV afterglow light curves. The fitting technique of the rest.frame (0.3-10) keV luminosity light curves represents the core of the Combo-relation. We separate the early steep decay, considered a part of the prompt emission, from the X-ray afterglow additional component. Data with the largest positive residual, identified as flares, are automatically eliminated until the p-value of the fit becomes greater than 0.3. Results: We strongly minimize the dependency of the Combo-GRB calibration on SNe Ia. We also measure a small extra-Poissonian scatter of the Combo-relation, which allows us to infer from GRBs alone $Ω_M =0.29^{+0.23}_{-0.15}$ (1$σ$) for the $Λ$CDM cosmological model, and $Ω_M =0.40^{+0.22}_{-0.16}$, $w_0 = -1.43^{+0.78}_{-0.66}$ for the flat-Universe variable equation of state case.
description: 10 pages, 9 figures, 3 tables. Accepted for publication in A&A. Truncated abstract text
Refraktometrie zur Messung des gastralen Nahrungstransportes in der neurologischen Intensivmedizin
Creators: name: Kästner, Matthias
Publisher: name: Universität Rostock
Year: 2020
Subjects: subject: 610 Medical sciences Medicine

description: Durch serielle Konzentrationsbestimmungen des Mageninhaltes kann das gastrale Residualvolumen berechnet werden. Die Konzentrationsbestimmung mittels Refraktometrie wurde mit der Glucosebestimmung mit einem Blutzuckermessgerät und dem Bradford-Test verglichen. Die Refraktometrie misst präziser und wird weniger durch Magensaft beeinflusst. Feeding-Intolerance und Unterernährung treten bei neurologischen, enteral ernährten Intensivpatienten häufig auf. In diesem Kollektiv zeigte sich die serielle Refraktometrie als praktikable und kostengünstige Methode zur Erfassung der Magenentleerung.
Efficient genome ancestry inference in complex pedigrees with inbreeding
Creators: name: Zhang, Qi
name: Liu, Eric Yi
name: Wang, Wei
name: McMillan, Leonard
name: de Villena, Fernando Pardo Manuel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation.
Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.
Creators: name: Rose, Peter W.
name: Godzik, Adam
name: Bliven, Spencer
name: Prlić, Andreas
name: Bourne, Philip E.
name: Bluhm, Wolfgang F.
name: Bizon, Chris
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Summary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.
Dynamical evolution of the Cybele asteroids
Creators: name: Carruba, Valerio
name: Nesvorný, David
name: Aljbaae, Safwan
name: Huaman, Mariela Espinoza
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The Cybele region, located between the 2J:-1A and 5J:-3A mean-motion resonances, is adjacent and exterior to the asteroid main belt. An increasing density of three-body resonances makes the region between the Cybele and Hilda populations dynamically unstable, so that the Cybele zone could be considered the last outpost of an extended main belt. The presence of binary asteroids with large primaries and small secondaries suggested that asteroid families should be found in this region, but only relatively recently the first dynamical groups were identified in this area. Among these, the Sylvia group has been proposed to be one of the oldest families in the extended main belt. In this work we identify families in the Cybele region in the context of the local dynamics and non-gravitational forces such as the Yarkovsky and stochastic YORP effects. We confirm the detection of the new Helga group at $\simeq$3.65~AU, that could extend the outer boundary of the Cybele region up to the 5J:-3A mean-motion resonance. We obtain age estimates for the four families, Sylvia, Huberta, Ulla and Helga, currently detectable in the Cybele region, using Monte Carlo methods that include the effects of stochastic YORP and variability of the Solar luminosity. The Sylvia family should be $T = 1220 \pm 40$ Myr old, with a possible older secondary solution. Any collisional Cybele group formed prior to the late heavy bombardment would have been most likely completely dispersed in the jumping Jupiter scenario of planetary migration.
description: This paper has 13 pages, 14 figures, and 4 tables. Accepted for publication in MNRAS
Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase
Creators: name: Carter Jr., Charles W.
name: Cammer, Stephen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Motivation: Similarities in core residue packing provide evidence for divergence or convergence not reported using other methods.
A latent profile analysis of students’ attitudes towards astronomy across grades 9–13
Creators: name: Galano, Silvia
name: Palazzo, Lucio
name: Testa, Italo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Astronomy is seen as a "gateway" science, inspiring students to pursue Science-Technology-Engineering-Mathematics (STEM) related careers. However, there is little evidence that students' attitudes towards astronomy remain stable over time. By integrating Self-Determination Theory (SDT) and Theory of Planned Behaviour (TPB), we identified three dimensions of students' attitudes towards astronomy - intrinsic, which refers to the enjoyment of studying astronomy, extrinsic, which refers to the will to pursue a career in astronomy, and utilitarian, which refers to the relevance of astronomy to society. We used these dimensions as indicators for a Latent Profile Analysis (LPA) to identify attitudinal profiles of 2650 Italian students in grades 9-13. We identified seven profiles, ranging from completely negative to completely positive attitudes. In particular, students enter secondary school mostly interested in astronomy and with a positive view of astronomy. By the end of secondary school, students have significantly lower attitudes towards astronomy in all three dimensions identified. From a theoretical perspective, our study shows that the SDT/TPB framework can be used to develop future instruments aimed at measuring students' attitudes towards science. From a practical point of view, our results call for better support for teachers to maintain students' attitudes towards astronomy throughout secondary school.
Näherungen an die Berufsbildung in Finnland
Creators: name: Kaiser, Franz
name: Kruse, Britta
name: Frind, Hanah
name: Alcala, Yannik
Publisher: name: Universität Rostock, Institut für Berufspädagogik
Year: 2021
Subjects: subject: 370 Education

description: Der vorliegende Band besteht überwiegend aus Beiträgen von Studierenden des Lehramts an berufsbildenden Schulen an der Universität Rostock, die sich mit der beruflichen Bildung in Finnland befasst und sich unterschiedlichen Schwerpunkten bei der Analyse des Berufsbildungssystems gewidmet haben. Dieser Band liefert einen Einblick in das finnische Bildungs- und Berufsbildungssystem, aber zugleich auch in die Lehr- und Lernformen des Instituts für Berufspädagogik.
全球公共物品供给与新兴大国参与—基于“非纯公共物品”概念的分析 / Global Public Goods and The Role of Emerging Power: Considering the Concept of Impure Public Goods
Creators: name: Yi, Liu Rieshøj
Publisher: name: Journal of China and International Relations
Year: 2016

description: 现有关于国际公共物品的论述过度关注“公益”性质，相对忽视国家特别是核心国家作为供给主体的主动地位及其战略考量。事实上，核心国家在提供各种国际公共物品时已经考虑到他国“搭便车”的可能性，纳入对外供给与消费模式设计。中国关于“欢迎周边国家搭便车”的提法可以视为此类战略动向的最新回应。为此，有必要重新审视原有理论，理解“搭便车”行为的可能性与现实性，从“非纯公共物品”角度出发讨论国际公共物品的推动因素以及运作机制。作为新兴大国，中国应该明确战略重点，注重“供给”与“营销”相互配合，创设或创新具体形式，提高国际公共物品供给效率与精致程度。 The existing analysis of global public goods over-emphasizes the significance of public. Great power as a main provider has played an active role in these strategic initiatives, which may be ignored. In fact, main power has thought about the possible free-riders when providing public goods and making its foreign strategic plan. China’s announcement to “welcome the neighbouring countries to be a free-rider and benefit from China’s rise” is a good example. It is necessary to think about the theory of public goods and take another look at the free-riding phenomenon. The concept of impure public goods may be useful and effective when we understand the reason why global public goods are being provided and are relatively efficient. As an emerging power, China should have a clear strategy on global public goods with a possible “marketing” viewpoint, including more initiatives and specific measures, so that the global public goods provision may be more diverse and well-planned.
description: Journal of China and International Relations, Vol 4 No 2 (2016)
TEAM: efficient two-locus epistasis tests in human genome-wide association study
Creators: name: Wang, Wei
name: Zhang, Xiang
name: Zou, Fei
name: Huang, Shunping
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene–gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.
On-Shell Calculation of Mixed Electromagnetic and Gravitational Scattering
Creators: name: Holstein, Barry R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Nuclear Theory (nucl-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The study of long-range effects arising from the higher order exchange of massless particles via summation of Feynman diagrams is well known, but recently it has been shown that the use of on-shell methods can provide a streamlined route to the calculation of both electromagnetic and gravitational effects. In this note we demonstrate that the use of on-shell methods yields a similar simplification in the evaluation of higher order effects in the case of mixed electromagnetic and gravitational scattering.
description: 18 page Latex manuscript, 3 figures
A powerful and flexible approach to the analysis of RNA sequence count data
Creators: name: Wright, Fred A.
name: Zhou, Yi Hui
name: Xia, Kai
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: A number of penalization and shrinkage approaches have been proposed for the analysis of microarray gene expression data. Similar techniques are now routinely applied to RNA sequence transcriptional count data, although the value of such shrinkage has not been conclusively established. If penalization is desired, the explicit modeling of mean–variance relationships provides a flexible testing regimen that ‘borrows’ information across genes, while easily incorporating design effects and additional covariates.
Model-based symbolic design space exploration at the electronic system level
Creators: name: Neubauer, Kai
Publisher: name: Universität Rostock
Year: 2021
Subjects: subject: 004 Data processing Computer sciences
subject: 621.3 Electrical Engineering, Electronics

description: In this thesis, a novel, fully systematic approach is proposed that addresses the automated design space exploration at the electronic system level. The problem is formulated as multi-objective optimization problem and is encoded symbolically using Answer Set Programming (ASP). Several specialized solvers are tightly coupled as background theories with the foreground ASP solver under the ASP modulo Theories (ASPmT) paradigm. By utilizing the ASPmT paradigm, the search is executed entirely systematically and the disparate synthesis steps can be coupled to explore the search space effectively.
A variable selection method for genome-wide association studies
Creators: name: He, Qianchuan
name: Lin, Dan Yu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: Genome-wide association studies (GWAS) involving half a million or more single nucleotide polymorphisms (SNPs) allow genetic dissection of complex diseases in a holistic manner. The common practice of analyzing one SNP at a time does not fully realize the potential of GWAS to identify multiple causal variants and to predict risk of disease. Existing methods for joint analysis of GWAS data tend to miss causal SNPs that are marginally uncorrelated with disease and have high false discovery rates (FDRs).
Application of the disk instability model to all Quasi-Periodic Eruptions
Creators: name: Pan, Xin
name: Li, Shuang-Liang
name: Cao, Xinwu
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: After the first quasi-periodic eruptions (QPEs, GSN069) was reported in 2019, four other sources have been identified as QPEs or its candidate. However, the physics behind QPEs is still unclear so far, though several models have been proposed. Pan et al. (2022) proposed an instability model for the accretion disk with magnetically driven outflows in the first QPEs GSN 069, which is able to reproduce both the light curve and the evolution of spectrum fairly well. In this work, we exploit this model to all the QPEs. We imporve the calculations of the spectrum of disk by introducing a hardening factor, which is caused by the deviation of opacity from the blackbody. We find that the light curves and evolution of the spectra of the four QPEs or candidate can all be well reproduced by our model calculations.
description: 8 pages, 7 figures, accepted for publication in ApJ
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data
Creators: name: Jefferys, Stuart R.
name: Giddings, Morgan C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: Post-translational modifications are vital to the function of proteins, but are hard to study, especially since several modified isoforms of a protein may be present simultaneously. Mass spectrometers are a great tool for investigating modified proteins, but the data they provide is often incomplete, ambiguous and difficult to interpret. Combining data from multiple experimental techniques—especially bottom-up and top-down mass spectrometry—provides complementary information. When integrated with background knowledge this allows a human expert to interpret what modifications are present and where on a protein they are located. However, the process is arduous and for high-throughput applications needs to be automated.
Einfluss der intrastriatalen Botulinumneurotoxin-A-Applikation auf die Rezeptordichte im Hemi-Parkinson-Modell der Ratte
Creators: name: Findeisen, Julia Isabel
Publisher: name: Universität Rostock
Year: 2020
Subjects: subject: 610 Medical sciences Medicine

description: In Rostock wurde eine experimentelle Therapieoption mittels einer lokalen intrastriatalen Injektion von Botulinumneurotoxin-A zur Behandlung von Parkinson entwickelt. Um das therapeutische Potenzial von BoNT-A im Tiermodell weiter zu untersuchen, wurde die Wirkung von intrastriatal injiziertem BoNT-A auf die Rezeptordichten zahlreicher Areale innerhalb und außerhalb der Basalganglienschleife des Gehirns von gesunden Ratten untersucht. Die Ergebnisse zeigen, dass intrastriatal injiziertes BoNT-A zu keiner signifikanten Änderung der Rezeptordichte der 16 untersuchten Rezeptoren führte.
Gabriel Chapotat, Vienne gauloise
Creators: name: Jacobi, Gerhard
Publisher: name: Germania : Anzeiger der Römisch-Germanischen Kommission des Deutschen Archäologischen Instituts
Year: 2023

description: Rezension zu: Gabriel Chapotat, Vienne gauloise. Le matériel de La Tène III trouvé sur la colline de Sainte-Blandine. Publications du Centre d’Études Romaines et Gallo-Romaines de la Faculté des Lettres et Sciences Humaines de Lyon. Fasc. II. En dépôt aux Éditions de Boccard, Lyon 1970. Textteil: 186 Seiten und 34 Abbil- dungen; Tafelteil: 56 Tafeln.
description: Germania : Anzeiger der Römisch-Germanischen Kommission des Deutschen Archäologischen Instituts, Bd. 52 Nr. 2 (1974)
Counterdiabatic driving for long-lived singlet state preparation
Creators: name: Suresh, Abhinav
name: Varma, Vishal
name: Batra, Priya
name: Mahesh, T S
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The quantum adiabatic method, which maintains populations in their instantaneous eigenstates throughout the state evolution, is an established and often a preferred choice for state preparation and manipulation. Though it minimizes the driving cost significantly, its slow speed is a severe limitation in noisy intermediate-scale quantum (NISQ) era technologies. Since adiabatic paths are extensive in many physical processes, it is of broader interest to achieve adiabaticity at a much faster rate. Shortcuts to adiabaticity techniques which overcome the slow adiabatic process by driving the system faster through non-adiabatic paths, have seen increased attention recently. The extraordinarily long lifetime of the long-lived singlet states (LLS) in nuclear magnetic resonance, established over the past decade, has opened several important applications ranging from spectroscopy to biomedical imaging. Various methods, including adiabatic methods, are already being used to prepare LLS. In this article, we report the use of counterdiabatic driving (CD) to speed up LLS preparation with faster drives. Using NMR experiments, we show that CD can give stronger LLS order in shorter durations than conventional adiabatic driving.
PBL and the Postmodern Condition - Knowledge Production in University Education
Creators: name: Ravn, Ole
name: Jensen, Annie Aarup
Publisher: name: Journal of Problem Based Learning in Higher Education
Year: 2016

description: In this article we discuss the contemporary conditions for running the Aalborg Problem Based Learning-model (PBL). We try to pinpoint key characteristics of these conditions emphasising Lyotard’s conception of knowledge production referred to as the move towards a postmodern condition for knowledge. Through discussions of this alleged condition for university curricula development we investigate its connections to the PBL-model. Some of the explored conditions highlight strong potentials for the PBL-model but the postmodern condition also raises a number of changes and challenges in relation to the original PBL-model as an educational setting.
description: Journal of Problem Based Learning in Higher Education, Vol 4 No 1 (2016)
$\texttt{Wapiti}$: a data-driven approach to correct for systematics in RV data -- Application to SPIRou data of the planet-hosting M dwarf GJ 251
Creators: name: Ould-Elhkim, M.
name: Moutou, C.
name: Donati, J-F.
name: Artigau, É.
name: Fouqué, P.
name: Cook, N. J.
name: Carmona, A.
name: Cristofari, P. I.
name: Martioli, E.
name: Debras, F.
name: Dumusque, X.
name: Martins, J. H. C.
name: Hébrard, G.
name: Cadieux, C.
name: Delfosse, X.
name: Doyon, R.
name: Klein, B.
name: da Silva, J. Gomes
name: Forveille, T.
name: Hood, T.
name: Charpentier, P.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Context: Recent advances in the development of precise radial velocity (RV) instruments in the near-infrared (nIR) domain, such as SPIRou, have facilitated the study of M-type stars to more effectively characterize planetary systems. However, the nIR presents unique challenges in exoplanet detection due to various sources of planet-independent signals which can result in systematic errors in the RV data. Aims: In order to address the challenges posed by the detection of exoplanetary systems around M-type stars using nIR observations, we introduce a new data-driven approach for correcting systematic errors in RV data. The effectiveness of this method is demonstrated through its application to the star GJ 251. Methods: Our proposed method, referred to as $\texttt{Wapiti}$ (Weighted principAl comPonent analysIs reconsTructIon), uses a dataset of per-line RV time-series generated by the line-by-line (LBL) algorithm and employs a weighted principal component analysis (wPCA) to reconstruct the original RV time-series. A multi-step process is employed to determine the appropriate number of components, with the ultimate goal of subtracting the wPCA reconstruction of the per-line RV time-series from the original data in order to correct systematic errors. Results: The application of $\texttt{Wapiti}$ to GJ 251 successfully eliminates spurious signals from the RV time-series and enables the first detection in the nIR of GJ 251b, a known temperate super-Earth with an orbital period of 14.2 days. This demonstrates that, even when systematics in SPIRou data are unidentified, it is still possible to effectively address them and fully realize the instrument's capability for exoplanet detection. Additionally, in contrast to the use of optical RVs, this detection did not require to filter out stellar activity, highlighting a key advantage of nIR RV measurements.
description: Submitted to A&A. For the publicly available Wapiti code, see https://github.com/HkmMerwan/wapiti
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Creators: name: Wright, Fred A.
name: Nobel, Andrew B.
name: Walter, Vonn
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: DNA copy number gains and losses are commonly found in tumor tissue, and some of these aberrations play a role in tumor genesis and development. Although high resolution DNA copy number data can be obtained using array-based techniques, no single method is widely used to distinguish between recurrent and sporadic copy number aberrations.Results: Here we introduce Discovering Copy Number Aberrations Manifested In Cancer (DiNAMIC), a novel method for assessing the statistical significance of recurrent copy number aberrations. In contrast to competing procedures, the testing procedure underlying DiNAMIC is carefully motivated, and employs a novel cyclic permutation scheme. Extensive simulation studies show that DiNAMIC controls false positive discoveries in a variety of realistic scenarios. We use DiNAMIC to analyze two publicly available tumor datasets, and our results show that DiNAMIC detects multiple loci that have biological relevance.Availability: Source code implemented in R, as well as text files containing examples and sample datasets are available at http://www.bios.unc.edu/research/genomic_software/DiNAMIC.Contact: vwalter@email.unc.edu; fwright@bios.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Magnetic Katok Examples on the two-sphere
Creators: name: Benedetti, Gabriele
Publisher: name: arXiv
Year: 2015
Subjects: subject: Symplectic Geometry (math.SG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 37J45, 53D25

description: We show that there exist non-exact magnetic flows on the two-sphere having an energy level whose double cover is strictly contactomorphic to an irrational ellipsoid in $\mathbb C^2$. Our construction generalizes the examples of integrable Finsler metrics on the two-sphere with only two closed geodesics due to A. Katok.
description: 13 pages. Second version. We have added a sharper example in the larger class of Lagrangians attaining a Morse-Bott non-degenerate minimum at the zero section. Comments, questions, and suggestions are very welcome. To appear in the Bulletin of the London Mathematical Society
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
Creators: name: Liu, Yufeng
name: Jones, Corbin D.
name: Prins, Jan F.
name: Singh, Darshan
name: Orellana, Christian F.
name: Chiang, Derek Y.
name: Liu, Jinze
name: Hu, Yin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: In eukaryotic cells, alternative splicing expands the diversity of RNA transcripts and plays an important role in tissue-specific differentiation, and can be misregulated in disease. To understand these processes, there is a great need for methods to detect differential transcription between samples. Our focus is on samples observed using short-read RNA sequencing (RNA-seq).Methods: We characterize differential transcription between two samples as the difference in the relative abundance of the transcript isoforms present in the samples. The magnitude of differential transcription of a gene between two samples can be measured by the square root of the Jensen Shannon Divergence (JSD*) between the gene's transcript abundance vectors in each sample. We define a weighted splice-graph representation of RNA-seq data, summarizing in compact form the alignment of RNA-seq reads to a reference genome. The flow difference metric (FDM) identifies regions of differential RNA transcript expression between pairs of splice graphs, without need for an underlying gene model or catalog of transcripts. We present a novel non-parametric statistical test between splice graphs to assess the significance of differential transcription, and extend it to group-wise comparison incorporating sample replicates.Results: Using simulated RNA-seq data consisting of four technical replicates of two samples with varying transcription between genes, we show that (i) the FDM is highly correlated with JSD* (r=0.82) when average RNA-seq coverage of the transcripts is sufficiently deep; and (ii) the FDM is able to identify 90% of genes with differential transcription when JSD* >0.28 and coverage >7. This represents higher sensitivity than Cufflinks (without annotations) and rDiff (MMD), which respectively identified 69 and 49% of the genes in this region as differential transcribed. Using annotations identifying the transcripts, Cufflinks was able to identify 86% of the genes in this region as differentially transcribed. Using experimental data consisting of four replicates each for two cancer cell lines (MCF7 and SUM102), FDM identified 1425 genes as significantly different in transcription. Subsequent study of the samples using quantitative real time polymerase chain reaction (qRT-PCR) of several differential transcription sites identified by FDM, confirmed significant differences at these sites.Availability: http://csbio-linux001.cs.unc.edu/nextgen/software/FDMContact: darshan@email.unc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
supplement table 1 .docx
Creators: name: Wang, Li
name: Zuo, Houjuan
name: Peng, Xiangyang
name: Zhang, Kaiyue
name: Yang, Zhenjia
name: Jiang, Luying
name: Nie, Xiang
Publisher: name: figshare
Year: 2022
Subjects: Cardiology (incl. cardiovascular diseases)

description: Clinical characteristics of six patients for sequencing analysis
Gaia: automated quality assessment of protein structure models
Creators: name: Dokholyan, Nikolay V.
name: Kota, Pradeep
name: Ramachandran, Srinivas
name: Ding, Feng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Motivation: Increasing use of structural modeling for understanding structure–function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.