cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Unscreening Modified Gravity in the Matter Power Spectrum
Creators: name: Lombriser, Lucas
name: Simpson, Fergus
name: Mead, Alexander
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Viable modifications of gravity that may produce cosmic acceleration need to be screened in high-density regions such as the Solar System, where general relativity is well tested. Screening mechanisms also prevent strong anomalies in the large-scale structure and limit the constraints that can be inferred on these gravity models from cosmology. We find that by suppressing the contribution of the screened high-density regions in the matter power spectrum, allowing a greater contribution of unscreened low densities, modified gravity models can be more readily discriminated from the concordance cosmology. Moreover, by variation of density thresholds, degeneracies with other effects may be dealt with more adequately. Specializing to chameleon gravity as a worked example for screening in modified gravity, employing N-body simulations of f(R) models and the halo model of chameleon theories, we demonstrate the effectiveness of this method. We find that a percent-level measurement of the clipped power at k < 0.3 h/Mpc can yield constraints on chameleon models that are more stringent than what is inferred from Solar System tests or distance indicators in unscreened dwarf galaxies. Finally, we verify that our method is also applicable to the Vainshtein mechanism.
description: 5 pages, 2 figures; v2 matches published version, including application to Vainshtein mechanism
Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
Creators: name: Mieczkowski, Piotr A.
name: Lujan, Scott A.
name: Gordenin, Dmitry A.
name: Clark, Alan B.
name: Malc, Ewa P.
name: Clausen, Anders R.
name: MacAlpine, Heather K.
name: Fargo, David C.
name: Burkholder, Adam B.
name: MacAlpine, David M.
name: Kunkel, Thomas A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
Semiparametric Localized Bandwidth Selection in Kernel Density Estimation
Creators: name: Cheng, Tingting
name: Gao, Jiti
name: Zhang, Xibin
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: Since conventional cross-validation bandwidth selection methods do not work for the case where the data considered are serially dependent, alternative bandwidth selection methods are needed. In recent years, Bayesian based global bandwidth selection methods have been proposed. Our experience shows that the use of a global bandwidth is however less suitable than using a localized bandwidth in kernel density estimation in the case where the data are serially dependent. Nonetheless, a difficult issue is how we can consistently estimate a localized bandwidth. In this paper, we propose a semiparametric estimation method and establish an asymptotic theory for the proposed estimator. A by-product of this bandwidth estimate is a new sampling-based likelihood approach to hyperparameter estimation. Monte Carlo simulation studies show that the proposed hyperparameter estimation method works very well, and that the proposed bandwidth estimator outperforms its competitors. Applications of the new bandwidth estimator to the kernel density estimation of Eurodollar deposit rate, as well as the S&P 500 daily return under conditional heteroscedasticity, demonstrate the effectiveness and competitiveness of the proposed semiparametric localized bandwidth.
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
Creators: name: Chen, Jenny
name: Guturu, Harendra
name: Frank, Christopher L.
name: Crawford, Gregory E.
name: Bejerano, Gill
name: Camp, J. Gray
name: Rube, Tomas
name: Lickwar, Colin R.
name: Wenger, Aaron M.
name: Rawls, John F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Microbiota regulate intestinal physiology by modifying host gene expression along the length of the intestine, but the underlying regulatory mechanisms remain unresolved. Transcriptional specificity occurs through interactions between transcription factors (TFs) and cis-regulatory regions (CRRs) characterized by nucleosome-depleted accessible chromatin. We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin accessibility. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome-depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is preprogrammed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs.
Deformations of Yang-Mills theory
Creators: name: Cofano, Marco
name: Fu, Chih-Hao
name: Krasnov, Kirill
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We introduce and study a new class of power-counting non-renormalisable gauge theories in four space-time dimensions. The Lagrangian is an arbitrary function of the self-dual part of the field strength. The resulting perturbation theory has the property that whenever two derivatives act on an internal line propagator, the result is a delta-function and the line collapses to a point. This means that there remains at most one derivative on each internal line, which gives improved ulta-violet behaviour. For many purposes, this class of theories behaves just like ordinary Yang-Mills theory. In particular, they all share the Yang-Mills theory MHV amplitudes. Moreover, these theories remain constructible in the sense that higher-point tree level scattering amplitudes can be obtained from the lower-point amplitudes using the BCFW recursion relations. Also, the square of these gauge-theory amplitudes gives the scattering amplitudes of "deformations" of General Relativity, at least for the low particle numbers that we checked. We compute the one-loop beta-function of the first new coupling constant, and find it to be positive, which signals the associated non-renormalisable interaction becoming important in the ulta-violet.
description: v2: 38 pages, many figures, references added; v3: Typos corrected, version accepted for publication in PRD
Manipulation of a single magnetic atom using polarized single electron transport in a double quantum dot
Creators: name: Lai, Wenxi
name: Yang, Wen
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We consider theoretically a magnetic impurity spin driven by polarized electrons tunneling through a double quantum dot system. Spin blockade effect and spin conservation in the system make the magnetic impurity sufficiently interact with each transferring electron. As a results, a single collected electron carries information about spin change of the magnetic impurity. The scheme may develop all electrical manipulation of magnetic atoms by means of single electrons, which is significant for the implementation of scalable logical gates in information processing systems.
description: 5 figures
A Study on Improving Early Warning Models for World Grain Markets
Creators: name: Kim, Jongjin
name: Kim, Jongjin
Publisher: name: Unknown
Year: 2016
Subjects: subject: Demand and Price Analysis
subject: International Relations/Trade
subject: early warning model
subject: world grain prices
subject: signal approach model

description: To identify the best early warning index for world grain markets, this study compares the performance of early warning indices computed from a regression model, probit model and signal approach model. The main result of this study is that, in the view of predictive power, the early warning indices from the regression model or probit model show better performance than that from the signal approach model, which most of early warning systems constructed in Korea have adopted. In addition to this finding, this study suggests using principal component analysis as a way to sum up information of many explanatory variables into several variables and develops a way to guarantee early warning indices obtained from co-moving variables by using predictive values of co-moving variables.
Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
Creators: name: Jonasch, E.
name: Weiser, M.
name: Ho, T. H.
name: Furey, T. S.
name: Hacker, K. E.
name: Rathmell, W. K.
name: Kuan, P.-F.
name: Parker, J. S.
name: Simon, J. M.
name: Brannon, A. R.
name: Prins, J. F.
name: Davis, I. J.
name: Lieb, J. D.
name: Singh, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Comprehensive sequencing of human cancers has identified recurrent mutations in genes encoding chromatin regulatory proteins. For clear cell renal cell carcinoma (ccRCC), three of the five commonly mutated genes encode the chromatin regulators PBRM1, SETD2, and BAP1. How these mutations alter the chromatin landscape and transcriptional program in ccRCC or other cancers is not understood. Here, we identified alterations in chromatin organization and transcript profiles associated with mutations in chromatin regulators in a large cohort of primary human kidney tumors. By associating variation in chromatin organization with mutations in SETD2, which encodes the enzyme responsible for H3K36 trimethylation, we found that changes in chromatin accessibility occurred primarily within actively transcribed genes. This increase in chromatin accessibility was linked with widespread alterations in RNA processing, including intron retention and aberrant splicing, affecting ∼25% of all expressed genes. Furthermore, decreased nucleosome occupancy proximal to misspliced exons was observed in tumors lacking H3K36me3. These results directly link mutations in SETD2 to chromatin accessibility changes and RNA processing defects in cancer. Detecting the functional consequences of specific mutations in chromatin regulatory proteins in primary human samples could ultimately inform the therapeutic application of an emerging class of chromatin-targeted compounds.
Measure rigidity of Ricci curvature lower bounds
Creators: name: Cavalletti, Fabio
name: Mondino, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: Metric Geometry (math.MG)
subject: FOS: Mathematics

description: The measure contraction property, $\mathsf{MCP}$ for short, is a weak Ricci curvature lower bound conditions for metric measure spaces. The goal of this paper is to understand which structural properties such assumption (or even weaker modifications) implies on the measure, on its support and on the geodesics of the space. We start our investigation from the euclidean case by proving that if a positive Radon measure $\mathsf{m}$ over $\mathbb{R}^{d}$ is such that $(\mathbb{R}^{d},|\cdot |, \mathsf{m})$ verifies a weaker variant of $\mathsf{MCP}$, then its support $\text{spt}(\mathsf{m})$ must be convex and $\mathsf{m}$ has to be absolutely continuous with respect to the relevant Hausdorff measure of $\text{spt}(\mathsf{m})$. This result is then used as a starting point to investigate the rigidity of $\mathsf{MCP}$ in the metric framework. We introduce the new notion of $reference \ measure$ for a metric space and prove that if $(X,\mathsf{d},\mathsf{m})$ is essentially non-branching and verifies $\mathsf{MCP}$, and $μ$ is an essentially non-branching $\mathsf{MCP}$ reference measure for $(\text{spt}(\mathsf{m}), \mathsf{d})$, then $\mathsf{m}$ is absolutely continuous with respect to $μ$, on the set of points where an inversion plan exists. As a consequence, an essentially non-branching $\mathsf{MCP}$ reference measure enjoys a weak type of uniqueness, up to densities. We also prove a stability property for reference measures under measured Gromov-Hausdorff convergence, provided an additional uniform bound holds. In the final part we present concrete examples of metric spaces with reference measures, both in smooth and non-smooth setting.
Three-level Haldane-like model on dice optical lattice
Creators: name: Andrijauskas, T.
name: Anisimovas, E.
name: Račiūnas, M.
name: Mekys, A.
name: Kudriašov, V.
name: Spielman, I. B.
name: Juzeliūnas, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We consider ultracold atoms in a two-dimensional optical lattice of the dice geometry in a tight-binding regime. The atoms experience a laser-assisted tunneling between the nearest neighbour sites of the dice lattice accompanied by the momentum recoil. This allows one to engineer staggered synthetic magnetic fluxes over plaquettes, and thus pave a way towards a realization of topologically nontrivial band structures. In such a lattice the real-valued next-neighbour transitions are not needed to reach a topological regime. Yet, such transitions can increase a variety of the obtained topological phases. The dice lattice represents a triangular Bravais lattice with a three-site basis consisting of a hub site connected to two rim sites. As a consequence, the dice lattice supports three dispersion bands. From this point of view, our model can be interpreted as a generalization of the paradigmatic Haldane model which is reproduced if one of the two rim sub-lattices is eliminated. We demonstrate that the proposed upgrade of the Haldane model creates a significant added value, including an easy access to topological semimetal phases relying only on the nearest neighbour coupling, as well as enhanced topological band structures featuring Chern numbers higher than one. The numerical investigation is supported and complemented by an analytical scheme based on the study of singularities in the Berry connection.
description: 24 pages, 15 figures
Semiparametric Model Selection in Panel Data Models with Deterministic Trends and Cross-Sectional Dependence
Creators: name: Chen, Jia
name: Gao, Jiti
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: In this paper, we consider a model selection issue in semiparametric panel data models with fixed effects. The modelling framework under investigation can accommodate both nonlinear deterministic trends and cross-sectional dependence. And we consider the so-called "large panels" where both the time series and cross sectional sizes are very large. A penalised profile least squares method with first-stage local linear smoothing is developed to select the significant covariates and estimate the regression coefficients simultaneously. The convergence rate and the oracle property of the resulting semiparametric estimator are established by the joint limit approach. The developed semiparametric model selection methodology is illustrated by two Monte-Carlo simulation studies, where we compare the performance in model selection and estimation of three penalties, i.e., the least absolute shrinkage and selection operator (LASSO), the smoothly clipped absolute deviation (SCAD), and the minimax concave penalty (MCP).
Non-Global Logarithms, Factorization, and the Soft Substructure of Jets
Creators: name: Larkoski, Andrew J.
name: Moult, Ian
name: Neill, Duff
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: An outstanding problem in QCD and jet physics is the factorization and resummation of logarithms that arise due to phase space constraints, so-called non-global logarithms (NGLs). In this paper, we show that NGLs can be factorized and resummed down to an unresolved infrared scale by making sufficiently many measurements on a jet or other restricted phase space region. Resummation is accomplished by renormalization group evolution of the objects in the factorization theorem and anomalous dimensions can be calculated to any perturbative accuracy and with any number of colors. To connect with the NGLs of more inclusive measurements, we present a novel perturbative expansion which is controlled by the volume of the allowed phase space for unresolved emissions. Arbitrary accuracy can be obtained by making more and more measurements so to resolve lower and lower scales. We find that even a minimal number of measurements produces agreement with Monte Carlo methods for leading-logarithmic resummation of NGLs at the sub-percent level over the full dynamical range relevant for the Large Hadron Collider. We also discuss other applications of our factorization theorem to soft jet dynamics and how to extend to higher-order accuracy.
description: 46 pages + appendices, 10 figures. v2: added current figures 4 and 5, as well as corrected several typos in appendices. v3: corrected some typos, added current figure 9, and added more discussion of fixed-order versus dressed gluon expansions. v4: fixed an error in numerics of two-dressed gluon; corrected figure 8, modified comparison to BMS. Conclusions unchanged. v5: fixed minor typo
title: Liquefaction in Action video
Creators: name: D., Iffland
name: J., Fayle
Publisher: name: Commonwealth of Australia (Geoscience Australia)
Year: 2023
Subjects: subject: ENVIRONMENTAL SCIENCES
subject: EARTH SCIENCES
subject: Earthquake
subject: Natural hazard
subject: Liquefaction
subject: Published_External

description: This short video introduces liquefaction and its impact on buildings and other structures. Liquefaction is demonstrated using sand in a glass container and explains why it happens. The video contains images and short clips of liquefaction and introduces some ways engineers lessen the impact of earthquakes on buildings. The second half of the video includes instructions on how to make your own liquefaction demonstration and extend it into an inquiry activity.
Quantum Gravity as an Information Network: Self-Organization of a 4D Universe
Creators: name: Trugenberger, Carlo A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: I propose a quantum gravity model in which the fundamental degrees of freedom are information bits for both discrete space-time points and links connecting them. The Hamiltonian is a very simple network model consisting of a ferromagnetic Ising model for space-time vertices and an antiferromagnetic Ising model for the links. As a result of the frustration between these two terms, the ground state self-organizes as a new type of low-clustering graph with finite Hausdorff dimension 4. The spectral dimension is lower than the Hausdorff dimension: it coincides with the Hausdorff dimension 4 at a first quantum phase transition corresponding to an IR fixed point while at a second quantum phase transition describing small scales space-time dissolves into disordered information bits. The large-scale dimension 4 of the universe is related to the upper critical dimension 4 of the Ising model. At finite temperatures the universe graph emerges without big bang and without singularities from a ferromagnetic phase transition in which space-time itself forms out of a hot soup of information bits. When the temperature is lowered the universe graph unfolds and expands by lowering its connectivity, a mechanism I have called topological expansion. The model admits topological black hole excitations corresponding to graphs containing holes with no space-time inside and with "Schwarzschild-like" horizons with a lower spectral dimension.
description: Revised version, to appear in Physical Review D
Generative Adversarial Networks for magnetic potential field image super-resolution
Creators: name: Benn, Anthony
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Magnetic data are one of the most common geophysical techniques in mineral and resources exploration. Developed nations have repositories of high-resolution geophysical datasets. However, these resources do not exist for many regions worldwide. Consequently, there is demand for new methodologies of image enhancement, to capitalise on existing low-resolution datasets. Generative Adversarial Networks (GANs) are a type of deep learning algorithm that have been used fruitfully on image enhancement problems in the computer vision field, but to date have received little attention in geophysics. This research uses GANs to enhance low-resolution magnetics data. Thirty thousand pairs of high- and low-resolution images are constructed from existing magnetic datasets in Australia. The dataset is split into training and validation sets and the training tiles are input into a GAN model for training. The GAN model attempts to predict the high-resolution images from the low-resolution input, effectively “learning” the geophysical and spatial characteristics of the data, and the transformation between resolutions. This new GAN-driven resolution enhancement model demonstrates the potential of this technique to be used on low-resolution datasets, particularly in areas where investment in high-resolution datasets is limited. GANs have wide-ranging applications to minerals exploration, groundwater studies, and planetary research.
Actionable exomic incidental findings in 6503 participants: challenges of variant classification
Creators: name: Taylor, Kent D.
name: Ranchalis, Jane
name: Murray, Mitzi L.
name: Foreman, Ann Katherine M.
name: Jamal, Seema M.
name: Johnson, Andrew D.
name: Gallego, Carlos J.
name: Jarvik, Ella R.
name: Shirts, Brian H.
name: Dulik, Matthew C.
name: Crosslin, David R.
name: Dorschner, Michael O.
name: Kim, Daniel Seung
name: Herman, Daniel S.
name: Lee, Kristy
name: Santani, Avni
name: Turner, Emily H.
name: Bennett, James T.
name: Abrudan, Jenica L.
name: Jones, Kelly L.
name: Itsara, Andy
name: Salama, Joseph S.
name: Robertson, Peggy D.
name: Amendola, Laura M.
name: Kelly, Melissa
name: Conlin, Laura K.
name: Schleit, Jennifer
name: Burt, Amber
name: Hart, Ragan
name: Tokita, Mari J.
name: Metterville, Danielle R.
name: Rosenthal, Elisabeth A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.
Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background
Creators: name: Zhang, Cheng-Zhong
name: Turner-Maier, Jason
name: Stewart, Chip
name: Koltookian, Michele
name: Palma, Federica Di
name: Swofford, Ross
name: Breen, Matthew
name: Elvers, Ingegerd
name: Modiano, Jaime F.
name: Beroukhim, Rameen
name: Thomas, Rachael
name: Getz, Gad
name: Alföldi, Jessica
name: Rosenberg, Mara
name: Lindblad-Toh, Kerstin
name: Johnson, Jeremy
name: Schumacher, Steven E.
name: Mauceli, Evan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Lymphoma is the most common hematological malignancy in developed countries. Outcome is strongly determined by molecular subtype, reflecting a need for new and improved treatment options. Dogs spontaneously develop lymphoma, and the predisposition of certain breeds indicates genetic risk factors. Using the dog breed structure, we selected three lymphoma predisposed breeds developing primarily T-cell (boxer), primarily B-cell (cocker spaniel), and with equal distribution of B- and T-cell lymphoma (golden retriever), respectively. We investigated the somatic mutations in B- and T-cell lymphomas from these breeds by exome sequencing of tumor and normal pairs. Strong similarities were evident between B-cell lymphomas from golden retrievers and cocker spaniels, with recurrent mutations in TRAF3-MAP3K14 (28% of all cases), FBXW7 (25%), and POT1 (17%). The FBXW7 mutations recurrently occur in a specific codon; the corresponding codon is recurrently mutated in human cancer. In contrast, T-cell lymphomas from the predisposed breeds, boxers and golden retrievers, show little overlap in their mutation pattern, sharing only one of their 15 most recurrently mutated genes. Boxers, which develop aggressive T-cell lymphomas, are typically mutated in the PTEN-mTOR pathway. T-cell lymphomas in golden retrievers are often less aggressive, and their tumors typically showed mutations in genes involved in cellular metabolism. We identify genes with known involvement in human lymphoma and leukemia, genes implicated in other human cancers, as well as novel genes that could allow new therapeutic options.
Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo
Creators: name: McKay, Daniel J.
name: Schulz, Katharine N.
name: Moshe, Arbel
name: Lieb, Jason D.
name: Harrison, Melissa M.
name: Bondra, Eliana R.
name: Kaplan, Tommy
name: Villalta, Jacqueline E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The transition from a specified germ cell to a population of pluripotent cells occurs rapidly following fertilization. During this developmental transition, the zygotic genome is largely transcriptionally quiescent and undergoes significant chromatin remodeling. In Drosophila, the DNA-binding protein Zelda (also known as Vielfaltig) is required for this transition and for transcriptional activation of the zygotic genome. Open chromatin is associated with Zelda-bound loci, as well as more generally with regions of active transcription. Nonetheless, the extent to which Zelda influences chromatin accessibility across the genome is largely unknown. Here we used formaldehyde-assisted isolation of regulatory elements to determine the role of Zelda in regulating regions of open chromatin in the early embryo. We demonstrate that Zelda is essential for hundreds of regions of open chromatin. This Zelda-mediated chromatin accessibility facilitates transcription-factor recruitment and early gene expression. Thus, Zelda possesses some key characteristics of a pioneer factor. Unexpectedly, chromatin at a large subset of Zelda-bound regions remains open even in the absence of Zelda. The GAGA factor-binding motif and embryonic GAGA factor binding are specifically enriched in these regions. We propose that both Zelda and GAGA factor function to specify sites of open chromatin and together facilitate the remodeling of the early embryonic genome.
More Is Different: Reconciling eV Sterile Neutrinos with Cosmological Mass Bounds
Creators: name: Tang, Yong
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: It is generally expected that adding light sterile species would increase the effective number of neutrinos, $N_{eff}$. In this paper we discuss a scenario that $N_{eff}$ can actually decrease due to the neutrino oscillation effect if sterile neutrinos have self-interactions. We specifically focus on the eV mass range, as suggested by the neutrino anomalies. With large self-interactions, sterile neutrinos are not fully thermalized in the early Universe because of the suppressed effective mixing angle or matter effect. As the Universe cools down, flavor equilibrium between active and sterile species can be reached after big bang nucleosynthesis (BBN) epoch, but leading to a decrease of $N_{eff}$. In such a scenario, we also show that the conflict with cosmological mass bounds on the additional sterile neutrinos can be relaxed further when more light species are introduced.
description: 17 pages, 4 figures; published version
Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms
Creators: name: Rothman, Nathaniel
name: Shen, Min
name: Rappaport, Stephen M.
name: Lan, Qing
name: Forrest, Matthew S.
name: Chen, Jinsong
name: McHale, Cliona M.
name: Zhang, Luoping
name: Smith, Martyn T.
name: Hubbard, Alan E.
name: Vermeulen, Roel
name: Yin, Songnian
name: Li, Guilan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Benzene is an established cause of leukemia, and possibly lymphoma, in humans, but the underlying molecular pathways remain largely undetermined. We used two microarray platforms to identify global gene expression changes associated with well-characterized occupational benzene exposure in the peripheral blood mononuclear cells (PBMC) of a population of shoefactory workers. Differential expression of 2692 genes (Affymetrix) and 1828 genes (Illumina) was found and the concordance was 50 % (based on an average fold-change ≥ 1.3 from the two platforms), with similar expression ratios among the concordant genes. Four genes (CXCL16, ZNF331, JUN and PF4), which we previously identified by microarray and confirmed by real-time PCR, were among the top 100 genes identified by both platforms in the current study. Gene Ontology analysis showed overrepresentation of genes involved in apoptosis among the concordant genes while pathway analysis identified pathways related to lipid metabolism. The two-platform approach allows for robust changes in the PBMC transcriptome of benzene-exposed individuals to be identified.
Spatial Search by Continuous-Time Quantum Walk with Multiple Marked Vertices
Creators: name: Wong, Thomas G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In the typical spatial search problems solved by continuous-time quantum walk, changing the location of the marked vertices does not alter the search problem. In this paper, we consider search when this is no longer true. In particular, we analytically solve search on the "simplex of $K_M$ complete graphs" with all configurations of two marked vertices, two configurations of $M+1$ marked vertices, and two configurations of $2(M+1)$ marked vertices, showing that the location of the marked vertices can dramatically influence the required jumping rate of the quantum walk, such that using the wrong configuration's value can cause the search to fail. This sensitivity to the jumping rate is an issue unique to continuous-time quantum walks that does not affect discrete-time ones.
description: 29 pages, 15 figures
REPORT 2022 DELLE ATTIVITÀ DI DIDATTICA E DIVULGAZIONE INAF - IRA
Creators: name: BIANCHI, GERMANO
name: BRIENZA, Marisa
name: CASSARO, Pietro Antonio
name: Gregorini, Loretta
name: GUIDETTI, DARIA
name: MONARI, Jader
name: NANNI, MAURO
name: NEGUSINI, MONIA
name: POLONI, MARCO
name: RICCI, ROBERTO
name: RIGHINI, SIMONA
name: TONIOLO, Rachele
name: TUGNOLI, MARCO
name: VARANO, Stefania
name: ZANICHELLI, Alessandra
Publisher: name: IRA Bologna
Year: 2023

description: Grazie a Marcello Giroletti e Roberto Orosei per la revisione del rapporto tecnico e per i preziosi consigli.
description: L'Istituto di Radioastronomia (IRA) dell’Istituto Nazionale di Astrofisica (INAF) è impegnato nella diffusione delle proprie attività presso le scuole e il pubblico, attraverso le visite guidate alle Stazioni Radioastronomiche di Medicina (BO) e Noto (SR) e la partecipazione alla realizzazione di mostre, eventi, ecc. Le attività di Didattica e Divulgazione IRA includono la progettazione di contenuti, la curatela e gestione del Centro Visite “Marcello Ceccarelli”, l’organizzazione di eventi in collaborazione con enti territoriali, nazionali e internazionali, la gestione amministrativa e finanziaria, la formazione di nuovo personale. In questo documento sono riportate le attività svolte nel 2022.
Strategies to fine-map genetic associations with lipid levels by combining epigenomic annotations and liver-specific transcription profiles
Creators: name: Mohlke, Karen L.
name: Vadlamudi, Swarooparani
name: Fogarty, Marie P.
name: Lettre, Guillaume
name: Lo, Ken Sin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Characterization of the epigenome promises to yield the functional elements buried in the human genome sequence, thus helping to annotate non-coding DNA polymorphisms with regulatory functions. Here, we develop two novel strategies to combine epigenomic data with transcriptomic profiles in humans or mice to prioritize potential candidate SNPs associated with lipid levels by genome-wide association study (GWAS). First, after confirming that lipid-associated loci that are also expression quantitative trait loci (eQTL) in human livers are enriched for ENCODE regulatory marks in the human hepatocellular HepG2 cell line, we prioritize candidate SNPs based on the number of these marks that overlap the variant position. This method recognized the known SORT1 rs12740374 regulatory SNP associated with LDL-cholesterol, and highlighted candidate functional SNPs at 15 additional lipid loci. In the second strategy, we combine ENCODE chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) data and liver expression datasets from knockout mice lacking specific transcription factors. This approach identified SNPs in specific transcription factor binding sites that are located near target genes of these transcription factors. We show that FOXA2 transcription factor binding sites are enriched at lipid-associated loci and experimentally validate that alleles of one such proxy SNP located near the FOXA2 target gene BIRC5 show allelic differences in FOXA2-DNA binding and enhancer activity. These methods can be used to generate testable hypotheses for many non-coding SNPs associated with complex diseases or traits.
Low-dimensional decomposition, smoothing and forecasting of sparse functional data
Creators: name: Dokumentov, Alexander
name: Hyndman, Rob J
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: We propose a new generic method ROPES (Regularized Optimization for Prediction and Estimation with Sparse data) for decomposing, smoothing and forecasting two-dimensional sparse data. In some ways, ROPES is similar to Ridge Regression, the LASSO, Principal Component Analysis (PCA) and Maximum-Margin Matrix Factorisation (MMMF). Using this new approach, we propose a practical method of forecasting mortality rates, as well as a new method for interpolating and extrapolating sparse longitudinal data. We also show how to calculate prediction intervals for the resulting estimates.
An Analysis of Economic Impacts of Horse Industry in Korea
Creators: name: Yu, Woong
name: Yu, Woong
Publisher: name: Unknown
Year: 2016
Subjects: subject: Demand and Price Analysis
subject: Livestock Production/Industries
subject: inter-industry analysis
subject: input-output analysis
subject: backward linkage effect

description: This paper presents the consistent and systematic basis of Inter-industry analysis for estimating the economic impact of the horse industry in Korea, which first incorporates a new approach of applying both demand-driven model and exogenous specification model to discover further realistic implications. We improve the estimation stability by resolving over-classification problems in horse-racing sector and redetermine the intermediate input structure of the horse industry following the current industry classification standard of the Bank of Korea which can be a good guide to various future researches. As a result, current market volume, production-inducing effect, value-added inducing effect, labor-inducing effect and employment-inducing effect are explored such as 2,284.5 billion won, 3,202.5 billion won, 2,174.6 billion won, 27,109 persons and 20,080 persons respectively. The horse-riding sector and horse-related sector in the horse industry have higher economic ripple effects that imply more invigoration of both sectors needs to be promoted by the policy judgement for the horse industry to settle down effectively in Korean economy.
Poincaré duality of wonderful compactifications and tautological rings
Creators: name: Petersen, Dan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: Let $g \geq 2$. Let $M_{g,n}^{rt}$ be the moduli space of $n$-pointed genus $g$ curves with rational tails. Let $C_g^n$ be the $n$-fold fibered power of the universal curve over $M_g$. We prove that the tautological ring of $M_{g,n}^{rt}$ has Poincaré duality if and only if the same holds for the tautological ring of $C_g^n$. We also obtain a presentation of the tautological ring of $M_{g,n}^{rt}$ as an algebra over the tautological ring of $C_g^n$. This proves a conjecture of Tavakol. Our results are valid in the more general setting of wonderful compactifications.
description: 11 pages. v2: Removed the incorrect Proposition 2.14, some other improvements and corrected inaccuracies. Final version, to appear in IMRN
Geomasking sensitive health data and privacy protection: an evaluation using an E911 database
Creators: name: Miller, William C.
name: Gesink, Dionne C.
name: Doherty, Irene A.
name: Fitch, Molly K.
name: Allshouse, William B.
name: Serre, Marc L.
name: Leone, Peter A.
name: Hampton, Kristen H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Geomasking is used to provide privacy protection for individual address information while maintaining spatial resolution for mapping purposes. Donut geomasking and other random perturbation geomasking algorithms rely on the assumption of a homogeneously distributed population to calculate displacement distances, leading to possible under-protection of individuals when this condition is not met. Using household data from 2007, we evaluated the performance of donut geomasking in Orange County, North Carolina. We calculated the estimated k-anonymity for every household based on the assumption of uniform household distribution. We then determined the actual k-anonymity by revealing household locations contained in the county E911 database. Census block groups in mixed-use areas with high population distribution heterogeneity were the most likely to have privacy protection below selected criteria. For heterogeneous populations, we suggest tripling the minimum displacement area in the donut to protect privacy with a less than 1% error rate.
Population growth and its spatial distribution as factors in the deforestation of Nang Rong, Thailand
Creators: name: Walsh, Stephen J.
name: Entwisle, Barbara
name: Rindfuss, Ronald R.
name: Page, Philip H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Frontiers constitute a major source of global land cover change hot spots, with forests and grass lands being converted into agricultural uses. As such, frontiers provide an opportunity to see how people manipulate the land and their lives in the context of social, cultural and environmental constraints. This paper examines frontier settlement and land cover change in Nang Rong district, Northeast Thailand for the last half century. It uses a Cellular Automata (CA) model to explore the land cover consequences of alternative patterns of settlement in a setting where people establish dwelling units in nucleated villages and work agricultural plots that surround villages. Forested land around the center of a village is converted into agricultural uses in an inverse relationship to the distance from the village center, but frequently modified by biophysical conditions. Land at the center of the village may be reforested after the village is established as a source of shade as well as fruit and other products. Model variation in land cover change is more sensitive to the spatial reach of village households than their temporal reach, suggesting the important role that technology plays in how villagers travel to their fields (walking versus motorized transit).
Collections Preservation HVAC Systems in Libraries, Archives and Museums
Creators: name: Cameron, Chris
name: Coulbourne, Mark
Publisher: name: Digital Repository at the University of Maryland
Year: 2021
Subjects: HVAC Systems
Collections Preservations

description: MARAC Educational Workshop recording of Collections Preservation: HVAC Systems in Libraries, Archives and Museums.
description: Heating, ventilation, and air conditioning systems play an integral role in libraries, archives, and museums. These systems help regulate our environments, filter pollutants, assist us in preserving our records, books, and artifacts and are now being called upon to help us decrease the chance of infection. Despite our dependence upon these systems there is little information given about them in our library and archival academic programs. This program will provide basic information about how HVAC systems function, the relationship between a properly functioning HVAC system and the long-term preservation of our collections, and ideas for advocating for a new or upgraded HVAC system.
Research Software Engineering in OpenLB: Refactoring a Legacy Code to State-Of-The-Art Performance
Creators: name: Kummerländer, Adrian
name: Krause, Mathias J.
Publisher: name: Zenodo
Year: 2023

description: Lattice Boltzmann Methods (LBM) are an established approach for simulating a wide variety of transport phenomena. The software framework OpenLB has been in continuous development for 15 years and counting as one of the major open source LBM research codes. Due to the need to develop the library alongside the primary research of the involved scientists, maintenance and performance-focused development was on the back burner for large stretches of its history, leading to it remaining a CPU-only code supporting neither SIMD nor GPUs. Within the last couple of year this was remedied by a focused refactoring effort leading to offering state-of-the-art performance on multi-GPU clusters with the latest release. This talk will revisit the steps leading to this significant advance of a feature-rich codebase, detailing the decision process between a full rewrite and incremental refactoring focused on maintaining and extending the usability of the existing feature set. In addition to this, the internal development processes w.r.t. continuous integration testing, validation and reproducability will be discussed alongside benchmarks on the HoreKa supercomputer.
Spontaneous PT symmetry breaking of a ferromagnetic superfluid in a gradient field
Creators: name: Vanderbruggen, Thomas
name: Palacios, Silvana
name: Coop, Simon
name: de Escobar, Natali Martinez
name: Mitchell, Morgan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We consider the interaction of a ferromagnetic spinor Bose-Einstein condensate with a magnetic field gradient. The magnetic field gradient realizes a spin-position coupling that explicitly breaks time-reversal symmetry T and space parity P, but preserves the combined PT symmetry. We observe using numerical simulations, a first-order phase transition spontaneously breaking this re-maining symmetry. The transition to a low-gradient phase, in which gradient effects are frozen out by the ferromagnetic interaction, suggests the possibility of high-coherence magnetic sensors unaffected by gradient dephasing.