bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Platform-as-a-Service paradigm meets ATLAS: Developing an automated analysis workflow on the newly established INFN CLOUD
Authors: Marcon Caterina , Carminati Leonardo , Rebatto David , Turra Ruggero 
Published: May 2024

The Worldwide LHC Computing Grid (WLCG) is a large-scale collaboration which gathers computing resources from more than 170 computing centers worldwide. To fulfill the requirements of new applications and to improve the long-term sustainability of the grid middleware, newly available solutions are being investigated. Like open-source and commercial players, the HEP community has also recognized the benefits of integrating cloud technologies into the legacy, grid-based workflows.
Since March 2021, INFN has entered the field of cloud computing establishing the INFN CLOUD infrastructure. This platform supports scientific computing, software development and training, and serves as an extension of local resources. Among available services, virtual machines, Docker-based deployments, HTCondor (deployed on Kubernetes) or general-purpose Kubernetes clusters can be deployed.
An ongoing R&D activity within the ATLAS experiment has the long-term objective to define an operation model which is efficient, versatile and scalable in terms of costs and computing power. As a part of this larger effort, this study investigates the feasibility of an automated, cloud-based data analysis workflow for the ATLAS experiment using INFN CLOUD resources. The scope of this research has been defined in a new INFN R&D project: the INfn Cloud based Atlas aNalysis faciliTy, or INCANT.
The long-term objective of INCANT is to provide a cloud-based system to support data preparation and data analysis. As a first project milestone, a proofof-concept has been developed. A Kubernetes cluster equipped with 7 nodes (total 28 vCPU, 56 GB of RAM and 700 GB of non-shared block storage) hosts an HTCondor cluster, federated with INFN’s IAM authentication platform, running in specialized Kubernetes pods. HTCondor worker nodes have direct access to CVMFS and EOS (via XRootD) for provisioning software and data, respectively. They are also connected to a NFS shared drive which can optionally be backed by an S3-compatible 2 TB storage. Jobs are submitted to the HTCondor cluster from a satellite, Dockerized submit node which is also federated with INFN’s IAM and connected to the same data and software resources. This proof-of-concept is being tested with actual analysis workflows.
Darshan for HEP applications
Authors: Wang Rui , Snyder Shane , Benjamin Douglas , Dong Zhihua , Gartung Patrick , Herner Kenneth 
Published: May 2024

Modern HEP workflows must manage increasingly large and complex data collections. HPC facilities may be employed to help meet these workflows’ growing data processing needs. However, a better understanding of the I/O patterns and underlying bottlenecks of these workflows is necessary to meet the performance expectations of HPC systems.
Darshan is a lightweight I/O characterization tool that captures concise views of HPC application I/O behavior. It intercepts application I/O calls at runtime, records file access statistics for each process, and generates log files detailing application I/O access patterns.
Typical HEP workflows include event generation, detector simulation, event reconstruction, and subsequent analysis stages. A study of the I/O behavior of the ATLAS simulation and filtering stage, and the CMS simulation workflow using Darshan is presented, including insights into the I/O operations and data access size.
Geant4 Monte-Carlo (GEMC) A database-driven simulation program
Authors: Ungaro Maurizio 
Published: May 2024

GEMC[1] is an application that harnesses the power of databases to execute Geant4 Monte-Carlo simulations.
The databases (MYSQL, CSQL, TEXT) define the geometry, materials, digitization algorithms, readout electronics and output formats.
Implemented in C++, GEMC also boasts a user-friendly Python API that facilitates detector construction and database population.
GEMC can handle real-life scenarios such as geometry variations and the run number-dependent calibration constants and digitization parameters.
This abstract provides an overview of GEMC, accompanied by examples that showcase its versatility. We delve into the practical application of GEMC within the the CLAS12 experimental program at Jefferson Lab.
Key4hep: Progress Report on Integrations
Authors: Brondolin Erica , Carceller Juan Miguel , Deconinck Wouter , Fang Wenxing , Francois Brieuc , Gaede Frank-Dieter , Ganis Gerardo , Hegner Benedikt , Helsens Clement , Huang Xingtao , Joosten Sylvester , Ko Sang Hyun , Lin Tao , Li Teng , Li Weidong , Madlener Thomas , Reichenbach Leonhard , Sailer André , Sasikumar Swathi , Smiesko Juraj , Stewart Graeme A. , Tolosa-Delgado Alvaro , Volkl Valentin , Zhang Xiaomei , Zou Jiaheng 
Published: May 2024

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.
Managing software build infrastructure at ALICE using Hashicorp Nomad
Authors: Wilken Timo , Eulisse Giulio 
Published: May 2024

The ALICE experiment at CERN uses a cluster consisting of virtual and bare-metal machines to build and test proposed changes to the ALICE Online–Offline (O2) software in addition to building and publishing regular software releases.
Nomad is a free and open-source job scheduler for containerised and noncontainerised applications developed by Hashicorp. It is integrated into an ecosystem of related software, including Consul and Vault, providing a consistent interface to orchestration, monitoring and secret storage. At ALICE, it recently replaced Apache Mesos, Aurora and Marathon as the primary tool for managing our computing resources.
First, we will describe the architecture of the build cluster at the ALICE experiment. After giving an overview of the advantages that Nomad gives us in managing our computing workload, and our reasons for switching away from the Mesos software stack, we will present concrete examples of improvements in monitoring and automatic configuration of web services that we are already benefiting from. Finally, we will discuss where we see opportunities for future work in integrating the ALICE build infrastructure more deeply with Nomad, in order to take advantage of its larger feature set compared to Mesos.
High-performance end-user analysis in pure Julia programming language
Authors: Ling Jerry , Gál Tamás 
Published: May 2024

We present tools for high-performance analysis written in pure Julia, a just-in-time (JIT) compiled dynamic programming language with a high-level syntax and performance. The packages we present center around UnROOT.jl, a pure Julia ROOT file I/O package that is optimized for speed, lazy reading, flexibility and thread safety.
We discuss what affects performance in Julia, the challenges, and their solutions during the development of UnROOT.jl. We highlight type stability as a challenge and discuss its implication whenever any “compilation” happens (incl. Numba, Jax, C++) as well as Julia’s specific ones.
We demonstrate the performance and “easy to use” claim by comparing UnROOT.jl against popular alternatives (RDataFrame, Uproot, etc.) in medium-size realistic benchmarks, comparing both performance and code complexity.
Finally, we also showcase real ATLAS analysis workflows both locally and on an HPC system, highlighting the composability of UnROOT.jl with multithread/process and out-of-core distributed computing libraries.
Modular toolsets for integrating HPC clusters in experiment control systems
Authors: Manafov Anar , Rybalchenko Alexey , Klein Dennis , Al-Turany Mohammad 
Published: May 2024

New particle/nuclear physics experiments require a massive amount of computing power that is only achieved by using high performance clusters directly connected to the data acquisition systems and integrated into the online systems of the experiments. However, integrating an HPC cluster into the online system of an experiment means: Managing and synchronizing thousands of processes that handle the huge throughput.
In this work, modular components that can be used to build and integrate such a HPC cluster in the experiment control systems (ECS) will be introduced.
The Online Device Control library (ODC) [1] in combination with the Dynamic Deployment System (DDS) [2, 3] and FairMQ [4] message queuing library offers a sustainable solution for integrating HPC cluster controls into an ECS. DDS as part of the ALFA framework [5] is a toolset that automates and significantly simplifies a dynamic deployment of user-defined processes and their dependencies on any resource management system (RMS) using a given process graph (topology).
ODC, in this architecture, is the tool to control and communicate with a topology of FairMQ processes using DDS. ODC is designed to act as a broker between a high level experiment control system and a low level task management system e.g.: DDS.
In this work the architecture of both DDS and ODC will be discussed, as well as the design decisions taken based on the experience gained of using these tools in production by the ALICE experiment at CERN to deploy and control thousands of processes (tasks) on the Event Processing Nodes cluster (EPN) during Run3 as a part of the ALICE O2 software ecosystem [6].
Particle identification with machine learning in ALICE Run 3
Authors: Karwowska Maja , Jakubowska Monika , Graczykowski Łukasz , Deja Kamil , Kasak Miłosz 
Published: May 2024

The main focus of the ALICE experiment, quark–gluon plasma measurements, requires accurate particle identification (PID). The ALICE subdetectors allow identifying particles over a broad momentum interval ranging from about 100 MeV/c up to 20 GeV/c. However, a machine learning (ML) model can explore more detector information. During LHC Run 2, preliminary studies with Random Forests obtained much higher efficiencies and purities for selected particles than standard techniques.
For Run 3, we investigate Domain Adaptation Neural Networks that account for the discrepancies between the Monte Carlo simulations and the experimental data. Preliminary studies show that domain adaptation improves particle classification. Moreover, the solution is extended with Feature Set Embedding and attention to give the network more flexibility to train on data with various sets of detector signals. PID ML is already integrated with the ALICE Run 3 Analysis Framework. Preliminary results for the PID of selected particle species, including real-world analyzes, are discussed as well as the possible optimizations.
Opticks: GPU Optical Photon Simulation via NVIDIA OptiX
Authors: Blyth Simon C. 
Published: May 2024

Opticks is an open source project that accelerates optical photon simulation by integrating GPU ray tracing, accessed via the NVIDIA OptiX 7+ API, with Geant4 based simulations. A single NVIDIA Turing GPU from the first RTX generation has been measured to provide optical photon simulation speedup factors exceeding 1500 times single threaded Geant4 with a full JUNO analytic GPU geometry automatically translated from the Geant4 geometry. Optical physics processes of scattering, absorption, scintillator reemission and boundary processes are implemented in CUDA programs based on Geant4. Wavelength-dependent material and surface properties as well as inverse cumulative distribution functions for reemission are interleaved into GPU textures providing fast interpolated property lookup or wavelength generation.
In this work we describe the near complete re-implementation required to adopt the entirely new NVIDIA OptiX 7+ API, with the implementation now directly CUDA based with OptiX usage restricted to providing intersects. The re-implementation features a modular many small header design that enables fine grained testing both on GPU and CPU together with large code reductions from CPU/GPU sharing. Enhanced modularity has enabled CSG tree generalization to support "list-nodes", similar to G4MultiUnion, that improve performance for complex CSG solids. In addition support for interference effects on boundaries with multiple thin layers, such as anti-reflection coatings and photocathodes, using CUDA compatible transfer matrix method (TMM) calculations of reflectance, transmittance and absorptance are reported.
Umbilical Catheter Extravasation Mimicking Necrotizing Enterocolitis
in a Preterm Neonate: A Diagnostic Challenge
Authors: Armağan Coşkun , Çapıtlı Tevfik , Dilmen Gülsüm , Kefeli Saadet Çağla , Ulusoy Oktay , Erdoğan Funda , Duman Nuray , Özkan Hasan 
Published: May 2024

AbstractManaging acute abdomen in very low birth weight (VLBW) and premature infants
presents a diagnostic challenge, often necessitating a thorough assessment to
discern underlying causes. Umbilical venous catheters (UVCs), commonly used in
neonatal intensive care, are essential but not without risks. A 29-week
premature male infant, born to a 23-year-old mother, was referred to our clinic
on the 16th day of life with a suspected diagnosis of necrotizing
enterocolitis (NEC). The infant had spent the first day intubated and received
non-invasive respiratory support for 15 days. A 5 French UVC was inserted at the
2nd hour of life, and by the 3rd day of life, the
infant transitioned to minimal enteral feeding. Between the 12th and
16th days of life, the infant initially diagnosed with NEC due to
symptoms such as decreased stool passage and abdominal distension. The patient
had been on a continuous course of antibiotic treatment throughout the entirety
of his life, commencing on the very first day due to suspected early neonatal
sepsis, followed by nosocomial sepsis during the hospitalization, and persisting
with antibiotic therapy for suspected NEC. The case took a unique turn upon
further evaluation after being referred to our unit. Despite a preliminary NEC
diagnosis, further evaluation revealed umbilical catheter complications, leading
to total parenteral nutrition extravasation. Removal of the catheter, drainage,
and antibiotic adjustment resulted in improved clinical outcomes. In neonatal
care, cautious management is vital when dealing with infants exhibiting
abdominal symptoms. A nuanced approach, including differential diagnosis and
careful antibiotic use, is essential.
Effekte einer motivationalen Intervention auf die Wirksamkeit und
Nachhaltigkeit der Sport- und Bewegungstherapie in der stationären
psychiatrischen Versorgung
Authors: Sauer Frank , Schmitz-Buhl Mario , Gouzoulis-Mayfrank Euphrosyne 
Published: May 2024

Zusammenfassung
Ziel Verstärkung und Nachhaltigkeit der Sport- und Bewegungstherapie in
der stationären Depressionsbehandlung.
Methodik Randomisierte kontrollierte Studie mit 3 Messzeitpunkten:
t0 Aufnahme in die Studie, t1 nach vier Wochen,
t2 zwei Monate nach Entlassung. Es wurden 96 stationäre Patienten
mit depressiver Störung (ICD-10 F32, F33) randomisiert einer Interventionsgruppe
(IG) oder einer Kontrollgruppe (KG) zugeteilt. Zusätzlich zur Sport- und
Bewegungstherapie (KG) erhielt die IG eine edukative und motivationsfördernde
Sitzung zur Bedeutung von Sport und Bewegung sowie ein motivationsförderndes
Abschlussgespräch.
Ergebnisse Die Ausdauerleistungsfähigkeit und die körperliche Fitness
verbesserten sich über die 3 Messzeitpunkte in der IG deutlicher als in der KG.
Das motivationale Abschlussgespräch wurde als hilfreicher bewertet.
Diskussion Die Intervention wurde von den Patienten gut angenommen und
konnte die Wirkungen der Sport- und Bewegungstherapie teilweise verstärken. Es
wurden nicht nur psychische Aspekte der Depressionsbehandlung beeinflusst,
sondern auch messbare physische Effekte.
Schlussfolgerung Die praxistaugliche und zeiteffiziente motivationale
Intervention kann in der stationären psychiatrischen Versorgung die Sport- und
Bewegungstherapie für depressive Patienten sinnvoll ergänzen.
N-Alkyl-1,2,4-triazole–Borane Complexes as High-Density Hypergolic Materials
Authors: He Chunlin , Jia Hongfu , Ma Wenqi , Chang Jinjie 
Published: May 2024

AbstractHydrazine and its derivatives have served as a conventional bipropellant fuel for several decades. However, their extremely acute toxicity and carcinogenicity, high volatility, and environmental impact have attracted significant attention. In order to synthesize green bipropellant fuels with high density, high specific impulse, and good thermal stability, three novel N-alkyl-1,2,4-triazole–borane complexes were successfully synthesized by reacting alkylated 1,2,4-triazole coordinated with sodium borohydride in the presence of ammonium sulfate. During the droplet test with white fuming nitric acid, there was a relatively short ignition delay time of 98 ms. Additionally, these hypergolic fuels possessed a high density exceeding 1.10 g cm–3, and the specific impulse is ranging from 187 to 199 s, and the highest decomposition temperature reaches 153.4 °C. These results demonstrate their great potential as hypergolic fuels or hypergolic ionic liquid additives in the field of hypergolic materials.
Rehabilitation Program for Postlaryngectomy Patients Following Ileocolon Flap Transfer for Voice Reconstruction: An Essential Part of Success
Authors: Lin Kai-Yuan Katie , Huang Chi-wen , Chen Shih-Heng , Lee Jian-Jr , Chen Hung-chi 
Published: May 2024

Abstract
Background Speech restoration is important for communication and social activities after pharyngolaryngectomy in head and neck cancer or corrosive injury. Several techniques of voice restoration have been developed to improve life quality. The aim of this paper was to focus on the microsurgical transfer of ileocolon flap and outcome of further voice rehabilitation.
Patients and Methods From 2010 to 2022, 69 patients had ileocolon flap at our hospital with postoperative speech training and regular follow-up for over 1 year. The patients received deglutition training first, followed by voice rehabilitation. Voice outcomes were evaluated at an interval of 3 months and finally at 12 months of voice training rehabilitation. Among other examinations, the speech function was evaluated using a 4-point Likert scale and senior surgeon (H-c.C.) scoring system.
Results The results showed that speech function reached 13.1% of excellent voice, 65.1% of good voice, 13.1% of fair result, and 8.7% of poor result by Likert scales. Meanwhile, the senior surgeon (H-c.C.) score showed 17.4% of excellent, 63.8% of moderate, and 18.8% of poor results. About voice laboratory results, maximal phonation time was 11.0 seconds, and the average number counted in one breath was 15. Loudness and frequency showed 56.0 dB and 105.0 Hz, respectively.
Conclusion The study showed that after voice reconstruction with ileocolon flap followed by the voice rehabilitation program, the patients would have a better understanding of the altered anatomical structures and practice in a more efficient way. Adequate recommendation by the therapists to plastic surgeons for revision surgeries optimized voice function of the patients.
One-Pot Synthesis of Diverse Anion-Binding Macrocycles
Authors: Madhavan Nandita , Baliarsingh Biswaranjan 
Published: May 2024

AbstractA one-pot synthetic protocol to access a diverse library of diamide–diester macrocycles from the same starting materials is reported. The molecular symmetry can be readily tuned based on the reaction sequence, while the core structure can be varied using amino acids and aromatic building blocks. The first class of macrocycles with C2 axes in their molecular plane were obtained in 24 h with 40–70% yield, while another class with C2 axes perpendicular to the plane were synthesized in 18 h in 10–30% yield. The phenyl- and serine-derived macrocycles of the first class could bind acetate, chloride, and phosphate ions. These macrocycles can be functionalized with hydrophobic groups and potentially be used as ion transporters.
A Convergent Approach to the Forskolin Skeleton
Authors: Ononiwu Fortune O. , Wang Bo , Totah Nancy I. 
Published: May 2024

AbstractA convergent approach to the forskolin skeleton is described. Assembly of a simplified tricyclic framework is achieved in a single step via the dihydropyrone Diels–Alder reaction. Selective manipulation of the resulting cycloadduct, in conjunction with an unusual equilibration of the C8 stereocenter, provides access to scaffolds that differ in relative stereochemistry at both the A/B and B/C ring junctions.
Environmental Homeopathy: Homeopathic Potencies Regulate the Toxicity and Growth of Raphidiopsis raciborskii (Cyanobacteria) and can be Tracked Physico-Chemically. Part 1: Biological Results
Authors: Mohammad Suham Nowrooz , Pinto Andreia Adelaide G. , Silva Rodrigo Augusto da , Suffredini Ivana Barbosa , Tournier Alexander L. , Cartwright Steven J. , Yunes João Sarkis , Bonamin Leoni V. 
Published: May 2024

Abstract
Introduction Cyanobacteria are microorganisms found in many parts of the world and several genera, such as Raphidiopsis raciborskii, are producers of cyanotoxins. Homeopathic potencies have been found to modulate toxicity in different biological models, and the present study endeavors to discover whether this might also be the case with cyanobacteria.
Objectives Our objective was to investigate the possible effects of homeopathic potencies on the resilience of Artemia franciscana (brine shrimp) embryos to saxitoxin (STX; cyanotoxin) and on controlling the growth of R. raciborskii in vitro.
Method A. franciscana cysts were cultivated in seawater in 96-well plates to evaluate the hatching rate and vitality, plus the gene expression of heat shock proteins (HSPs), after being challenged with R. raciborskii extract containing 2.5 µg/L of STX and treated with different homeopathic potencies. Untreated wells were used as controls (“base-line”). Potencies were chosen from a screening process based on seven selected homeopathic preparations according to the similitude of STX symptoms (Sulphur, Zincum metallicum, Nitric acidum, Plumbum metallicum, Mercurius solubilis, Phosphoric acidum, Isotherapic from R. raciborskii extract; all at 6cH, 30cH and 200cH). Cultures of R. raciborskii maintained in an artificial seawater medium were equally treated with screened homeopathic potencies selected from the same list but specifically for their growth control as a function of time.
Results A 15% lower rate of hatching of A. franciscana cysts was observed after treatment with Nitric acidum 6cH in comparison with baseline (p = 0.05). A complete toxicity reversal was seen after treatment with Isotherapic 200cH, with a 23-fold increase of Hsp 26 gene expression (p = 0.023) and a 24-fold increase of p26 gene expression (p ≤ 0.001) in relation to baseline. Nitric acidum 200cH and Mercurius solubilis 30cH limited the exponential growth of cyanobacteria up to 95% and 85% respectively (p ≤ 0.003) in relation to baseline. Succussed water presented only a transitory 50% inhibition effect.
Conclusion Isotherapic 200cH improved A. franciscana bioresilience to STX; Nitric acidum 200cH and Mercurius solubilis 30cH showed the optimal performance on limiting R. raciborskii growth. The results point to the potential of homeopathic potencies to mitigate environmental problems related to water quality.