Operation and performance of the ATLAS Tile Calorimeter in Run 1

The Tile Calorimeter is the hadron calorimeter covering the central region of the ATLAS experiment at the Large Hadron Collider. Approximately 10,000 photomultipliers collect light from scintillating tiles acting as the active material sandwiched between slabs of steel absorber. This paper gives an overview of the calorimeter’s performance during the years 2008–2012 using cosmic-ray muon events and proton–proton collision data at centre-of-mass energies of 7 and 8TeV with a total integrated luminosity of nearly 30 fb−1. The signal reconstruction methods, calibration systems as well as the detector operation status are presented. The energy and time calibration methods performed excellently, resulting in good stability of the calorimeter response under varying conditions during the LHC Run 1. Finally, the Tile Calorimeter response to isolated muons and hadrons as well as to jets from proton–proton collisions is presented. The results demonstrate excellent performance in accord with specifications mentioned in the Technical Design Report

Structural, Magnetic, and Electronic Properties of CaBaCo_4–<i>x</i>M_<i>x</i>O₇ (M = Fe, Zn)

The effect of substituting iron and zinc for cobalt in CaBaCo₄O₇ was investigated using neutron diffraction and X-ray absorption spectroscopy techniques. The orthorhombic distortion present in the parent compound CaBaCo₄O₇ decreases with increasing the content of either Fe or Zn. The samples CaBaCo₃ZnO₇ and CaBaCo_4–<i>x</i>Fe_<i>x</i>O₇ with <i>x</i> ≥ 1.5 are metrically hexagonal, but much better refinements in the neutron diffraction patterns are obtained using an orthorhombic unit cell. The two types of substitution have opposite effects on the structural and magnetic properties. Fe atoms preferentially occupy the sites at the triangular layer. Thus, the replacement of Co by Fe suppresses the ferrimagnetic ordering of the parent compound, and CaBaCo_4–<i>x</i>Fe_<i>x</i>O₇ (0.5 ≤ <i>x</i> ≤ 2) samples are antiferromagnetically ordered following a new propagation vector <i>k</i> = (1/3,0,0). However, the Zn atoms prefer occupying the Kagome layer, which is very detrimental for the long-range magnetic interactions giving rise to a magnetic glass-like behavior in the CaBaCo₃ZnO₇ sample. The oxidation states of iron and zinc are found to be 3+ and 2+, respectively, independently of the content, as confirmed by X-ray absorption spectroscopy. Therefore, the average Co oxidation state changes accordingly with the Fe³⁺ or Zn²⁺ doping. Also, X-ray absorption spectroscopy data confirm the different preferential occupation for both Fe and Zn cations. The combined information obtained by neutron diffraction and X-ray absorption spectroscopy indicates that cobalt atoms can be either in a fluctuating Co²⁺/Co³⁺ valence state or, alternatively, Co²⁺ and Co³⁺ ions being randomly distributed in the lattice. These results explain the occurrence of local disorder in the CoO₄ tetrahedra obtained by EXAFS. An anomaly in the lattice parameters and an increase in the local disorder are observed only at the ferrimagnetic transition for CaBaCo₄O₇, revealing the occurrence of local magneto-elastic coupling

Integrative pathway enrichment analysis of multivariate omics data

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations

Author Correction: The landscape of viral associations in human cancers

author correctio

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these features. Indeed, domain disruptions in human cancers can lead to misregulation of gene expression. However, the frequency of domain disruptions in human cancers remains unclear. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we analyzed 288,457 somatic structural variations (SVs) to understand the distributions and effects of SVs across TADs. Notably, SVs can lead to the fusion of discrete TADs, and complex rearrangements markedly change chromatin folding maps in the cancer genomes. Notably, only 14% of the boundary deletions resulted in a change in expression in nearby genes of more than twofold.A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer