Shawn McKee

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

This white paper presents the current status of the R&D for Analysis Facilities (AFs) and attempts to summarize the views on the future direction of these facilities. These views have been collected through the High Energy Physics (HEP) Software Foundation's (HSF) Analysis Facilities forum, established in March 2022, the Analysis Ecosystems II workshop, that took place in May 2022, and the WLCG/HSF pre-CHEP workshop, that took place in May 2023. The paper attempts to cover all the aspects of an analysis facility.

The transition of the Worldwide Large Hadron Collider Computing Grid (WLCG) storage services to dual-stack IPv6/IPv4 is almost complete; all Tier-1 and 94% of Tier-2 storage are IPv6 enabled. While most data transfers now use IPv6, a significant number of IPv4 transfers still occur even when both endpoints support IPv6. This paper presents the ongoing efforts of the HEPiX IPv6 working group to steer WLCG toward IPv6-only services by investigating and fixing the obstacles to the use of IPv6 and identifying cases where IPv4 is used when IPv6 is available. Removing IPv4 use is essential for the long-term agreed goal of IPv6-only access to resources within WLCG, thus eliminating the complexity and security concerns associated with dual-stack services. We present our achievements and ongoing challenges as we navigate the final stages of the transition from IPv4 to IPv6 within WLCG.

The Snowmass 2021 CompF4 topical group’s scope is facilities R&D, where we consider “facilities” as the hardware and software infrastructure inside the data centers plus the networking between data centers, irrespective of who owns them, and what policies are applied for using them. In other words, it includes commercial clouds, federally funded High Performance Computing (HPC) systems for all of science, and systems funded explicitly for a given experimental or theoretical program. However, we explicitly consider any data centers that are integrated into data acquisition systems or trigger of the experiments out of scope here. Those systems tend to have requirements that are quite distinct from the data center functionality required for “offline” processing and storage.As well as submitted whitepapers, this report is the result of community discussions, including sessions in the Computational Frontier workshop …

The quest to understand the fundamental building blocks of nature and their interactions is one of the oldest and most ambitious of human scientific endeavors. CERN's Large Hadron Collider (LHC) represents a huge step forward in this quest. The discovery of the Higgs boson, the observation of exceedingly rare decays of mesons, and stringent constraints on many viable theories of physics beyond the Standard Model (SM) demonstrate the great scientific value of the LHC physics program. The next phase of this global scientific project will be the High-Luminosity LHC (HL-LHC) which will collect data starting circa 2029 and continue through the 2030s. The primary science goal is to search for physics beyond the SM and, should it be discovered, to study its implications. In the HL-LHC era, the ATLAS and CMS experiments will record around 100 times as many collisions as were used to discover the Higgs boson (and at twice the energy). Both NSF and DOE are making large detector upgrade investments so the HL-LHC can operate in this high-rate environment. Similar investment in software R&D; for acquiring, managing, processing and analyzing HL-LHC data is critical to maximize the return-on-investment in the upgraded accelerator and detectors. This report presents a strategic plan for a possible second 5-year funded phase (2023 through 2028) for the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) which will close remaining software and computing gaps to deliver HL-LHC science.

A technique is presented to measure the efficiency with which c-jets are mistagged as b-jets (mistagging efficiency) using events, where one of the W bosons decays into an electron or muon and a neutrino and the other decays into a quark–antiquark pair. The measurement utilises the relatively large and known branching ratio, which allows a measurement to be made in an inclusive c-jet sample. The data sample used was collected by the ATLAS detector at and corresponds to an integrated luminosity of 139 fb. Events are reconstructed using a kinematic likelihood technique which selects the mapping between jets and decay products that yields the highest likelihood value. The distribution of the b-tagging discriminant for jets from the hadronic W decays in data is compared with that in simulation to extract the mistagging efficiency as a function of jet transverse momentum. The total …

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino oscillation experiment with a primary physics goal of observing neutrino and antineutrino oscillation patterns to precisely measure the parameters governing long-baseline neutrino oscillation in a single experiment, and to test the three-flavor paradigm. DUNE's design has been developed by a large, international collaboration of scientists and engineers to have unique capability to measure neutrino oscillation as a function of energy in a broadband beam, to resolve degeneracy among oscillation parameters, and to control systematic uncertainty using the exquisite imaging capability of massive LArTPC far detector modules and an argon-based near detector. DUNE's neutrino oscillation measurements will unambiguously resolve the neutrino mass ordering and provide the sensitivity to discover CP violation in neutrinos for a wide range of possible values of . DUNE is also uniquely sensitive to electron neutrinos from a galactic supernova burst, and to a broad range of physics beyond the Standard Model (BSM), including nucleon decays. DUNE is anticipated to begin collecting physics data with Phase I, an initial experiment configuration consisting of two far detector modules and a minimal suite of near detector components, with a 1.2 MW proton beam. To realize its extensive, world-leading physics potential requires the full scope of DUNE be completed in Phase II. The three Phase II upgrades are all necessary to achieve DUNE's physics goals: (1) addition of far detector modules three and four for a total FD fiducial mass of at least 40 kt, (2 …

SARS-CoV-2 has been associated with an increased rate of venous thromboembolism in critically ill patients. Since surgical patients are already at higher risk of venous thromboembolism than general populations, this study aimed to determine if patients with peri-operative or prior SARS-CoV-2 were at further increased risk of venous thromboembolism. We conducted a planned sub-study and analysis from an international, multicentre, prospective cohort study of elective and emergency patients undergoing surgery during October 2020. Patients from all surgical specialties were included. The primary outcome measure was venous thromboembolism (pulmonary embolism or deep vein thrombosis) within 30 days of surgery. SARS-CoV-2 diagnosis was defined as peri-operative (7 days before to 30 days after surgery); recent (1-6 weeks before surgery); previous (≥7 weeks before surgery); or none. Information on prophylaxis regimens or pre-operative anti-coagulation for baseline comorbidities was not available. Postoperative venous thromboembolism rate was 0.5% (666/123,591) in patients without SARS-CoV-2; 2.2% (50/2317) in patients with peri-operative SARS-CoV-2; 1.6% (15/953) in patients with recent SARS-CoV-2; and 1.0% (11/1148) in patients with previous SARS-CoV-2. After adjustment for confounding factors, patients with peri-operative (adjusted odds ratio 1.5 (95%CI 1.1-2.0)) and recent SARS-CoV-2 (1.9 (95%CI 1.2-3.3)) remained at higher risk of venous thromboembolism, with a borderline finding in previous SARS-CoV-2 (1.7 (95%CI 0.9-3.0)). Overall, venous thromboembolism was independently associated with 30-day …