Concepts, Design and Implementation of the ATLAS New Tracking (NEWT)

The track reconstruction of modern high energy physics experiments is a very complex task that puts stringent requirements onto the software realisation. The ATLAS track reconstruction software has been in the past dominated by a collection of individual packages, each of which incorporating a different intrinsic event data model, different data flow sequences and calibration data. Invoked by the Final Report of the Reconstruction Task Force, the ATLAS track reconstruction has undergone a major design revolution to ensure maintainability during the long lifetime of the ATLAS experiment and the flexibility needed for the startup phase. The entire software chain has been re-organised in modular components and a common Event Data Model has been deployed during the last three years. A complete new track reconstruction that concentrates on common tools aimed to be used by both ATLAS tracking devices, the Inner Detector and the Muon System, has been established. It has been already used during many large scale tests with data from Monte Carlo simulation and from detector commissioning projects such as the combined test beam 2004 and cosmic ray events. This document concentrates on the technical and conceptual details of the newly developed track reconstruction, also known as New Tracking

Updates of the ATLAS Tracking Event Data Model (Release 13)

In a previous document we have presented the ATLAS tracking Event Data Model (EDM) that has been developed during the recent restructuring of the ATLAS offline track reconstruction. The tracking EDM has become a cornerstone of the new modular track reconstruction algorithms of both tracking devices of the ATLAS detector, the Inner Detector and the Muon System. Recently, some components have undergone yet another design evolution targeted at completing missing modules and at establishing anticipated functionality for the startup of the ATLAS experiment. One particular aspect of the EDM is that is does not only have to fulfill the requirements of today's algorithmic modules, but has to provide the flexibility for future developments. This document is based on ATLAS software release 13.0.0

ATLAS Tracking Event Data Model

In this report the event data model (EDM) relevant for tracking in the ATLAS experiment is presented. The core component of the tracking EDM is a common track object which is suited to describe tracks in the innermost tracking sub-detectors and in the muon detectors in offline as well as online reconstruction. The design of the EDM was driven by a demand for modularity and extensibility while taking into account the different requirements of the clients. The structure of the track object and the representation of the tracking-relevant information are described in detail

ATLAS Inner Detector Event Data Model

The data model for event reconstruction (EDM) in the Inner Detector of the ATLAS experiment is presented. Different data classes represent evolving stages in the reconstruction data flow, and specific derived classes exist for the sub-detectors. The Inner Detector EDM also extends the data model for common tracking in ATLAS and is integrated into the modular design of the ATLAS high-level trigger and off-line software

Blood ties: ABO is a trans-species polymorphism in primates

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World Monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multi-allelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the ABO polymorphism is a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years, to date, the only such example in Hominoids and Old World Monkeys outside of the Major Histocompatibility Complex.Comment: 45 pages, 4 Figures, 4 Supplementary Figures, 5 Supplementary Table

Editorial: Vagus nerve-mediated drive in supporting homeostasis: optimizing global health through monitoring and stimulating vagal function

Epigenetics encompasses the changes in gene expression triggered by environmental cues that occur without altering the underlying DNA sequences. Although epigenetics involves a limited number of identified mechanisms so far (DNA methylation, histone modifications and noncoding RNAs), the field of Epigenetics is spreading rapidly over integrated physiopathology (Jeffries, 2020). The importance of epigenetics has been acknowledged in cancer (Sun et al., 2022), sepsis (Binnie et al., 2020), autoimmune/inflammatory diseases (Surace and Hedrich, 2019), addiction (Hamilton and Nestler, 2019), aging (Pal and Tyler, 2016; Pérez et al., 2022), neurodegenerative diseases (Berson et al., 2018; Zhang et al., 2022) and even in neurodevelopmental (Esposito et al., 2018; Wu et al., 2020) and psychiatric diseases (Abdolmaleky et al., 2023). Likewise, a broad and expanding set of therapies in clinics have been potentialized by tuning the vagal complex of brainstem, i.e., the key neural node of homeostasis, via non-invasive Vagus Nerve Stimulation (VNS) (Hilz, 2022). Moreover, Heart Rate Variability (HRV), a physiologically validated and easily accessible read-out of the vagal tone (Lewis et al., 2012), is acknowledged as a polyvalent prognostic tool (Gidron et al., 2018; Mol et al., 2021). This is not surprising, since Epigenome is considered as a “mediator for host-microbiome crosstalk” (Peery et al., 2021) and since vagus nerve represents the fastest pathway of the Microbiota-Gut-brain Axis (Fülling et al., 2019). However, except for regulating neuro-inflammation (Chen et al., 2022), the mechanisms through which VNS influences peripheral and central nervous system plasticity are not well described yet, limiting therapeutic optimization (Morrison et al., 2020; Keute and Gharabaghi, 2021). Therefore, as the vagal complex (i.e., peripheral and brainstem components) is definitely prone to bring about epigenetic modulations, notably through neuro-endocrine stimuli (Gil et al., 2013), we questioned the epigenetic role of vagus nerve, in order to promote noninvasive VNS, guided by HRV monitoring, as a universal therapy to stay healthy

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV

Search for squarks and gluinos in events with isolated leptons, jets and missing transverse momentum at s√=8 TeV with the ATLAS detector

The results of a search for supersymmetry in final states containing at least one isolated lepton (electron or muon), jets and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are reported. The search is based on proton-proton collision data at a centre-of-mass energy s√=8 TeV collected in 2012, corresponding to an integrated luminosity of 20 fb−1. No significant excess above the Standard Model expectation is observed. Limits are set on supersymmetric particle masses for various supersymmetric models. Depending on the model, the search excludes gluino masses up to 1.32 TeV and squark masses up to 840 GeV. Limits are also set on the parameters of a minimal universal extra dimension model, excluding a compactification radius of 1/R c = 950 GeV for a cut-off scale times radius (ΛR c) of approximately 30