Operational model of the athos undulator beamline

Athos, the new Soft X-ray beamline of SwissFEL, operates 16 Apple X undulators and 15 compact chicanes to implement novel lasing schemes. With the data available after the end of the magnetic measurement campaign (middle 2020), a self-consistent set of equations will be used to summarize all the relevant properties of those devices to start their commissioning. The analytic approach planned will be discussed in great detail and tested with the preliminary experimental data available. Finally, the accuracy of this approach will be evaluated and critically compared to the requirements of the new FEL beamline.peer-reviewe

Advanced operational models of the apple X undulator

Athos is a new soft X-ray beamline at SwissFEL, where the Apple X type undulators will be equipped. These devices are flexible to produce light in different polarization modes. An adequate magnetic field model is required for the operation of undulator. The undulator deflection parameter K and its gradient are calculated starting from the Fourier series of the magnetic field. In the classical parallel and anti-parallel operational modes - respectively elliptical and linear modes, the variation of the magnetic field as well as its parameters are evaluated by computer modeling. The results are compared to the magnetic measurements of the first Apple X prototype.peer-reviewe

Characterization of large area photomultipliers and its application to dark matter search with noble liquid detectors

There is growing interest in the use of noble liquid detectors to study particle properties and search for new phenomena. In particular, they are extremely suitable for performing direct searches for dark matter. In this kind of experiments, the light produced after an interaction within the sensitive volume is usually read-out by photomultipliers. The need to go to masses in the tonne scale to explore deeper regions of the parameter space, calls for the use of large area photomultipliers. In this paper we address the need to perform laboratory calibration measurements of these large photomultipliers, in particular to characterize its behaviour at cryogenic temperatures where no reference from the manufacturer is available. We present comparative tests of phototubes from two companies. The tests are performed in conditions similar to those of operation in a real experiment. Measurements of the most relevant phototube parameters (quantum efficiency, gain, linearity, etc.) both at room and liquid Argon temperatures are reported. The results show that the studied phototubes comply with the stringent requirements posed by current dark matter searches performed with noble-liquid detectors.This work has been supported by CICYT Grants FPA-2006-00684, FPA-2002-01835 and FPA- 2005-07605-C02-01

Experience with short-period, small gap undulators at the SwissFEL aramis beamline

The SwissFEL Aramis beamline provides hard X-ray FEL radiation down to 1 Angström with 5.8 GeV and short period, 15mm, in-vacuum undulators (U15). To reach the maximum designed K-value of 1.8 the U15s have to be operated with vacuum gaps down to 3.0 mm. The thirteen-undulator modules are 4m long and each of them is equipped with a pair of permanent magnet quadrupoles at the two ends, aligned magnetically to the undulator axis. Optical systems and dedicated photon diagnostics are used to check the alignment and improve the K-value calibration. In this talk the main steps of the undulator commissioning will be recalled and a systematic comparison between the magnetic results and the electron and photon based measurements will be reported to highlight achievements and open issues.peer-reviewe

Solutions of the Two-Dimensional Hubbard Model: Benchmarks and Results from a Wide Range of Numerical Algorithms

Numerical results for ground-state and excited-state properties (energies, double occupancies, and Matsubara-axis self-energies) of the single-orbital Hubbard model on a two-dimensional square lattice are presented, in order to provide an assessment of our ability to compute accurate results in the thermodynamic limit. Many methods are employed, including auxiliary-field quantum Monte Carlo, bare and bold-line diagrammatic Monte Carlo, method of dual fermions, density matrix embedding theory, density matrix renormalization group, dynamical cluster approximation, diffusion Monte Carlo within a fixed-node approximation, unrestricted coupled cluster theory, and multireference projected Hartree-Fock methods. Comparison of results obtained by different methods allows for the identification of uncertainties and systematic errors. The importance of extrapolation to converged thermodynamic-limit values is emphasized. Cases where agreement between different methods is obtained establish benchmark results that may be useful in the validation of new approaches and the improvement of existing methods

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

SummaryWe describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers