Polyglot Jet Finding

The evaluation of new computing languages for a large community, like HEP, involves comparison of many aspects of the languages' behaviour, ecosystem and interactions with other languages. In this paper we compare a number of languages using a common, yet non-trivial, HEP algorithm: the \akt\ clustering algorithm used for jet finding. We compare specifically the algorithm implemented in Python (pure Python and accelerated with numpy and numba), and Julia, with respect to the reference implementation in C++, from Fastjet. As well as the speed of the implementation we describe the ergonomics of the language for the coder, as well as the efforts required to achieve the best performance, which can directly impact on code readability and sustainability

Polyglot Jet Finding

The evaluation of new computing languages for a large community, like HEP, involves comparison of many aspects of the languages’ behaviour, ecosystem and interactions with other languages. In this paper we compare a number of languages using a common, yet non-trivial, HEP algorithm: the anti- kT clustering algorithm used for jet finding. We compare specifically the algorithm implemented in Python (pure Python and accelerated with numpy and numba), and Julia, with respect to the reference implementation in C++, from Fastjet. As well as the speed of the implementation we describe the ergonomics of the language for the coder, as well as the efforts required to achieve the best performance, which can directly impact on code readability and sustainability

HEP Community White Paper on Software trigger and event reconstruction

Realizing the physics programs of the planned and upgraded high-energy physics (HEP) experiments over the next 10 years will require the HEP community to address a number of challenges in the area of software and computing. For this reason, the HEP software community has engaged in a planning process over the past two years, with the objective of identifying and prioritizing the research and development required to enable the next generation of HEP detectors to fulfill their full physics potential. The aim is to produce a Community White Paper which will describe the community strategy and a roadmap for software and computing research and development in HEP for the 2020s. The topics of event reconstruction and software triggers were considered by a joint working group and are summarized together in this document.Comment: Editors Vladimir Vava Gligorov and David Lang

CaMKIIδ-dependent dysregulation of atrial Na+ homeostasis promotes pro-arrhythmic activity in an obstructive sleep apnea mouse model

BackgroundObstructive sleep apnea (OSA) has been linked to various pathologies, including arrhythmias such as atrial fibrillation. Specific treatment options for OSA are mainly limited to symptomatic approaches. We previously showed that increased production of reactive oxygen species (ROS) stimulates late sodium current through the voltage-dependent Na+ channels via Ca2+/calmodulin-dependent protein kinase IIδ (CaMKIIδ), thereby increasing the propensity for arrhythmias. However, the impact on atrial intracellular Na+ homeostasis has never been demonstrated. Moreover, the patients often exhibit a broad range of comorbidities, making it difficult to ascertain the effects of OSA alone.ObjectiveWe analyzed the effects of OSA on ROS production, cytosolic Na+ level, and rate of spontaneous arrhythmia in atrial cardiomyocytes isolated from an OSA mouse model free from comorbidities.MethodsOSA was induced in C57BL/6 wild-type and CaMKIIδ-knockout mice by polytetrafluorethylene (PTFE) injection into the tongue. After 8 weeks, their atrial cardiomyocytes were analyzed for cytosolic and mitochondrial ROS production via laser-scanning confocal microscopy. Quantifications of the cytosolic Na+ concentration and arrhythmia were performed by epifluorescence microscopy.ResultsPTFE treatment resulted in increased cytosolic and mitochondrial ROS production. Importantly, the cytosolic Na+ concentration was dramatically increased at various stimulation frequencies in the PTFE-treated mice, while the CaMKIIδ-knockout mice were protected. Accordingly, the rate of spontaneous Ca2+ release events increased in the wild-type PTFE mice while being impeded in the CaMKIIδ-knockout mice.ConclusionAtrial Na+ concentration and propensity for spontaneous Ca2+ release events were higher in an OSA mouse model in a CaMKIIδ-dependent manner, which could have therapeutic implications

CaMKII-Dependent Contractile Dysfunction and Pro-Arrhythmic Activity in a Mouse Model of Obstructive Sleep Apnea

Left ventricular contractile dysfunction and arrhythmias frequently occur in patients with sleep-disordered breathing (SDB). The CaMKII-dependent dysregulation of cellular Ca homeostasis has recently been described in SDB patients, but these studies only partly explain the mechanism and are limited by the patients’ heterogeneity. Here, we analyzed contractile function and Ca homeostasis in a mouse model of obstructive sleep apnea (OSA) that is not limited by confounding comorbidities. OSA was induced by artificial tongue enlargement with polytetrafluorethylene (PTFE) injection into the tongue of wildtype mice and mice with a genetic ablation of the oxidative activation sites of CaMKII (MMVV knock-in). After eight weeks, cardiac function was assessed with echocardiography. Reactive oxygen species (ROS) and Ca transients were measured using confocal and epifluorescence microscopy, respectively. Wildtype PTFE mice exhibited an impaired ejection fraction, while MMVV PTFE mice were fully protected. As expected, isolated cardiomyocytes from PTFE mice showed increased ROS production. We further observed decreased levels of steady-state Ca transients, decreased levels of caffeine-induced Ca transients, and increased pro-arrhythmic activity (defined as deviations from the diastolic Ca baseline) only in wildtype but not in MMVV PTFE mice. In summary, in the absence of any comorbidities, OSA was associated with contractile dysfunction and pro-arrhythmic activity and the inhibition of the oxidative activation of CaMKII conveyed cardioprotection, which may have therapeutic implications

Towards podio v1.0 - A first stable release of the EDM toolkit

A performant and easy-to-use event data model (EDM) is a key component of any HEP software stack. The podio EDM toolkit provides a user friendly way of generating such a performant implementation in C++ from a high level description in yaml format. Finalizing a few important developments, we are in the final stretches for release v1.0 of podio, a stable release with backward compatibility for datafiles written with podio from then on. We present an overview of the podio basics, and go into slighty more technical detail on the most important topics and developments. These include: schema evolution for generated EDMs, multithreading with podio generated EDMs, the implementation of them as well as the basics of I/O. Using EDM4hep, the common and shared EDM of the Key4hep project, we highlight a few of the smaller features in action as well as some lessons learned during the development of EDM4hep and podio. Finally, we show how podio has been integrated into the Gaudi based event processing framework that is used by Key4hep, before we conclude with a brief outlook on potential developments after v1.0

CaMKIIδ-dependent dysregulation of atrial Na+ homeostasis promotes pro-arrhythmic activity in an obstructive sleep apnea mouse model

Background: Obstructive sleep apnea (OSA) has been linked to various pathologies, including arrhythmias such as atrial fibrillation. Specific treatment options for OSA are mainly limited to symptomatic approaches. We previously showed that increased production of reactive oxygen species (ROS) stimulates late sodium current through the voltage-dependent Na+ channels via Ca2+/calmodulin-dependent protein kinase IIδ (CaMKIIδ), thereby increasing the propensity for arrhythmias. However, the impact on atrial intracellular Na+ homeostasis has never been demonstrated. Moreover, the patients often exhibit a broad range of comorbidities, making it difficult to ascertain the effects of OSA alone. Objective: We analyzed the effects of OSA on ROS production, cytosolic Na+ level, and rate of spontaneous arrhythmia in atrial cardiomyocytes isolated from an OSA mouse model free from comorbidities. Methods: OSA was induced in C57BL/6 wild-type and CaMKIIδ-knockout mice by polytetrafluorethylene (PTFE) injection into the tongue. After 8 weeks, their atrial cardiomyocytes were analyzed for cytosolic and mitochondrial ROS production via laser-scanning confocal microscopy. Quantifications of the cytosolic Na+ concentration and arrhythmia were performed by epifluorescence microscopy. Results: PTFE treatment resulted in increased cytosolic and mitochondrial ROS production. Importantly, the cytosolic Na+ concentration was dramatically increased at various stimulation frequencies in the PTFE-treated mice, while the CaMKIIδ-knockout mice were protected. Accordingly, the rate of spontaneous Ca2+ release events increased in the wild-type PTFE mice while being impeded in the CaMKIIδ-knockout mice. Conclusion: Atrial Na+ concentration and propensity for spontaneous Ca2+ release events were higher in an OSA mouse model in a CaMKIIδ-dependent manner, which could have therapeutic implications

Is Julia ready to be adopted by HEP?

The Julia programming language was created 10 years ago and is now a mature and stable language with a large ecosystem including more than 8,000 third-party packages. It was designed for scientific programming to be a high-level and dynamic language as Python is, while achieving runtime performances comparable to C/C++ or even faster. With this, we ask ourselves if the Julia language and its ecosystem is ready now for its adoption by the High Energy Physics community. We will report on a number of investigations and studies of the Julia language that have been done for various representative HEP applications, ranging from computing intensive initial data processing of experimental data and simulation, to final interactive data analysis and plotting. Aspects of collaborative code development of large software within a HEP experiment has also been investigated: scalability with large development teams, continuous integration and code test, code reuse, language interoperability to enable an adiabatic migration of packages and tools, software installation and distribution, training of the community, benefit from development from industry and academia from other fields

Key4hep: Progress Report on Integrations

Detector studies for future experiments rely on advanced software tools to estimate performance and optimize their design and technology choices. The Key4hep project provides a flexible turnkey solution for the full experiment life-cycle based on established community tools such as ROOT, Geant4, DD4hep, Gaudi, podio and spack. Members of the CEPC, CLIC, EIC, FCC, and ILC communities have joined to develop this framework and have merged, or are in the progress of merging, their respective software environments into the Key4hep stack. These proceedings will give an overview over the recent progress in the Key4hep project: covering the developments towards adaptation of state-of-theart tools for simulation (DD4hep, Gaussino), track and calorimeter reconstruction (ACTS, CLUE), particle flow (PandoraPFA), analysis via RDataFrame, and visualization with Phoenix, as well as tools for testing and validation

HEP Software Foundation Community White Paper Working Group - Data Analysis and Interpretation

At the heart of experimental high energy physics (HEP) is the development of facilities and instrumentation that provide sensitivity to new phenomena. Our understanding of nature at its most fundamental level is advanced through the analysis and interpretation of data from sophisticated detectors in HEP experiments. The goal of data analysis systems is to realize the maximum possible scientific potential of the data within the constraints of computing and human resources in the least time. To achieve this goal, future analysis systems should empower physicists to access the data with a high level of interactivity, reproducibility and throughput capability. As part of the HEP Software Foundation Community White Paper process, a working group on Data Analysis and Interpretation was formed to assess the challenges and opportunities in HEP data analysis and develop a roadmap for activities in this area over the next decade. In this report, the key findings and recommendations of the Data Analysis and Interpretation Working Group are presented.Comment: arXiv admin note: text overlap with arXiv:1712.0659