cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
New recurrent balanced translocations in acute myeloid leukemia and myelodysplastic syndromes: Cancer and leukemia group B 8461
Creators: name: Rao, Kathleen W.
name: Pettenati, Mark J.
name: Bloomfield, Clara D.
name: Kohlschmidt, Jessica
name: Mrózek, Krzysztof
name: Carroll, Andrew J.
name: Walker, Alison
name: Sterling, Lisa J.
name: Marcucci, Guido
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Acquired chromosome abnormalities in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are among the most valuable determinants of diagnosis and prognosis. In search of new recurrent balanced translocations we reviewed the Cancer and Leukemia Group B (CALGB) cytogenetics database containing pretreatment and relapse karyotypes of 4,701 adults with AML and 565 with MDS who were treated on CALGB trials. We identified all cases with balanced structural rearrangements occurring as a sole abnormality or in addition to one other abnormality, excluded abnormalities known to be recurrent, and then reviewed the literature to determine whether any of what we considered unique, previously unknown abnormalities had been reported. As a result, we identified seven new recurrent balanced translocations in AML or MDS: t(7;11)(q22;p15.5), t(10;11)(q23;p15), t(2;12)(p13;p13), t(12;17)(p13;q12), t(2;3)(p21;p21), t(5;21)(q31;q22) and t(8;14)(q24.1;q32.2), and, additionally, t(10;12)(p11;q15), a new translocation in AML previously reported in a case of acute lymphoblastic leukemia. Herein we report hematologic and clinical characteristics, and treatment outcomes of patients with these newly recognized recurrent translocations. We also report 52 unique balanced translocations, together with the clinical data of patients harboring them, that to our knowledge have not been previously published. We hope that once the awareness of their existence is increased, some of these translocations may become recognized as novel recurring abnormalities. Identification of additional cases with both the new recurrent and the unique balanced translocations will enable determination of their prognostic significance and help to provide insights into the mechanisms of disease pathogenesis in patients with these rare abnormalities.
Decoding development inXenopus tropicalis
Creators: name: Conlon, Frank L.
name: Showell, Chris
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Xenopus tropicalis is rapidly being adopted as a model organism for developmental biology research and has enormous potential for increasing our understanding of how embryonic development is controlled. In recent years there has been a well-organized initiative within the Xenopus community, funded largely through the support of the National Institutes of Health in the US, to develop X. tropicalis as a new genetic model system with the potential to impact diverse fields of research. Concerted efforts have been made both to adapt established methodologies for use in X. tropicalis and to develop new techniques. A key resource to come out of these efforts is the genome sequence, produced by the US Department of Energy’s Joint Genome Institute and made freely available to the community in draft form for the past three years. In this review, we focus on how advances in X. tropicalis genetics coupled with the sequencing of its genome are likely to form a foundation from which we can build a better understanding of the genetic control of vertebrate development and why, when we already have other vertebrate genetic models, we should want to develop genetic analysis in the frog.
Small heat shock protein Hsp27 is required for proper heart tube formation
Creators: name: Conlon, Frank L.
name: Brown, Daniel D.
name: Christine, Kathleen S.
name: Showell, Christopher
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The small heat shock protein Hsp27 has been shown to be involved in a diverse array of cellular processes, including cellular stress response, protein chaperone activity, regulation of cellular glutathione levels, apoptotic signaling, and regulation of actin polymerization and stability. Furthermore, mutation within Hsp27 has been associated with the human congenital neuropathy Charcot-Marie Tooth (CMT) disease. Hsp27 is known to be expressed in developing embryonic tissues; however, little has been done to determine the endogenous requirement for Hsp27 in developing embryos. In this study, we show that depletion of XHSP27 protein results in a failure of cardiac progenitor fusion resulting in cardia bifida. Furthermore, we demonstrate a concomitant disorganization of actin filament organization and defects in myofibril assembly. Moreover, these defects are not associated with alterations in specification or differentiation. We have thus demonstrated a critical requirement for XHSP27 in developing cardiac and skeletal muscle tissues.
Die Orchideenstandorte in Württemberg und Hohenzollern
Creators: name: Mayer, Adolf
Publisher: name: unkn
Year: 2021

description: Jahreshefte des Vereins für Vaterländische Naturkunde in Württemberg : zugl. Jahrbuch d. Staatlichen Museums für Naturkunde in Stuttgart
description: Bd. 69, 1913
Berry-phase effects and electronic dynamics in noncollinear antiferromagnetic texture
Creators: name: Olena, Gomonay
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Antiferromagnets (AFMs), in contrast to ferromagnets, show a nontrivial magnetic structure with zero net magnetization. However, they share a number of spintronic effects with ferromagnets, including spin-pumping and spin transfer torques. Both phenomena stem from the coupled dynamics of free carriers and localized magnetic moments. In the present paper I study the adiabatic dynamics of a spin-polarized electrons in a metallic AFM exhibiting a noncollinear 120$^\circ$ magnetic structure. I show that the slowly varying AFM spin texture produces a non-Abelian gauge potential related to the time/space gradients of the Néel vectors. Corresponding emergent electric and magnetic fields induce rotation of spin and influence the orbital dynamics of free electrons. I discuss both the possibility of a topological spin Hall effect in the vicinity of topological AFM solitons with nonzero curvature and rotation of the electron spin traveling through the AFM domain wall.
Focal adhesion kinase is essential for cardiac looping and multichamber heart formation
Creators: name: Mack, Christopher P.
name: Taylor, Joan M.
name: Doherty, Jason T.
name: Conlon, Frank L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Focal adhesion kinase (FAK) is a critical mediator of matrix- and growth factor-induced signaling during development. Myocyte-restricted FAK deletion in mid-gestation mice results in impaired ventricular septation and cardiac compaction. However, whether FAK regulates early cardiogenic steps remains unknown. To explore a role for FAK in multi-chambered heart formation, we utilized anti-sense morpholinos to deplete FAK in Xenopus laevis. Xenopus FAK morphants exhibited impaired cardiogenesis, pronounced pericardial edema, and lethality by tadpole stages. Spatial-temporal assessment of cardiac marker gene expression revealed that FAK was not necessary for midline migration, differentiation, fusion of cardiac precursors, or linear heart tube formation. However, myocyte proliferation was significantly reduced in FAK morphant heart tubes and these tubes failed to undergo proper looping morphogenesis. Collectively our data imply that FAK plays an essential role in chamber outgrowth and looping morphogenesis likely stimulated by fibroblast growth factors (and possibly other) cardiotrophic factors.
CANDID: a flexible method for prioritizing candidate genes for complex human traits
Creators: name: Hutz, Janna E.
name: McLeod,, Howard L.
name: Province, Michael A.
name: Kraja, Aldi T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Genomewide studies and localized candidate gene approaches have become everyday study designs for identifying polymorphisms in genes that influence complex human traits. Yet, in general, the number of significant findings and the need to focus in smaller regions require a prioritization of genes for further study. Some candidate gene identification algorithms have been proposed in recent years to attempt to streamline this prioritization, but many suffer from limitations imposed by the source data or are difficult to use and understand. CANDID is a prioritization algorithm designed to produce impartial, accurate rankings of candidate genes that influence complex human traits. CANDID can use information from publications, protein domain descriptions, cross-species conservation measures, gene expression profiles, and protein-protein interactions in its analysis. Additionally, users may supplement these data sources with results from linkage, association and other studies. CANDID was tested on well-known complex trait genes using data from the Online Mendelian Inheritance in Man (OMIM) database. Additionally, CANDID was evaluated in a modeled gene discovery environment, where it ranked genes whose trait associations were published after CANDID’s databases were compiled. In all settings, CANDID exhibited high sensitivity and specificity, indicating an improvement upon previously published algorithms. Its accuracy and ease of use make CANDID a highly useful tool in study design and analysis for complex human traits.
Statistical methods for exoplanet detection with radial velocities
Creators: name: Hara, Nathan C.
name: Ford, Eric B.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Applications (stat.AP)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Exoplanets can be detected with various observational techniques. Among them, radial velocity (RV) has the key advantages of revealing the architecture of planetary systems and measuring planetary mass and orbital eccentricities. RV observations are poised to play a key role in the detection and characterization of Earth twins. However, the detection of such small planets is not yet possible due to very complex, temporally correlated instrumental and astrophysical stochastic signals. Furthermore, exploring the large parameter space of RV models exhaustively and efficiently presents difficulties. In this review, we frame RV data analysis as a problem of detection and parameter estimation in unevenly sampled, multivariate time series. The objective of this review is two-fold: to introduce the motivation, methodological challenges, and numerical challenges of RV data analysis to nonspecialists, and to unify the existing advanced approaches in order to identify areas for improvement.
description: Published in Annual Reviews of Statistics and Its Application, contains the main text and supplemental appendix
Trading in Onion Futures: Effect on Cash Prices
Creators: name: Jesse, Edward
name: Jesse, Edward
Publisher: name: Unknown
Year: 1973
Subjects: subject: Crop Production/Industries
subject: Demand and Price Analysis
subject: Marketing
subject: FOS: Economics and business
subject: Onions
subject: prices
subject: price performance
subject: futures trading

description: Futures trading in perishable commodities has frequently been cited as having undesirable effects on cash market prices. This article reports the results of an extensive study of the behavior of cash market prices for dry onions, a perishable commodity which was traded on the Chicago Mercantile Exchange from 1942 until a Congressional ban on trading became effective in 1959. The study detected no differences in cash onion price performance between periods before, during, and after trading.
description: Reprinted From The Marketing and Transportation Situation • Feb. 1973
Avoiding progenitor bias: The structural and mass evolution of Brightest Group and Cluster Galaxies in Hierarchical models since z~1
Creators: name: Shankar, Francesco
name: Buchan, Stewart
name: Rettura, Alessandro
name: Bouillot, Vincent
name: Moreno, Jorge
name: Licitra, Rossella
name: Bernardi, Mariangela
name: Huertas-Company, Marc
name: Mei, Simona
name: Ascaso, Begoña
name: Sheth, Ravi
name: Delaye, Lauriane
name: Raichoor, Anand
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The mass and structural evolution of massive galaxies is one of the hottest topics in galaxy formation. This is because it may reveal invaluable insights into the still debated evolutionary processes governing the growth and assembly of spheroids. However, direct comparison between models and observations is usually prevented by the so-called "progenitor bias", i.e., new galaxies entering the observational selection at later epochs, thus eluding a precise study of how pre-existing galaxies actually evolve in size. To limit this effect, we here gather data on high-redshift brightest group and cluster galaxies, evolve their (mean) host halo masses down to z=0 along their main progenitors, and assign as their "descendants" local SDSS central galaxies matched in host halo mass. At face value, the comparison between high redshift and local data suggests a noticeable increase in stellar mass of a factor of >2 since z~1, and of >2.5 in mean effective radius. We then compare the inferred stellar mass and size growth with those predicted by hierarchical models for central galaxies, selected at high redshifts to closely match the halo and stellar mass bins as in the data. Only hierarchical models characterized by very limited satellite stellar stripping and parabolic orbits are capable of broadly reproducing the stellar mass and size increase of a factor ~2-4 observed in cluster galaxies since z ~1. The predicted, average (major) merger rate since z~1 is in good agreement with the latest observational estimates.
description: 9 pages, 5 figures. ApJ, in press. Additional (minor) editing included in text and figure captions
Approaches to Open Access in Scientific Publishing
Creators: name: Harnad, J.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Popular Physics (physics.pop-ph)
subject: FOS: Physical sciences

description: Approaches to scientific journal publishing that provide free access to all readers are challenging the standard subscription-based model. But in domains that have a well-functioning system of publicly accessible preprint repositories like arXiv, Open Access is already effectively available. In physics, such repositories have long coexisted constructively with refereed, subscription based journals. Trying to replace this by a system based on journals whose revenue is derived primarily from fees charged to authors is unlikely to provide a better guarantee of Open Access, and may be in conflict with the maintenance of high quality standards.
description: 5 pages. Detailed version of an article to appear in Physics World, in an abbreviated form, under the title "Free For All"
Avoiding the high Bonferroni penalty in genome-wide association studies
Creators: name: Starmer, Joshua D.
name: Becker, Diane M.
name: Gao, Xiaoyi
name: Becker, Lewis C.
name: Province, Michael A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: A major challenge in genome-wide association studies (GWASs) is to derive the multiple testing threshold when hypothesis tests are conducted using a large number of single nucleotide polymorphisms. Permutation tests are considered the gold standard in multiple testing adjustment in genetic association studies. However, it is computationally intensive, especially for GWASs, and can be impractical if a large number of random shuffles are used to ensure accuracy. Many researchers have developed approximation algorithms to relieve the computing burden imposed by permutation. One particularly attractive alternative to permutation is to calculate the effective number of independent tests, Meff, which has been shown to be promising in genetic association studies. In this study, we compare recently developed Meff methods and validate them by the permutation test with 10,000 random shuffles using two real GWAS data sets: an Illumina 1M BeadChip and an Affymetrix GeneChip® Human Mapping 500K Array Set. Our results show that the simpleM method produces the best approximation of the permutation threshold, and it does so in the shortest amount of time. We also show that Meff is indeed valid on a genome-wide scale in these data sets based on statistical theory and significance tests. The significance thresholds derived can provide practical guidelines for other studies using similar population samples and genotyping platforms.
Considerations When Learning Additive Explanations for Black-Box Models
Creators: name: Tan, Sarah
name: Hooker, Giles
name: Koch, Paul
name: Gordo, Albert
name: Caruana, Rich
Publisher: name: arXiv
Year: 2018
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Many methods to explain black-box models, whether local or global, are additive. In this paper, we study global additive explanations for non-additive models, focusing on four explanation methods: partial dependence, Shapley explanations adapted to a global setting, distilled additive explanations, and gradient-based explanations. We show that different explanation methods characterize non-additive components in a black-box model's prediction function in different ways. We use the concepts of main and total effects to anchor additive explanations, and quantitatively evaluate additive and non-additive explanations. Even though distilled explanations are generally the most accurate additive explanations, non-additive explanations such as tree explanations that explicitly model non-additive components tend to be even more accurate. Despite this, our user study showed that machine learning practitioners were better able to leverage additive explanations for various tasks. These considerations should be taken into account when considering which explanation to trust and use to explain black-box models.
description: Published at Machine Learning (2023). Previously titled "Learning Global Additive Explanations for Neural Nets Using Model Distillation". A short version was presented at NeurIPS 2018 Machine Learning for Health Workshop
SousLeSensVocables
Creators: name: Fauconnet, Claude
Publisher: name: Zenodo
Year: 2023
Subjects: ontology
standard
data management
global workshop
ontology commons ecosystem
FAIR

description: SousLeSens Vocables is an extensible platform with tools designed to visually manipulate, compare, create and enrich OWL ontologies and knowledge graphs. It is under MIT license.
Haplotype associations with quantitative traits in the presence of complex multilocus and heterogeneous effects
Creators: name: Diatchenko, Luda
name: Zaykin, Dmitri V.
name: Shibata, Kyoko
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: In genetic mapping of complex traits, scored haplotypes are likely to represent only a subset of all causal polymorphisms. At the extreme of this scenario, observed polymorphisms are not themselves functional, and only linked to causal ones via linkage disequilibrium (LD). We will demonstrate that due to such incomplete knowledge regarding the underlying genetic mechanism, the variance of a trait may become different between the scored haplotypes. Thus, unequal variances between haplotypes may be indicative of additional functional polymorphisms affecting the trait. Methods accounting for such haplotype-specific variance may also provide an increased power to detect complex associations. We suggest ways to estimate and test these haplotypic variance contrasts, and incorporate them into the haplotypic tests for association. We further extend this approach to data with unknown gametic phase via likelihood-based simultaneous estimation of haplotypic effects and their frequencies. We find our approach to provide additional power, especially under the following types of models: (a) where scored and unobserved variants are epistatically interacting with each other; and (b) under heterogeneity models, where multiple unobserved mutations are linked to nonfunctional observed polymorphisms via LD. An illustrative example of usefulness of the method is discussed, utilizing analysis of multilocus effects within the catechol-O-methyl transferase (COMT) gene.
Renormalization of the conduction band spectrum in HgTe quantum wells by electron-electron interaction
Creators: name: Minkov, G. M.
name: Aleshkin, V. Ya.
name: Rut, O. E.
name: Sherstobitov, A. A.
name: Germanenko, A. V.
name: Dvoretski, S. A.
name: Mikhailov, N. N.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The energy spectrum of the conduction band in HgTe/Cd$_x$Hg$_{1-x}$Te quantum wells of a width $d=(4.6-20.2)$ nm has been experimentally studied in a wide range of electron density. For this purpose, the electron density dependence of the effective mass was measured by two methods: by analyzing the temperature dependence of the Shubnikov-de Haas oscillations and by means of the quantum capacitance measurements. There was shown that the effective mass obtained for the structures with $d(7-8)$ nm, the experimental effective mass becomes noticeably less than the calculated ones. This difference increases with the electron density decrease, i.e., with lowering the Fermi energy; the maximal difference between the theory and experiment is achieved at $d = (15-18)$ nm, where the ratio between the calculated and experimental masses reaches the value of two and begins to decrease with a further $d$ increase. We assume that observed behavior of the electron effective mass results from the spectrum renormalization due to electron-electron interaction.
description: 8 pages, 10 figures
title: Transnationale Migration von Polinnen und ihre Auswirkungen auf das Familienleben
Creators: name: Skrzypczak, Aneta Malgorzata
Year: 2023

description: In der Arbeit werden die transnationale Migration und ihre Auswirkung auf das Familienleben am Beispiel von polnischen Familien präsentiert. Ich habe mich ausschließlich auf weibliche Tranmigrantinnen aus meinem Heimatland - Polen - konzentriert, weil die Gruppe immer noch nicht ausreichend erforscht wurde. In den 1990er fingen WissenschaftlerInnen an, verstärkt Transmigration und die daraus entstandenen transnationalen Räume zu untersuchen. Die wichtigsten internationalen und polnischen Publikationen zu diesem Thema werden in dieser Arbeit kurz präsentiert. Da mich besonders der Einfluss der Transmigration auf das Familienleben interessiert hat, habe ich mehrere Migrantinnen und ihre Kinder dazu befragt und die Veränderungen beschrieben. Das Thema ist höchst relevant, da die transnationale Migration einen großen Einfluss auf die Institution “Familie“ hat. Die empirische Untersuchung umfasste sieben leitfadengestützte Interviews mit polnischen Transmigratinnen und ihren Familienmitgliedern. Aus dem Material haben sich elf unterschiedliche Themen herauszukristallisiert: Materielle Vorteile aus der Transmigration, Materialisierte Mutterschaft, Paradigmenwechsel bei TransmigrantInnen, der Einfluss der Transmigration auf die Kinder, Familientrennung, Gefühlslage der Kinder, Kinderbetreuung, Schulleistungen der Kinder, Haushaltstätigkeiten, neue Technologien und Kommunikationswege, Pflege von älteren Familienmitgliedern. Dazu haben sich die von mir untersuchten Frauen oder ihre Kinder am häufigsten geäußert. Intensiv habe ich mich dann mit der Thematik schlechter Kinderbetreuung auseinandergesetzt, die ich feinstrukturanalytisch untersuchte. Das unverantwortliche Verhalten eines Ehemannes und Vater, der auf die zwei gemeinsamen Kinder aufpassen sollte, während die Mutter in den USA erwerbstätig war, um die Familie finanziell zu stützen, hat tiefe Gräben in dieser Familie hinterlassen. Weiters hat man gemerkt, wie schnell solche wichtigen Angelegenheiten zur Überforderung der Tranmigratinnen im Aufnahmeland führen können. Veränderungen der Auswanderungsmotive und des tatsächlichen Migrationsgeschehens legen nahe, dass Transmigration und transnationale Migranten sowie die verstärkte Pendelmobilität in der wissenschaftlichen Forschung und politischen Debatte mehr Aufmerksamkeit bedürfen.
Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data
Creators: name: Lin, D. Y.
name: Zeng, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: To identify genetic variants with modest effects on complex human diseases, a growing number of networks or consortia are created for sharing data from multiple genome-wide association studies on the same disease or related disorders. A central question in this enterprise is whether to obtain summary results or individual participant data from relevant studies. We show theoretically and numerically that meta-analysis of summary results is statistically as efficient as joint analysis of individual participant data (provided that both analyses are performed properly under the same modeling assumptions). We illustrate this equivalence with case-control data from the Finland-United States Investigation of NIDDM Genetics (FUSION) study. Collating only summary results will increase the number and representativeness of available studies, simplify data collection and analysis, reduce resource utilization, and accelerate discovery.
title: Sharing-Modelle für innovative unternehmerische Initiativen - ein Thema der Regionalentwicklung im steirischen Zentralraum!?
Creators: name: Arbesleitner, Nora
Year: 2023

description: Diese Masterarbeit geht der Frage nach, wie die Region Steirischer Zentralraum auf regionaler Ebene und in interkommunaler bzw. regionaler Zusammenarbeit den Bereich der Sharing-Modelle für innovative unternehmerische Initiativen unterstützen kann. Insbesondere werden die bestehenden Potentiale, Synergien, Akteur:innen und ebenso Bedarfe, die es in diesem Bereich in der Region gibt, aufgezeigt. Daraus resultierend galt es zu erforschen, welche Maßnahmen es zu setzen bzw. Synergien zu nützen und / oder aufzubauen gilt, um im Sinne des Forschungsziels entsprechende Handlungsempfehlungen aussprechen zu können. Mit der Arbeit wird an das Projekt ROBUST, ein durch Horizon 2020 gefördertes EU-Projekt in dem der Steirische Zentralraum als living lab (Reallabor) fungiert, angeknüpft. Die Masterarbeit ist als Mehrwert für ROBUST zu erachten.
Proper analysis of secondary phenotype data in case-control association studies
Creators: name: Zeng, D.
name: Lin, D. Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Case-control association studies often collect extensive information on secondary phenotypes, which are quantitative or qualitative traits other than the case-control status. Exploring secondary phenotypes can yield valuable insights into biological pathways and identify genetic variants influencing phenotypes of direct interest. All publications on secondary phenotypes have used standard statistical methods, such as least-squares regression for quantitative traits. Because of unequal selection probabilities between cases and controls, the case-control sample is not a random sample from the general population. As a result, standard statistical analysis of secondary phenotype data can be extremely misleading. Although one may avoid the sampling bias by analyzing cases and controls separately or by including the case-control status as a covariate in the model, the associations between a secondary phenotype and a genetic variant in the case and control groups can be quite different from the association in the general population. In this article, we present novel statistical methods that properly reflect the case-control sampling in the analysis of secondary phenotype data. The new methods provide unbiased estimation of genetic effects and accurate control of false-positive rates while maximizing statistical power. We demonstrate the pitfalls of the standard methods and the advantages of the new methods both analytically and numerically. The relevant software is available at our website.
Spin-orbit splitting of the conduction band in HgTe quantum wells: role of different mechanisms
Creators: name: Minkov, G. M.
name: Aleshkin, V. Ya.
name: Rut, O. E.
name: Sherstobitov, A. A.
name: Germanenko, A. V.
name: Dvoretski, S. A.
name: Mikhailov, N. N.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Spin-orbit splitting of conduction band in HgTe quantum wells was studied experimentally. In order to recognize the role of different mechanisms, we carried out detailed measurements of the Shubnikov-de Haas oscillations in gated structures with a quantum well widths from $8$ to $18$ nm over a wide range of electron density. With increasing electron density controlled by the gate voltage, splitting of the maximum of the Fourier spectrum $f_0$ into two components $f_1$ and $f_2$ and the appearance of the low-frequency component $f_3$ was observed. Analysis of these results shows that the components $f_1$ and $f_2$ give the electron densities $n_1$ and $n_2$ in spin-orbit split subbands while the $f_3$ component results from magneto-intersubband oscillations so that $f_3=f_1 - f_2$. Comparison of these data with results of self-consistent calculations carried out within the framework of four-band \emph{kP}-model shows that a main contribution to spin-orbit splitting comes from the Bychkov-Rashba effect. Contribution of the interface inversion asymmetry to the splitting of the conduction band turns out to be four-to-five times less than that for the valence band in the same structures.
description: 6 pages, 6 figures
Use of longitudinal data in genetic studies in the genome-wide association studies era: summary of Group 14
Creators: name: North, Kari E.
name: Fallin, M. Daniele
name: Kerner, Berit
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Participants analyzed actual and simulated longitudinal data from the Framingham Heart Study for various metabolic and cardiovascular traits. The genetic information incorporated into these investigations ranged from selected single-nucleotide polymorphisms to genome-wide association arrays. Genotypes were incorporated using a broad range of methodological approaches including conditional logistic regression, linear mixed models, generalized estimating equations, linear growth curve estimation, growth modeling, growth mixture modeling, population attributable risk fraction based on survival functions under the proportional hazards models, and multivariate adaptive splines for the analysis of longitudinal data. The specific scientific questions addressed by these different approaches also varied, ranging from a more precise definition of the phenotype, bias reduction in control selection, estimation of effect sizes and genotype associated risk, to direct incorporation of genetic data into longitudinal modeling approaches and the exploration of population heterogeneity with regard to longitudinal trajectories. The group reached several overall conclusions: 1) The additional information provided by longitudinal data may be useful in genetic analyses. 2) The precision of the phenotype definition as well as control selection in nested designs may be improved, especially if traits demonstrate a trend over time or have strong age-of-onset effects. 3) Analyzing genetic data stratified for high-risk subgroups defined by a unique development over time could be useful for the detection of rare mutations in common multi-factorial diseases. 4) Estimation of the population impact of genomic risk variants could be more precise. The challenges and computational complexity demanded by genome-wide single-nucleotide polymorphism data were also discussed.
Variance-components methods for linkage and association analysis of ordinal traits in general pedigrees
Creators: name: Diao, G.
name: Lin, D. Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Many complex human diseases such as alcoholism and cancer are rated on ordinal scales. Well-developed statistical methods for the genetic mapping of quantitative traits may not be appropriate for ordinal traits. We propose a class of variance-component models for the joint linkage and association analysis of ordinal traits. The proposed models accommodate arbitrary pedigrees and allow covariates and gene-environment interactions. We develop efficient likelihood-based inference procedures under the proposed models. The maximum likelihood estimators are approximately unbiased, normally distributed, and statistically efficient. Extensive simulation studies demonstrate that the proposed methods perform well in practical situations. An application to data from the Collaborative Study on the Genetics of Alcoholism is provided.
The Swift-UVOT ultraviolet and visible grism calibration
Creators: name: Kuin, N. P. M.
name: Landsman, W.
name: Breeveld, A. A.
name: Page, M. J.
name: James, C.
name: Lamoureux, H.
name: Mehdipour, M.
name: Still, M.
name: Yershov, V.
name: Brown, P. J.
name: Carter, M.
name: Mason, K. O.
name: Kennedy, T.
name: Marshall, F.
name: Roming, P. W. A.
name: Siegel, M.
name: Oates, S.
name: Smith, P. J.
name: De Pasquale, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present the calibration of the Swift UVOT grisms, of which there are two, providing low-resolution field spectroscopy in the ultraviolet and optical bands respectively. The UV grism covers the range 1700-5000 Angstrom with a spectral resolution of 75 at 2600 Angstrom for source magnitudes of u=10-16 mag, while the visible grism covers the range 2850-6600 Angstrom with a spectral resolution of 100 at 4000 Angstrom for source magnitudes of b=12-17 mag. This calibration extends over all detector positions, for all modes used during operations. The wavelength accuracy (1-sigma) is 9 Angstrom in the UV grism clocked mode, 17 Angstrom in the UV grism nominal mode and 22 Angstrom in the visible grism. The range below 2740 Angstrom in the UV grism and 5200 Angstrom in the visible grism never suffers from overlapping by higher spectral orders. The flux calibration of the grisms includes a correction we developed for coincidence loss in the detector. The error in the coincidence loss correction is less than 20%. The position of the spectrum on the detector only affects the effective area (sensitivity) by a few percent in the nominal modes, but varies substantially in the clocked modes. The error in the effective area is from 9% in the UV grism clocked mode to 15% in the visible grism clocked mode .
description: 27 pages, 31 figures; MNRAS accepted 23 February 2015
Sharp decay estimates and smoothness for solutions to nonlocal semilinear equations
Creators: name: Cappiello, Marco
name: Nicola, Fabio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We consider semilinear equations of the form p(D)u=F(u), with a locally bounded nonlinearity F(u), and a linear part p(D) given by a Fourier multiplier. The multiplier p(ξ) is the sum of positively homogeneous terms, with at least one of them non smooth. This general class of equations includes most physical models for traveling waves in hydrodynamics, the Benjamin-Ono equation being a basic example. We prove sharp pointwise decay estimates for the solutions to such equations, depending on the degree of the non smooth terms in p(ξ). When the nonlinearity is smooth we prove similar estimates for the derivatives of the solution, as well holomorphic extension to a strip, for analytic nonlinearity.
Analysis of untyped SNPs: maximum likelihood and imputation methods
Creators: name: Lin, D.Y.
name: Hu, Y.J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Analysis of untyped single nucleotide polymorphisms (SNPs) can facilitate the localization of disease-causing variants and permit meta-analysis of association studies with different genotyping platforms. We present two approaches for using the linkage disequilibrium structure of an external reference panel to infer the unknown value of an untyped SNP from the observed genotypes of typed SNPs. The maximum-likelihood approach integrates the prediction of untyped genotypes and estimation of association parameters into a single framework and yields consistent and efficient estimators of genetic effects and gene-environment interactions with proper variance estimators. The imputation approach is a two-stage strategy, which first imputes the untyped genotypes by either the most likely genotypes or the expected genotype counts and then uses the imputed values in a downstream association analysis. The latter approach has proper control of type I error in single-SNP tests with possible covariate adjustments even when the reference panel is misspecified; however, type I error may not be properly controlled in testing multiple-SNP effects or gene-environment interactions. In general, imputation yields biased estimators of genetic effects and gene-environment interactions, and the variances are underestimated. We conduct extensive simulation studies to compare the bias, type I error, power, and confidence interval coverage between the maximum likelihood and imputation approaches in the analysis of single-SNP effects, multiple-SNP effects, and gene-environment interactions under cross-sectional and case-control designs. In addition, we provide an illustration with genome-wide data from the Wellcome Trust Case-Control Consortium (WTCCC) [2007].
A nearby M star with three transiting super-Earths discovered by K2
Creators: name: Crossfield, Ian J. M.
name: Petigura, Erik
name: Schlieder, Joshua
name: Howard, Andrew W.
name: Fulton, B. J.
name: Aller, Kimberly M.
name: Ciardi, David R.
name: Lepine, Sebastien
name: Barclay, Thomas
name: de Pater, Imke
name: de Kleer, Katherine
name: Quintana, Elisa V.
name: Christiansen, Jessie L.
name: Schlafly, Eddie
name: Kaltenegger, Lisa
name: Crepp, Justin R.
name: Henning, Thomas
name: Obermeier, Christian
name: Deacon, Niall
name: Weiss, Lauren M.
name: Isaacson, Howard T.
name: Hansen, Brad M. S.
name: Liu, Michael C.
name: Greene, Tom
name: Howell, Steve B.
name: Barman, Travis
name: Mordasini, Christoph
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Small, cool planets represent the typical end-products of planetary formation. Studying the archi- tectures of these systems, measuring planet masses and radii, and observing these planets' atmospheres during transit directly informs theories of planet assembly, migration, and evolution. Here we report the discovery of three small planets orbiting a bright (Ks = 8.6 mag) M0 dwarf using data collected as part of K2, the new transit survey using the re-purposed Kepler spacecraft. Stellar spectroscopy and K2 photometry indicate that the system hosts three transiting planets with radii 1.5-2.1 R_Earth, straddling the transition region between rocky and increasingly volatile-dominated compositions. With orbital periods of 10-45 days the planets receive just 1.5-10x the flux incident on Earth, making these some of the coolest small planets known orbiting a nearby star; planet d is located near the inner edge of the system's habitable zone. The bright, low-mass star makes this system an excellent laboratory to determine the planets' masses via Doppler spectroscopy and to constrain their atmospheric compositions via transit spectroscopy. This discovery demonstrates the ability of K2 and future space-based transit searches to find many fascinating objects of interest.
description: ApJ accepted. Spectra and light curves available at ApJ or via arXiv source
A proof that artificial neural networks overcome the curse of dimensionality in the numerical approximation of Black-Scholes partial differential equations
Creators: name: Grohs, Philipp
name: Hornung, Fabian
name: Jentzen, Arnulf
name: von Wurstemberger, Philippe
Publisher: name: arXiv
Year: 2018
Subjects: subject: Numerical Analysis (math.NA)
subject: Machine Learning (cs.LG)
subject: Probability (math.PR)
subject: Mathematical Finance (q-fin.MF)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: FOS: Economics and business

description: Artificial neural networks (ANNs) have very successfully been used in numerical simulations for a series of computational problems ranging from image classification/image recognition, speech recognition, time series analysis, game intelligence, and computational advertising to numerical approximations of partial differential equations (PDEs). Such numerical simulations suggest that ANNs have the capacity to very efficiently approximate high-dimensional functions and, especially, indicate that ANNs seem to admit the fundamental power to overcome the curse of dimensionality when approximating the high-dimensional functions appearing in the above named computational problems. There are a series of rigorous mathematical approximation results for ANNs in the scientific literature. Some of them prove convergence without convergence rates and some even rigorously establish convergence rates but there are only a few special cases where mathematical results can rigorously explain the empirical success of ANNs when approximating high-dimensional functions. The key contribution of this article is to disclose that ANNs can efficiently approximate high-dimensional functions in the case of numerical approximations of Black-Scholes PDEs. More precisely, this work reveals that the number of required parameters of an ANN to approximate the solution of the Black-Scholes PDE grows at most polynomially in both the reciprocal of the prescribed approximation accuracy $\varepsilon > 0$ and the PDE dimension $d \in \mathbb{N}$. We thereby prove, for the first time, that ANNs do indeed overcome the curse of dimensionality in the numerical approximation of Black-Scholes PDEs.
description: To appear in Mem. Amer. Math. Soc.; 126 pages
Memory Vulnerability: A Case for Delaying Error Reporting
Creators: name: Jaulmes, Luc
name: Moretó, Miquel
name: Valero, Mateo
name: Casas, Marc
Publisher: name: arXiv
Year: 2018
Subjects: subject: Hardware Architecture (cs.AR)
subject: FOS: Computer and information sciences

description: To face future reliability challenges, it is necessary to quantify the risk of error in any part of a computing system. To this goal, the Architectural Vulnerability Factor (AVF) has long been used for chips. However, this metric is used for offline characterisation, which is inappropriate for memory. We survey the literature and formalise one of the metrics used, the Memory Vulnerability Factor, and extend it to take into account false errors. These are reported errors which would have no impact on the program if they were ignored. We measure the False Error Aware MVF (FEA) and related metrics precisely in a cycle-accurate simulator, and compare them with the effects of injecting faults in a program's data, in native parallel runs. Our findings show that MVF and FEA are the only two metrics that are safe to use at runtime, as they both consistently give an upper bound on the probability of incorrect program outcome. FEA gives a tighter bound than MVF, and is the metric that correlates best with the incorrect outcome probability of all considered metrics.
Relativistic extended coupled cluster method for magnetic hyperfine structure constant
Creators: name: Sasmal, Sudip
name: Pathak, Himadri
name: Nayak, Malaya K.
name: Vaval, Nayana
name: Pal, Sourav
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: This article deals with the general implementation of 4-component spinor relativistic extended coupled cluster (ECC) method to calculate first order property of atoms and molecules in their open-shell ground state configuration. The implemented relativistic ECC is employed to calculate hyperfine structure (HFS) constant of alkali metals (Li, Na, K, Rb and Cs), singly charged alkaline earth metal atoms (Be+, Mg+, Ca+ and Sr+) and molecules (BeH, MgF and CaH). We have compared our ECC results with the calculations based on restricted active space configuration interaction (RAS-CI) method. Our results are in better agreement with the available experimental values than those of the RAS-CI values.
description: 14 pages, 6 figures
Impact of repeated measures and sample selection on genome-wide association studies of fasting glucose
Creators: name: Bielinski, Suzette J.
name: Couper, David
name: Yan, Yu
name: Boerwinkle, Eric
name: Rasmussen-Torvik, Laura J.
name: Li, Man
name: Kao, Wen
name: Köttgen, Anna
name: Pankow, James S.
name: Alonso, Alvaro
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Although GWAS have been performed in longitudinal studies, most used only a single trait measure. GWAS of fasting glucose have generally included only normoglycemic individuals. We examined the impact of both repeated measures and sample selection on GWAS in ARIC, a study which obtained four longitudinal measures of fasting glucose and included both individuals with and without prevalent diabetes. The sample included Caucasians and the Affymetrix 6.0 chip was used for genotyping. Sample sizes for GWAS analyses ranged from 8372 (first study visit) to 5782 (average fasting glucose). Candidate SNP analyses with SNPs identified through fasting glucose or diabetes GWAS were conducted in 9133 individuals, including 761 with prevalent diabetes. For a constant sample size, smaller p-values were obtained for the average measure of fasting glucose compared to values at any single visit, and two additional significant GWAS signals were detected. For four candidate SNPs (rs780094, rs10830963, rs7903146, and rs4607517), the strength of association between genotype and glucose was significantly (p-interaction < .05) different in those with and without prevalent diabetes and for all five fasting glucose candidate SNPs (rs780094, rs10830963, rs560887, rs4607517, rs13266634) the association with measured fasting glucose was more significant in the smaller sample without prevalent diabetes than in the larger combined sample of those with and without diabetes. This analysis demonstrates the potential utility of averaging trait values in GWAS studies and explores the advantage of using only individuals without prevalent diabetes in GWAS of fasting glucose.