Light colored scalars from grand unification and the forward-backward asymmetry in top quark pair production

The experimental results on the t bar t production cross section at the Tevatron are well described by the QCD contributions within the standard model, while the recent measurement of the forward-backward asymmetry cannot be accounted for within this framework. We consider light colored scalars appearing in a particular SU(5) GUT model within the 45-dimensional Higgs representation. A virtue of the model is that it connects the presence of a light colored SU(2) singlet (Delta_6) and a color octet weak doublet (Delta_1) with bounds on the proton lifetime, which constrain the parameter space of both scalars. We find that both the t bar t production cross section and the forward-backward asymmetry can be accommodated simultaneously within this model. The experimental results prefer a region for the mass of Delta_6 around 400 GeV, while Delta_1 is then constrained to have a mass around the TeV scale as well. We analyze possible experimental signatures and find that Delta_6 associated top production could be probed in the t bar t + jets final states at Tevatron and the LHC.Comment: 12 pages, 13 figures, version as publishe

Charm meson resonances in D→PℓνD \to P \ell \nu decays

Motivated by recent experimental results we reconsider semileptonic $D \to P \ell \nu_{\ell}$ decays within a model which combines heavy quark symmetry and properties of the chiral Lagrangian. We include excited charm meson states, some of them recently observed, in our Lagrangian and determine their impact on the charm meson semileptonic form factors. We find that the inclusion of excited charm meson states in the model leads to a rather good agreement with the experimental results on the $q^2$ shape of the $F_+(q^2)$ form factor. We also calculate branching ratios for all $D \to P \ell \nu_{\ell}$ decays.Comment: 9 pages, 4 figures; minor corrections, added some discussion, version as publishe

Light Colored Scalar as Messenger of Up-Quark Flavor Dynamics in Grand Unified Theories

The measured forward-backward asymmetry in the t tbar production at the Tevatron might be explained by the additional exchange of a colored weak singlet scalar. Such state appears in some of the grand unified theories and its interactions with the up-quarks are purely antisymmetric in flavor space. We systematically investigate the resulting impact on charm and top quark physics. The constraints on the relevant Yukawa couplings come from the experimentally measured observables related to D0--D0bar oscillations, as well as di-jet and single top production measurements at the Tevatron. After fully constraining the relevant Yukawa couplings, we predict possible signatures of this model in rare top quark decays. In a class of grand unified models we demonstrate how the obtained information enables to constrain the Yukawa couplings of the up-quarks at very high energy scale.Comment: 13 pages, 11 figures, version as published in PR

clipplotr - a comparative visualisation and analysis tool for CLIP data

CLIP technologies are now widely used to study RNA-protein interactions and many datasets are now publicly available. An important first step in CLIP data exploration is the visual inspection and assessment of processed genomic data on selected genes or regions and performing comparisons: either across conditions within a particular project, or incorporating publicly available data. However, the output files produced by data processing pipelines or preprocessed files available to download from data repositories are often not suitable for direct comparison and usually need further processing. Furthermore, to derive biological insight it is usually necessary to visualise CLIP signal alongside other data such as annotations, or orthogonal functional genomic data (e.g. RNA-seq). We have developed a simple, but powerful, command-line tool: clipplotr, which facilitates these visual comparative and integrative analyses with normalisation and smoothing options for CLIP data and the ability to show these alongside reference annotation tracks and functional genomic data. These data can be supplied as input to clipplotr in a range of file formats, which will output a publication quality figure. It is written in R and can both run on a laptop computer independently, or be integrated into computational workflows on a high-performance cluster. Releases, source code and documentation are freely available at: https://github.com/ulelab/clipplotr

Bump Hunting in Latent Space

Unsupervised anomaly detection could be crucial in future analyses searching for rare phenomena in large datasets, as for example collected at the LHC. To this end, we introduce a physics inspired variational autoencoder (VAE) architecture which performs competitively and robustly on the LHC Olympics Machine Learning Challenge datasets. We demonstrate how embedding some physical observables directly into the VAE latent space, while at the same time keeping the classifier manifestly agnostic to them, can help to identify and characterise features in measured spectra as caused by the presence of anomalies in a dataset.Comment: 5 pages, 4 figure

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ∼10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between transcripts with STAU1-bound 3' UTR duplexes and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3' UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions

RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis

Valosin-containing protein (VCP) is a hexameric ATPase associated with diverse cellular activities. Genetic mutations in VCP are associated with several forms of muscular and neuronal degeneration, including amyotrophic lateral sclerosis (ALS). Moreover, VCP mediates UV-induced proteolysis of RNA polymerase II (RNAPII), but little is known about the effects of VCP mutations on the transcriptional machinery. Here, we used silica particle-assisted chromatin enrichment and mass spectrometry to study proteins co-localized with RNAPII in precursor neurons differentiated from VCP-mutant or control induced pluripotent stem cells. Remarkably, we observed diminished RNAPII binding of proteins involved in transcription elongation and mRNA splicing in mutant cells. One of these is SART3, a recycling factor of the splicing machinery, whose knockdown leads to perturbed intron retention in several ALS-associated genes. Additional reduced proteins are RBM45, EIF5A and RNF220, mutations in which are associated with various neurodegenerative disorders and are linked to TDP-43 aggregation. Conversely, we observed increased RNAPII binding of heat shock proteins such as HSPB1. Together, these findings shed light on how transcription and splicing machinery are impaired by VCP mutations, which might contribute to aberrant alternative splicing and proteinopathy in neurodegeneration.journal articl