cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
Creators: name: Bhinge, A. A.
name: Lee, B.-K.
name: Crawford, G. E.
name: McDaniell, R. M.
name: Lieb, J. D.
name: Furey, T. S.
name: Birney, E.
name: Ni, Y.
name: Song, L.
name: Battenhouse, A.
name: Liu, Z.
name: Iyer, V. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII), and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, while MYC showed the greatest cell-type specificity. MYC and RNAPII co-localized at many of their binding sites and putative target genes. Cell-type specific binding sites, in particular for MYC and RNAPII, were associated with cell-type specific functions. Patterns of binding in relation to gene features were generally conserved across different cell types. RNAPII occupancy was higher over exons than adjacent introns, likely reflecting a link between transcriptional elongation and splicing. TF binding was positively correlated with the expression levels of their putative target genes, but combinatorial binding, in particular of MYC and RNAPII, was even more strongly associated with higher gene expression. These data illuminate how combinatorial binding of transcription factors in diverse cell types is associated with gene expression and cell-type specific biology.
Estimation for Single-index and Partially Linear Single-index Nonstationary Time Series Models
Creators: name: Dong, Chaohua
name: Gao, Jiti
name: Tjostheim, Dag
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: Estimation in two classes of popular models, single-index models and partially linear single-index models, is studied in this paper. Such models feature nonstationarity. Orthogonal series expansion is used to approximate the unknown integrable link function in the models and a profile approach is used to derive the estimators. The findings include dual convergence rates of the estimators for the single-index models and a trio of convergence rates for the partially linear single-index models. More precisely, the estimators for single-index model converge along the direction of the true parameter vector at rate of n^(-1/4), while at rate of n^(-3/4) along all directions orthogonal to the true parameter vector; on the other hand, the estimators of the index vector for the partially single-index model retain the dual convergence rates as in the single-index model but the estimators of the coefficients in the linear part of the model possess rate
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Creators: name: Hartemink, A. J.
name: Gerstein, M.
name: Park, P. J.
name: Kellis, M.
name: Pazin, M. J.
name: Fisher-Aylor, K. I.
name: Myers, R. M.
name: Chen, Y.
name: Pauli, F.
name: Gertz, J.
name: Epstein, C.
name: Li, Q.
name: Brown, J. B.
name: Cayting, P.
name: Iyer, V. R.
name: Kundaje, A.
name: Kharchenko, P. V.
name: Bickel, P.
name: Karmakar, S.
name: Euskirchen, G.
name: DeSalvo, G.
name: Ma, L.
name: Landt, S. G.
name: Milosavljevic, A.
name: Hoffman, M. M.
name: Liu, X. S.
name: Liu, T.
name: Batzoglou, S.
name: Bernstein, B. E.
name: Kheradpour, P.
name: Jung, Y. L.
name: Marinov, G. K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.
Feasibility Studies of Exclusive Diffractive Bremsstrahlung Measurement at RHIC Energies
Creators: name: Chwastowski, J.
name: Cyz, A.
name: Fulek, L.
name: Kycia, R.
name: Pawlik, B.
name: Sikora, R.
name: Turnau, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Feasibility studies of an observation of the exclusive diffractive bremsstrahlung at RHIC at $\sqrt{s} = 200$~GeV and at $\sqrt{s} = 500$~GeV are reported. A simplified approach to the photon and the scattered proton energy reconstruction is used. Influence of possible backgrounds is discussed.
description: 15 pages, 9 figures
Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets
Creators: name: Ancona, N.
name: Mukherjee, S.
name: Hauser, E. R.
name: Furey, T. S.
name: Xiong, Q.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Single variant or single gene analyses generally account for only a small proportion of the phenotypic variation in complex traits. Alternatively, gene set or pathway association analyses are playing an increasingly important role in uncovering genetic architectures of complex traits through the identification of systematic genetic interactions. Two dominant paradigms for gene set analyses are association analyses based on SNP genotypes and those based on gene expression profiles. However, gene–disease association can manifest in many ways, such as alterations of gene expression, genotype, and copy number; thus, an integrative approach combining multiple forms of evidence can more accurately and comprehensively capture pathway associations. We have developed a single statistical framework, Gene Set Association Analysis (GSAA), that simultaneously measures genome-wide patterns of genetic variation and gene expression variation to identify sets of genes enriched for differential expression and/or trait-associated genetic markers. Simulation studies illustrate that joint analyses of genomic data increase the power to detect real associations when compared with gene set methods that use only one genomic data type. The analysis of two human diseases, glioblastoma and Crohn's disease, detected abnormalities in previously identified disease-associated pathways, such as pathways related to PI3K signaling, DNA damage response, and the activation of NFKB. In addition, GSAA predicted novel pathway associations, for example, differential genetic and expression characteristics in genes from the ABC transporter family in glioblastoma and from the HLA system in Crohn's disease. These demonstrate that GSAA can help uncover biological pathways underlying human diseases and complex traits.
Specification Testing for Nonlinear Multivariate Cointegrating Regressions
Creators: name: Dong, Chaohua
name: Gao, Jiti
name: Tjostheim, Dag
name: Yin, Jiying
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: This paper considers a general model specification test for nonlinear multivariate cointegrating regressions where the regressor consists of a univariate integrated time series and a vector of stationary time series. The regressors and the errors are generated from the same innovations, so that the model accommodates endogeniety. A new and simple test is proposed and the resulting asymptotic theory is established. The test statistic is constructed based on a natural distance function between a nonparametric estimate and a smoothed parametric counterpart. The asymptotic distribution of the test statistic under the parametric specification is proportional to that of a local-time random variable with a known distribution. In addition, the finite sample performance of the proposed test is evaluated through using both simulated and real data examples.
Large exchange bias in polycrystalline MnN/CoFe bilayers at room temperature
Creators: name: Meinert, Markus
name: Büker, Björn
name: Graulich, Dominik
name: Dunz, Mareike
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report on the new polycrystalline exchange bias system MnN/CoFe, which shows exchange bias of up to 1800Oe at room temperature with a coercive field around 600Oe. The room temperature values of the interfacial exchange energy and the effective uniaxial anisotropy are estimated to be $J_\mathrm{eff} = 0.41\,\mathrm{mJ}/\mathrm{m}^2$ and $K_\mathrm{eff} = 37\,\mathrm{kJ}\,/\,\mathrm{m}^3$. The thermal stability was found to be tunable by controlling the nitrogen content of the MnN. The maximum blocking temperature exceeds $325^\circ$C, however the median blocking temperature in the limit of thick MnN is $160^\circ$C. Good oxidation stability through self-passivation was observed, enabling the use of MnN in lithographically defined microstructures. As a proof-of-principle we demonstrate a simple GMR stack exchange biased with MnN, which shows clear separation between parallel and antiparallel magnetic states. These properties come along with a surprisingly simple manufacturing process for the MnN films.
description: 7 pages, 6 figures
GCM selection Task Team in Med-CORDEX: summary of the work so far
Creators: name: Somot, Samuel
name: Fernandez, Jesus
name: Jordà, Gabriel
name: Soto-Navarro, Javier
name: Reale, Marco
name: Coppola, Erika
name: Mindlin, Julia
Publisher: name: Zenodo
Year: 2023
Subjects: Med-CORDEX GCM RCM selection scenario baseline

description: In the framework of the phase 3 of the so-called Med-CORDEX baseline runs, a Task Team in 2022 has been set to prepare the GCM selection for the scenario runs. Here is the current status of the Task Team work. This document will be updated with time
Oral beclomethasone dipropionate is an effective treatment for immune checkpoint inhibitor induced colitis.
Creators: name: Alexander, James L
name: Ibraheim, Hajir
name: Richards, Camellia
name: Shum, Ben
name: Pavlidis, Polychronis
name: Hunter, Nikki
name: Teare, Julian P
name: Wotherspoon, Andrew
name: Furness, Andrew
name: Turajlic, Samra
name: Pickering, Lisa
name: Larkin, James
name: Speight, Ally
name: Papa, Sophie
name: Powell, Nick
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: Tumour Biology
Signalling & Oncogenes
Genetics & Genomics
Genome Integrity & Repair
Computational & Systems Biology

description: INTRODUCTION: Systemic corticosteroids are the mainstay of treatment for immune checkpoint inhibitor induced (CPI) colitis but are associated with complications including life-threatening infection. The topically acting oral corticosteroid beclomethasone dipropionate (BD) is an effective treatment for mild to moderate flares of ulcerative colitis, and has fewer side effects than systemic corticosteroids. We hypothesized that BD would be an effective treatment for CPI-induced colitis. METHODS: We performed a retrospective analysis of all patients who started BD for CPI-induced colitis at three UK cancer centers between November 2017 and October 2020. All patients underwent endoscopic assessment and biopsy. The initial regimen of BD was 5 mg once daily for 28 days. Data were collected from electronic patient records. Clinical outcomes were assessed at 28 days after initiation of treatment. RESULTS: Twenty-two patients (14 male) with a median age of 64 (range 45-84) with CPI-induced colitis were treated with BD. At baseline, the median number of loose stools in a 24-hour period was six (common terminology criteria for adverse events, CTCAE grade diarrhea=2). Thirteen patients (59%) were dependent on systemic corticosteroids prior to starting BD. Baseline sigmoidoscopy showed moderate inflammation (Mayo Endoscopic Score (MES) = 2) in two patients (9%), mild inflammation (MES=1) in nine patients (41%) and normal findings (MES=0) in eleven patients (50%). Twenty patients (91%) had histopathological features of inflammation. All 22 patients (100%) had a clinical response to BD and 21 (95%) achieved clinical remission with a return to baseline stool frequency (CTCAE diarrhea=0). Ten patients (45%) had symptomatic relapse on cessation of BD, half within 7 days of stopping. All patients recaptured response on restarting BD. No adverse events were reported in patients treated with BD. CONCLUSIONS: Topical BD represents an appealing alternative option to systemic immunosuppressive treatments to treat colonic inflammation. In this study, BD was effective and safe at inducing remission in CPI-induced colitis, which was refractory to systemic corticosteroids. Further randomized studies are needed to confirm these findings and determine the optimum dosing regimen.
Long noncoding RNAs are rarely translated in two human cell lines
Creators: name: Brown, J. B.
name: Giddings, M. C.
name: Chen, X.
name: Gundling, W. E.
name: Risk, B.
name: Khatun, J.
name: Bickel, P.
name: Gunawardena, H. P.
name: Lipovich, L.
name: Xie, L.
name: Strahl, B. D.
name: Banfai, B.
name: Yu, Y.
name: Jia, H.
name: Wood, E.
name: Kundaje, A.
name: Krajewski, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ∼100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA− fractions in the cell lines K562 and GM12878. We used the machine-learning algorithm RuleFit3 to regress the peptide data against RNA expression data. The most important covariate for predicting translation was, surprisingly, the Cytosol polyA− fraction in both cell lines. LncRNAs are ∼13-fold less likely to produce detectable peptides than similar mRNAs, indicating that ∼92% of GENCODE v7 lncRNAs are not translated in these two ENCODE cell lines. Intersecting 9640 lncRNA loci with 79,333 peptides yielded 85 unique peptides matching 69 lncRNAs. Most cases were due to a coding transcript misannotated as lncRNA. Two exceptions were an unprocessed pseudogene and a bona fide lncRNA gene, both with open reading frames (ORFs) compromised by upstream stop codons. All potentially translatable lncRNA ORFs had only a single peptide match, indicating low protein abundance and/or false-positive peptide matches. We conclude that with very few exceptions, ribosomes are able to distinguish coding from noncoding transcripts and, hence, that ectopic translation and cryptic mRNAs are rare in the human lncRNAome.
On contact numbers of totally separable unit sphere packings
Creators: name: Bezdek, Karoly
name: Szalkai, Balazs
name: Szalkai, Istvan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: 52C17, 05B40, 11H31, 52C45

description: Contact numbers are natural extensions of kissing numbers. In this paper we give estimates for the number of contacts in a totally separable packing of n unit balls in Euclidean d-space for all n>1 and d>1.
description: 11 pages
Semiparametric Single-Index Panel Data Models with Cross-Sectional Dependence
Creators: name: Peng, Bin
name: Dong, Chaohua
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 semiparametric single index panel data mode with cross-sectional dependence, high-dimensionality and stationarity. Meanwhile, we allow fixed effects to be correlated with the regressors to capture unobservable heterogeneity. Under a general spatial error dependence structure, we then establish some consistent closed-form estimates for both the unknown parameters and a link function for the case where both N and T go to ∞. Rates of convergence and asymptotic normality consistencies are established for the proposed estimates. Our experience suggests that the proposed estimation method is simple and thus attractive for finite-sample studies and empirical implementations. Moreover, both the finite-sample performance and the empirical applications show that the proposed estimation method works well when the cross-sectional dependence exists in the data set.
Structure Preserving Parallel Algorithms for Solving the Bethe-Salpeter Eigenvalue Problem
Creators: name: Shao, Meiyue
name: da Jornada, Felipe H.
name: Yang, Chao
name: Deslippe, Jack
name: Louie, Steven G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: The Bethe-Salpeter eigenvalue problem is a dense structured eigenvalue problem arising from discretized Bethe-Salpeter equation in the context of computing exciton energies and states. A computational challenge is that at least half of the eigenvalues and the associated eigenvectors are desired in practice. We establish the equivalence between Bethe-Salpeter eigenvalue problems and real Hamiltonian eigenvalue problems. Based on theoretical analysis, structure preserving algorithms for a class of Bethe-Salpeter eigenvalue problems are proposed. We also show that for this class of problems all eigenvalues obtained from the Tamm-Dancoff approximation are overestimated. In order to solve large scale problems of practical interest, we discuss parallel implementations of our algorithms targeting distributed memory systems. Several numerical examples are presented to demonstrate the efficiency and accuracy of our algorithms.
A Case Study of India’s Janmabhoomi as Voluntary Adoption of Saemaul Undong
Creators: name: Choi, Jungug
name: Choi, Jungug
Publisher: name: Unknown
Year: 2015
Subjects: subject: Community/Rural/Urban Development
subject: Saemaul Undong
subject: Janmabhoomi
subject: rural development program

description: For most developing countries, the most pressing development issue lies in the agricultural sector. This is why more attention should be paid to Saemaul Undong, one of the most successful models of rural development. Despite the recently increased interest in the globalization of Saemaul Undong, Janmabhoomi has barely been known. It is most likely the first ever self-motivated initiative by a foreign government to adopt Saemaul Undong without any financial or logistical assistance from the Korean government. This article is designed to introduce Janmabhoomi to Koreans, compare it with Saemaul Undong in terms of its key features, and provide some policy implications for the globalization of Saemaul Undong.
Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription
Creators: name: Iglesia, M. D.
name: Simon, J. M.
name: Wu, S. B.
name: Patel, M.
name: Davis, I. J.
name: McFadden, A. W.
name: Lieb, J. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Chromosomal translocations involving transcription factor genes have been identified in an increasingly wide range of cancers. Some translocations can create a protein “chimera” that is composed of parts from different proteins. How such chimeras cause cancer, and why they cause cancer in some cell types but not others, is not understood. One such chimera is EWS–FLI, the most frequently occurring translocation in Ewing Sarcoma, a malignant bone and soft tissue tumor of children and young adults. Using EWS–FLI and its parental transcription factor, FLI1, we created a unique experimental system to address questions regarding the genomic mechanisms by which chimeric transcription factors cause cancer. We found that in tumor cells, EWS–FLI targets regions of the genome distinct from FLI1, despite identical DNA-binding domains. In primary endothelial cells, however, EWS–FLI and FLI1 demonstrate similar targeting. To understand this mistargeting, we examined chromatin organization. Regions targeted by EWS–FLI are normally repressed and nucleosomal in primary endothelial cells. In tumor cells, however, bound regions are nucleosome depleted and harbor the chromatin signature of enhancers. We next demonstrated that through chimerism, EWS–FLI acquired the ability to alter chromatin. Expression of EWS–FLI results in nucleosome depletion at targeted sites, whereas silencing of EWS–FLI in tumor cells restored nucleosome occupancy. Thus, the EWS–FLI chimera acquired chromatin-altering activity, leading to mistargeting, chromatin disruption, and ultimately, transcriptional dysregulation.
Data Product Specification for Biodiversity indicator Tier 1 (computed at km grid cell level).
Creators: name: Laurent, Dominique
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity, Agro-environmental monitoring, environment, agruclutre

description: The NIVA UC1b pilot has developed a set of tools to compute agro-environmental indicators about carbon storage, nitrate leaching and biodiversity. This data product specification aims to document the characteristics of data about biodiversity indicator Tier 1 . It is organised following the principles of ISO 19131 (Data Specification Product for geographic information). This indicator is based on a scientific method elaborated by a previous European project (Farmland) and is based on data widely available in EU: agricultural parcels coming from national or regional IACS (CAP payment information system including the GSAA: Geo-Spatial Aid Application) and topographic data. The computation open-source tool was developed by INRAE, one of the French partners of the NIVA project and tested in several areas in Europe by other NIVA partners. The computation tool and its documentation is available on https://gitlab.com/nivaeu/uc1b_tier1_co2
 The NIVA project decided to publish the geographic data resulting from these tests, in order to make it available to any potential user. The data is coming from an innovation project and shall be considered as research data.
Bias Reduction of Long Memory Parameter Estimators via the Pre-filtered Sieve Bootstrap
Creators: name: Poskitt, D.S.
name: Martin, Gael M.
name: Grose, Simone D.
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: This paper investigates the use of bootstrap-based bias correction of semi-parametric estimators of the long memory parameter in fractionally integrated processes. The re-sampling method involves the application of the sieve boot-strap to data pre-filtered by a preliminary semi-parametric estimate of the long memory parameter. Theoretical justification for using the bootstrap techniques to bias adjust log-periodogram and semi-parametric local Whittle estimators of the memory parameter is provided. Simulation evidence comparing the performance of the bootstrap bias correction with analytical bias correction techniques is also presented. The bootstrap method is shown to produce notable bias reductions, in particular when applied to an estimator for which analytical adjustments have already been used. The empirical coverage of confidence intervals based on the bias-adjusted estimators is very close to the nominal, for a reasonably large sample size, more so than for the comparable analytically adjusted estimators. The precision of inferences (as measured by interval length) is also greater when the bootstrap is used to bias correct rather than analytical adjustments.
Continuous Hamiltonian dynamics and area-preserving homeomorphism group of $D^2$
Creators: name: Oh, Yong-Geun
Publisher: name: arXiv
Year: 2015
Subjects: subject: Symplectic Geometry (math.SG)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 53D05, 53D35, 53D40, 28D10

description: The main purpose of this paper is to propose a scheme of a proof of the nonsimpleness of the group $Homeo^Ω(D^2,\partial D^2)$ of area preserving homeomorphisms of the 2-disc $D^2$. We first establish the existence of Alexander isotopy in the category of Hamiltonian homeomorphisms. This reduces the question of extendability of the well-known Calabi homomorphism ${\rm Cal}:Diff^Ω(D^1,\partial D^2) \to \mathbb R$ to a homomorphism $\overline{\rm Cal}:Hameo(D^2,\partial D^2) \to \mathbb R$ to that of the vanishing of the basic phase function $f_{\underline{\mathbb F}}$, a Floer theoretic graph selector previously constructed by the author, that is associated to the graph of the topological Hamiltonian loop and its normalized Hamiltonian $\underline{F}$ on $S^2$ that is obtained via the natural embedding $D^2 \hookrightarrow S^2$. Here $Hameo(D^2,\partial D^2)$ is the group of Hamiltonian homeomorphisms introduced by Müller and the author. We then provide an evidence of this vanishing conjecture by proving the conjecture for the special class of \emph{weakly graphical} topological Hamiltonian loops on $D^2$ via a study of the associated Hamilton-Jacobi equation.
description: 32 pages, Comments welcome; v2) 35 pages, an error in the proof of Theorem 1.8 corrected, a new section 9 added, many typos corrected and overall presentation improved
Fragmentation functions of polarized heavy quarkonium
Creators: name: Ma, Yan-Qing
name: Qiu, Jian-Wei
name: Zhang, Hong
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Study of the polarized heavy quarkonium production in recently proposed QCD factorization formalism requires knowledge of a large number of input fragmentation functions (FFs) from a single parton or a heavy quark-antiquark pair to a polarized heavy quarkonium. In this paper, we calculate these FFs at the input scale in terms of nonrelativistic QCD (NRQCD) factorization. We derive all relevant polarized NRQCD long-distance matrix elements based symmetries and propose a self-consistent scheme to define them in arbitrary $d$ dimensions. We then calculate polarized input FFs contributed from all $S$-wave and $P$-wave NRQCD intermediate states. With our calculation of the polarized input FFs, and the partonic hard part available in literatures, the QCD factorization formalism is ready to be applied to polarized heavy quarkonium production.
description: 30 pages, 1 figure
DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
Creators: name: Crawford, G. E.
name: Mukherjee, S.
name: Winter, D. R.
name: Furey, T. S.
name: Song, L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ∼40 yr ago it was demonstrated that DNase I also digests with a ∼10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation.
Bagging Exponential Smoothing Methods using STL Decomposition and Box-Cox Transformation
Creators: name: Bergmeir, Christoph
name: Hyndman, Rob J
name: Benitez, Jose M
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: Exponential smoothing is one of the most popular forecasting methods. We present a method for bootstrap aggregation (bagging) of exponential smoothing methods. The bagging uses a Box-Cox transformation followed by an STL decomposition to separate the time series into trend, seasonal part, and remainder. The remainder is then bootstrapped using a moving block bootstrap, and a new series is assembled using this bootstrapped remainder. On the bootstrapped series, an ensemble of exponential smoothing models is estimated. The resulting point forecasts are averaged using the mean. We evaluate this new method on the M3 data set, showing that it consistently outperforms the original exponential smoothing models. On the monthly data, we achieve better results than any of the original M3 participants. We also perform statistical testing to explore significance of the results. Using the MASE, our method is significantly better than all the M3 participants on the monthly data.
A solution to the non-linear equations of D=10 super Yang-Mills theory
Creators: name: Mafra, Carlos R.
name: Schlotterer, Oliver
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this letter, we present a formal solution to the non-linear field equations of ten-dimensional super Yang--Mills theory. It is assembled from products of linearized superfields which have been introduced as multiparticle superfields in the context of superstring perturbation theory. Their explicit form follows recursively from the conformal field theory description of the gluon multiplet in the pure spinor superstring. Furthermore, superfields of higher mass dimensions are defined and their equations of motion spelled out.
description: 6 pages, v2: published version
Genotype calling and haplotyping in parent-offspring trios
Creators: name: Chen, W.
name: Sidore, C.
name: Li, Y.
name: Sanna, S.
name: Busonero, F.
name: Zeng, Z.
name: Li, B.
name: Kang, H. M.
name: Abecasis, G. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Emerging sequencing technologies allow common and rare variants to be systematically assayed across the human genome in many individuals. In order to improve variant detection and genotype calling, raw sequence data are typically examined across many individuals. Here, we describe a method for genotype calling in settings where sequence data are available for unrelated individuals and parent-offspring trios and show that modeling trio information can greatly increase the accuracy of inferred genotypes and haplotypes, especially on low to modest depth sequencing data. Our method considers both linkage disequilibrium (LD) patterns and the constraints imposed by family structure when assigning individual genotypes and haplotypes. Using simulations, we show that trios provide higher genotype calling accuracy across the frequency spectrum, both overall and at hard-to-call heterozygous sites. In addition, trios provide greatly improved phasing accuracy—improving the accuracy of downstream analyses (such as genotype imputation) that rely on phased haplotypes. To further evaluate our approach, we analyzed data on the first 508 individuals sequenced by the SardiNIA sequencing project. Our results show that our method reduces the genotyping error rate by 50% compared with analysis using existing methods that ignore family structure. We anticipate our method will facilitate genotype calling and haplotype inference for many ongoing sequencing projects.
Efficient Identification of the Pareto Optimal Set
Creators: name: Steponavice, Ingrida
name: Hyndman, Rob J
name: Smith-Miles, Kate
name: Villanova, Laura
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: In this paper, we focus on expensive multiobjective optimization problems and propose a method to predict an approximation of the Pareto optimal set using classification of sampled decision vectors as dominated or nondominated. The performance of our method, called EPIC, is demonstrated on a set of benchmark problems used in the multiobjective optimization literature and compared with state-of the-art methods, ParEGO and PAL. The initial results are promising and encourage further research in this direction.
iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data
Creators: name: Smith, E. J. M.
name: Savich, G. L.
name: Brudno, M.
name: Fiume, M.
name: Goldenberg, A.
name: Chiang, D. Y.
name: Buske, O.
name: Aparicio, S.
name: Shah, S.
name: Mezlini, A. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: High-throughput RNA sequencing (RNA-seq) promises to revolutionize our understanding of genes and their role in human disease by characterizing the RNA content of tissues and cells. The realization of this promise, however, is conditional on the development of effective computational methods for the identification and quantification of transcripts from incomplete and noisy data. In this article, we introduce iReckon, a method for simultaneous determination of the isoforms and estimation of their abundances. Our probabilistic approach incorporates multiple biological and technical phenomena, including novel isoforms, intron retention, unspliced pre-mRNA, PCR amplification biases, and multimapped reads. iReckon utilizes regularized expectation-maximization to accurately estimate the abundances of known and novel isoforms. Our results on simulated and real data demonstrate a superior ability to discover novel isoforms with a significantly reduced number of false-positive predictions, and our abundance accuracy prediction outmatches that of other state-of-the-art tools. Furthermore, we have applied iReckon to two cancer transcriptome data sets, a triple-negative breast cancer patient sample and the MCF7 breast cancer cell line, and show that iReckon is able to reconstruct the complex splicing changes that were not previously identified. QT-PCR validations of the isoforms detected in the MCF7 cell line confirmed all of iReckon's predictions and also showed strong agreement (r2 = 0.94) with the predicted abundances.
Designed-walk replica-exchange method for simulations of complex systems
Creators: name: Urano, Ryo
name: Okamoto, Yuko
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfies the detailed balance condition in the proposed route. The method forces tunneling events between the highest and lowest temperatures to happen with an almost constant period. The number of tunneling counts is proportional to that of the random-walk REM multiplied by the square root of moving distance in temperature space. We applied this new implementation to two kinds of REM and compared the results with those of the conventional random-walk REM. The test system was a two-dimensional Ising model, and our new method reproduced the results of the conventional random-walk REM and improved the tunneling counts by three times or more than that of the random-walk REM.
description: 6 pages, 3 figures, 1 table; methods are the same before, but results and some references are added, table is updated
Effects of Tariff Reduction on Welfare in Korean Orange Market
Creators: name: Choi, Yongho
name: Choi, Yongho
Publisher: name: Unknown
Year: 2016
Subjects: subject: International Relations/Trade
subject: tariff reduction
subject: equilibrium displacement model
subject: market power

description: This paper analyzes how tariff reductions on fresh oranges by the KOR-US FTA have changed each economic player's welfare. By reviews on the characteristics of Korea's orange market, we first detect that a small number of US exporters have relatively much stronger market power than Korean importers, implying imperfect competition. Second, we theoretically explain and empirically examine that exporters may adjust exporting prices based on the size of tariff reduction. Finally, we employ the Equilibrium Displacement Models to estimate each economic player's welfare and discuss the implications on the changes in the welfare under imperfect competition, compared to perfect competition. This paper provides the evidence that the tariff reduction affects the price decision of the U.S. orange exporters. The main results furthermore suggest that under imperfect competition, import price in Korean market is higher and consumer welfare is lower than under perfect competition.
A European Desert? The Territorial Economics and Politics of Emigration in Crisis Regions
Creators: name: Crevoisier, Olivier
name: Arrighi, Jean-Thomas
name: Mueller, Sean
Publisher: name: Zenodo
Year: 2022
Subjects: Migration
Research

description: A European Desert? The Territorial Economics and Politics of Emigration in Crisis Regions is a project of the National Center of Competence "nccr – on the move "
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
Creators: name: Furey, T. S.
name: Thurman, R. E.
name: Crawford, G. E.
name: Song, L.
name: Lenhard, B.
name: Sheffield, N. C.
name: Stamatoyannopoulos, J. A.
name: Safi, A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Regulatory elements recruit transcription factors that modulate gene expression distinctly across cell types, but the relationships among these remains elusive. To address this, we analyzed matched DNase-seq and gene expression data for 112 human samples representing 72 cell types. We first defined more than 1800 clusters of DNase I hypersensitive sites (DHSs) with similar tissue specificity of DNase-seq signal patterns. We then used these to uncover distinct associations between DHSs and promoters, CpG islands, conserved elements, and transcription factor motif enrichment. Motif analysis within clusters identified known and novel motifs in cell-type-specific and ubiquitous regulatory elements and supports a role for AP-1 regulating open chromatin. We developed a classifier that accurately predicts cell-type lineage based on only 43 DHSs and evaluated the tissue of origin for cancer cell types. A similar classifier identified three sex-specific loci on the X chromosome, including the XIST lincRNA locus. By correlating DNase I signal and gene expression, we predicted regulated genes for more than 500K DHSs. Finally, we introduce a web resource to enable researchers to use these results to explore these regulatory patterns and better understand how expression is modulated within and across human cell types.
Bound states of a ferromagnetic wire in a superconductor
Creators: name: Sau, Jay D.
name: Brydon, P. M. R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We consider the problem of bound states in strongly anisotropic ferromagnetic impurities in a superconductor, motivated by recent experiments that claim to observe Majorana modes at the ends of ferromagnetic wires on a superconducting substrate [S. Nadj-Perge et al., Science 346, 602 (2014)]. Generalizing the successful theory of bound states of spherically symmetric impurities, we consider a wire-like potential using both analytical and numerical approaches. We find that away from the ends of the wire the bound states form bands with pronounced van Hove singularities, giving rise to subgap peaks in the local density of states. For sufficiently strong magnetization of the wire, we show that this process generically produces a sharp peak at zero energy in the local density of states near the ends of the wire. This zero-energy peak has qualitative similarities to the claimed signature of a Majorana mode observed in the aforementioned experiment.
Boosting multi-step autoregressive forecasts
Creators: name: Taieb, Souhaib Ben
name: Hyndman, Rob J
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: Multi-step forecasts can be produced recursively by iterating a one-step model, or directly using a specific model for each horizon. Choosing between these two strategies is not an easy task since it involves a trade-off between bias and estimation variance over the forecast horizon. Using a nonlinear machine learning model makes the tradeoff even more difficult. To address this issue, we propose a new forecasting strategy which boosts traditional recursive linear forecasts with a direct strategy using a boosting autoregression procedure at each horizon. First, we investigate the performance of the proposed strategy in terms of bias and variance decomposition of the error using simulated time series. Then, we evaluate the proposed strategy on real-world time series from two forecasting competitions. Overall, we obtain excellent performance with respect to the standard forecasting strategies.
Macroscopic non-contextuality as a principle for Almost Quantum Correlations
Creators: name: Henson, Joe
name: Sainz, Ana Belén
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum mechanics allows only certain sets of experimental results (or "probabilistic models") for Bell-type quantum non-locality experiments. A derivation of this set from simple physical or information theoretic principles would represent an important step forward in our understanding of quantum mechanics, and this problem has been intensely investigated in recent years. "Macroscopic locality," which requires the recovery of locality in the limit of large numbers of trials, is one of several principles discussed in the literature that place a bound on the set of quantum probabilistic models. A similar question can also be asked about probabilistic models for the more general class of quantum contextuality experiments. Here, we extend the Macroscopic Locality principle to this more general setting, using the hypergraph approach of Acín, Fritz, Leverrier and Sainz [Comm. Math. Phys. 334(2), 533-628 (2015)], which provides a framework to study both phenomena of nonlocality and contextuality in a unified manner. We find that the set of probabilistic models allowed by our Macroscopic Non-Contextuality principle is equivalent to an important and previously studied set in this formalism, which is slightly larger than the quantum set. In the particular case of Bell Scenarios, this set is equivalent to the set of "Almost Quantum" models, which is of particular interest since the latter was recently shown to satisfy all but one of the principles that have been proposed to bound quantum probabilistic models, without being implied by any of them (or even their conjunction). Our condition is the first characterisation of the almost quantum set from a simple physical principle.
description: 21 pages (main text 12 pages); v2 minor typos corrected, extended presentation and discussion, published version
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures
Creators: name: Egelhofer, T. A.
name: Jeffers, T. E.
name: Down, T. A.
name: Chen, Q. B.
name: Stempor, P.
name: Ahringer, J.
name: Chen, R. A.- J.
name: Hillier, L. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. The initial 5′ end of most protein-coding transcripts is removed by trans-splicing, and noncoding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is frequent, with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. Our results provide a new resource to investigate transcription regulation in metazoans.