Heavy Quark Production in the ACOT Scheme Beyond NLO

We analyze the properties of the ACOT scheme for heavy quark production and make use of the MS-Bar massless results at NNLO and N3LO for the structure functions F2 and FL in neutral current deep-inelastic scattering to estimate the higher order corrections. The dominant heavy quark mass effects at higher orders can be taken into account using the massless Wilson coefficients together with an appropriate slow-rescaling prescription implementing the phase space constraints. Combining the exact ACOT scheme at NLO with these expressions should provide a good approximation to the full calculation in the ACOT scheme at NNLO and N3LO.Comment: 4 pages, 2 figures. Presented at DIS12, March 2012, Bonn, German

A Hybrid Scheme for Heavy Flavors: Merging the FFNS and VFNS

We introduce a Hybrid Variable Flavor Number Scheme for heavy flavors, denoted H-VFNS, which incorporates the advantages of both the traditional Variable Flavor Number Scheme (VFNS) as well as the Fixed Flavor Number Scheme (FFNS). By including an explicit $N_F$-dependence in both the Parton Distribution Functions (PDFs) and the strong coupling constant $\alpha_S$, we generate coexisting sets of PDFs and $\alpha_S$ for $N_F=\{3,4,5,6\}$ at any scale $\mu$, that are related analytically by the $\overline{\text{MS}}$ matching conditions. The H-VFNS resums the heavy quark contributions and provides the freedom to choose the optimal $N_F$ for each particular data set. Thus, we can fit selected HERA data in a FFNS framework, while retaining the benefits of the VFNS to analyze LHC data at high scales. We illustrate how such a fit can be implemented for the case of both HERA and LHC data.Comment: 15 pages, 11 figures, updated to match journa

CTEQ nuclear parton distribution functions

We show for the first time preliminary results of nuclear parton distribution function analysis of charged lepton DIS and Drell-Yan data within the CTEQ framework including error PDFs. We compare our error estimates to estimates of different nPDF groups.Comment: 5 pages, to appear in the proceedings of XXI International Workshop on Deep-Inelastic Scattering and Related Subjects, Marseilles, Franc

Update on nCTEQ PDFs: nuclear PDF uncertainties and LHC applications

We present updated nCTEQ nuclear parton distribution functions with errors including pion production data from RHIC. We compare them with the results of other groups and present selected LHC applications.Comment: Presented at DIS2014, 28 April - 2 May 2014, Warsaw, Poland. PoS(DIS2014)04

nCTEQ15 - Global analysis of nuclear parton distributions with uncertainties in the CTEQ framework

We present the new nCTEQ15 set of nuclear parton distribution functions with uncertainties. This fit extends the CTEQ proton PDFs to include the nuclear dependence using data on nuclei all the way up to 208^Pb. The uncertainties are determined using the Hessian method with an optimal rescaling of the eigenvectors to accurately represent the uncertainties for the chosen tolerance criteria. In addition to the Deep Inelastic Scattering (DIS) and Drell-Yan (DY) processes, we also include inclusive pion production data from RHIC to help constrain the nuclear gluon PDF. Furthermore, we investigate the correlation of the data sets with specific nPDF flavor components, and asses the impact of individual experiments. We also provide comparisons of the nCTEQ15 set with recent fits from other groups.Comment: 35 page

Strange Quark PDFs and Implications for Drell-Yan Boson Production at the LHC

Global analyses of Parton Distribution Functions (PDFs) have provided incisive constraints on the up and down quark components of the proton, but constraining the other flavor degrees of freedom is more challenging. Higher-order theory predictions and new data sets have contributed to recent improvements. Despite these efforts, the strange quark PDF has a sizable uncertainty, particularly in the small x region. We examine the constraints from experiment and theory, and investigate the impact of this uncertainty on LHC observables. In particular, we study W/Z production to see how the s-quark uncertainty propagates to these observables, and examine the extent to which precise measurements at the LHC can provide additional information on the proton flavor structure.Comment: 14 pages, 11 figures, added reference

Odnos strukture i aktivnosti u reaktivaciji tabunom fosforilirane ljudske acetilkolinesteraze bispiridinijevim para-aldoksimima

We investigated interactions of bispyridinium para-aldoximes N,N’-(propano)bis(4-hydroxyiminomethyl) pyridinium bromide (TMB-4), N,N’-(ethano)bis(4-hydroxyiminomethyl)pyridinium methanosulphonate (DMB-4), and N,N’-(methano)bis(4-hydroxyiminomethyl)pyridinium chloride (MMB-4) with human erythrocyte acetylcholinesterase phosphorylated by tabun. We analysed aldoxime conformations to determine the flexibility of aldoxime as an important feature for binding to the acetylcholinesterase active site. Tabun-inhibited human erythrocyte acetylcholinesterase was completely reactivated only by the most flexible bispyridinium aldoxime - TMB-4 with a propylene chain between two rings. Shorter linkers than propylene (methylene or ethylene) as in MMB-4 and DMB-4 did not allow appropriate orientation in the active site, and MMB-4 and DMB-4 were not efficient reactivators of tabun-phosphorylated acetylcholinesterase. Since aldoximes are also reversible inhibitors of native acetylcholinesterase, we determined dissociation constants and their protective index against acetylcholinesterase inactivation by tabun.Proučavali smo interakcije bispiridinijevih para-oksima N,N’-(propano)bis(4-hidroksiiminometil)piridinijeva bromida (TMB-4), N,N’-(etanano)bis(4-hidroksiiminometil)piridinijeva metanosulfonata (DMB-4) i N,N’- (metano)bis(4-hidroksiiminometil)piridinijeva klorida (MMB-4) s ljudskom eritrocitnom acetilkolinesterazom fosforiliranom tabunom. Da bismo odredili fleksibilnosti aldoksima, što je važna osobina kod njihova vezanja u aktivno mjesto acetilkolinesteraze, analizirali smo i konformacijske odlike aldoksima. Ljudska acetilkolinesteraza inhibirana tabunom bila je potpuno reaktivirana samo najfleksibilnijim bispiridinijevim aldoksimom – TMB-4. Aldoksimi MMB-4 i DMB-4 nisu bili efikasni reaktivatori acetilkolinesteraze fosforilirane tabunom jer je kod tih spojeva lanac koji povezuje dva prstena kraći od propilena (metilen u MMB-4 i etilen u DMB-4), što ne dopušta povoljnu orijentaciju tih aldoksima unutar aktivnog mjesta enzima. S obzirom na to da su aldoksimi i reverzibilni inhibitori nativne acetilkolinesteraze, odredili smo njihove disocijacijske konstante, kao i zaštitu acetilkolinesteraze od inhibiranja tabunom reverzibilnim vezanjem aldoksima

Mega-sized pericentromeric blocks of simple telomeric repeats and their variants reveal patterns of chromosome evolution in ancient Cycadales genomes

Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads.This project was supported by the Czech Academy of Science, Czech Science Foundation (22-16826S), Czech National Infrastructure for Biological data (ELIXIR CZ, LM2018131), NERC and China Scholarship Council (CSC). JP benefited from a Ramón y Cajal grant Ref: RYC-2017-2274 funded by MCIN/AEI/INTRODUCTION RESULTS Identification and quantification of telomeric repeats in high-throughput reads In silico identification of telomeric repeat variants Southern blot hybridization analysis of telomeric variants Identification of cycad centromeres by immunostaining of chromatin FISH analysis of telomeric variants Evolution of chromosome numbers and genome sizes across cycads DISCUSSION Variable abundance of telomeric repeats in plant genomes Origin of telomeric repeat variants in cycad genomes Epigenetic modification of telomeric repeats Chromosome evolution in cycads CONCLUSION EXPERIMENTAL PROCEDURES Plant material DNA isolation and Illumina sequencing Estimation of telomeric repeats abundance and diversity from high-throughput sequencing data Ancestral chromosome and genome size reconstruction Southern blot hybridization and DNA methylation analysis DNA probe preparation for FISH and southern blotting FISH Immunohistochemical staining of chromosomes ACKNOWLEDGEMENTS Author CONTRIBUTION

AREsite: a database for the comprehensive investigation of AU-rich elements

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3′-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential role of the structural mRNA context in which these sequence motifs are embedded. AREsite is the first database that allows to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. Moreover, we also provide a detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite