bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated machine learning model for fundus image classification by health-care professionals with no coding experience
Authors: Zago Ribeiro Lucas , Nakayama Luis Filipe , Malerbi Fernando Korn , Regatieri Caio Vinicius Saito
Published: May 2024

To assess the feasibility of code-free deep learning (CFDL) platforms in the prediction of binary outcomes from fundus images in ophthalmology, evaluating two distinct online-based platforms (Google Vertex and Amazon Rekognition), and two distinct datasets. Two publicly available datasets, Messidor-2 and BRSET, were utilized for model development. The Messidor-2 consists of fundus photographs from diabetic patients and the BRSET is a multi-label dataset. The CFDL platforms were used to create deep learning models, with no preprocessing of the images, by a single ophthalmologist without coding expertise. The performance metrics employed to evaluate the models were F1 score, area under curve (AUC), precision and recall. The performance metrics for referable diabetic retinopathy and macular edema were above 0.9 for both tasks and CFDL. The Google Vertex models demonstrated superior performance compared to the Amazon models, with the BRSET dataset achieving the highest accuracy (AUC of 0.994). Multi-classification tasks using only BRSET achieved similar overall performance between platforms, achieving AUC of 0.994 for laterality, 0.942 for age grouping, 0.779 for genetic sex identification, 0.857 for optic, and 0.837 for normality with Google Vertex. The study demonstrates the feasibility of using automated machine learning platforms for predicting binary outcomes from fundus images in ophthalmology. It highlights the high accuracy achieved by the models in some tasks and the potential of CFDL as an entry-friendly platform for ophthalmologists to familiarize themselves with machine learning concepts.
Radiation-induced DNA double-strand breaks in cortisol exposed fibroblasts as quantified with the novel foci-integrated damage complexity score (FIDCS)
Authors: Radstake Wilhelmina E. , Parisi Alessio , Miranda Silvana , Gautam Kiran , Vermeesen Randy , Rehnberg Emil , Tabury Kevin , Coppes Rob , van Goethem Marc-Jan , Brandenburg Sytze , Weber Ulrich , Fournier Claudia , Durante Marco , Baselet Bjorn , Baatout Sarah
Published: May 2024

Without the protective shielding of Earth’s atmosphere, astronauts face higher doses of ionizing radiation in space, causing serious health concerns. Highly charged and high energy (HZE) particles are particularly effective in causing complex and difficult-to-repair DNA double-strand breaks compared to low linear energy transfer. Additionally, chronic cortisol exposure during spaceflight raises further concerns, although its specific impact on DNA damage and repair remains unknown. This study explorers the effect of different radiation qualities (photons, protons, carbon, and iron ions) on the DNA damage and repair of cortisol-conditioned primary human dermal fibroblasts. Besides, we introduce a new measure, the Foci-Integrated Damage Complexity Score (FIDCS), to assess DNA damage complexity by analyzing focus area and fluorescent intensity. Our results show that the FIDCS captured the DNA damage induced by different radiation qualities better than counting the number of foci, as traditionally done. Besides, using this measure, we were able to identify differences in DNA damage between cortisol-exposed cells and controls. This suggests that, besides measuring the total number of foci, considering the complexity of the DNA damage by means of the FIDCS can provide additional and, in our case, improved information when comparing different radiation qualities.
Angulation and curvature of aortic landing zone affect implantation depth in transcatheter aortic valve implantation
Authors: Gorla Riccardo , Oliva Omar A. , Arzuffi Luca , Milani Valentina , Saitta Simone , Squillace Mattia , Poletti Enrico , Tusa Maurizio , Votta Emiliano , Brambilla Nedy , Testa Luca , Bedogni Francesco , Sturla Francesco
Published: May 2024

In transcatheter aortic valve implantation (TAVI), final device position may be affected by device interaction with the whole aortic landing zone (LZ) extending to ascending aorta. We investigated the impact of aortic LZ curvature and angulation on TAVI implantation depth, comparing short-frame balloon-expanding (BE) and long-frame self-expanding (SE) devices. Patients (n = 202) treated with BE or SE devices were matched based on one-to-one propensity score. Primary endpoint was the mismatch between the intended (HPre) and the final (HPost) implantation depth. LZ curvature and angulation were calculated based on the aortic centerline trajectory available from pre-TAVI computed tomography. Total LZ curvature ($${k}_{LZ,tot}$$

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) were greater in the SE compared to the BE group (P < 0.001 for both). In the BE group, HPost was significantly higher than HPre at both cusps (P < 0.001). In the SE group, HPost was significantly deeper than HPre only at the left coronary cusp (P = 0.013). At multivariate analysis, $${\alpha }_{LZ,Distal}$$

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was the only independent predictor (OR = 1.11, P = 0.002) of deeper final implantation depth with a cut-off value of 17.8°. Aortic LZ curvature and angulation significantly affected final TAVI implantation depth, especially in high stent-frame SE devices reporting, upon complete release, deeper implantation depth with respect to the intended one.
Validity and reliability of the heart failure-specific health literacy scale in Turkish
Authors: Kalkim Asli , Karaman Emine , Birdal Oğuzhan , Tosun Taşar Pinar
Published: May 2024

Inadequate health literacy is common among adults with HF. The disease management process in HF closely depends on health literacy. No questionnaire is used to assess health literacy among Turkish patients with heart failure. This study aimed to determine the validity and reliability of the Turkish form of the ‘Heart Failure-Specific Health Literacy Scale’. The research is a methodological study design. The study was conducted at the cardiology clinic between May and July 2021, located in the eastern part of Türkiye. The study sample consisted of 121 patients with HF. Data were collected using the Personal Information Form and the Heart Failure-Specific Health Literacy Scale. The patients’ mean age was 62.88 ± 12.55 and 66.9% were men. Based on the factor analysis, three factors with eigenvalue above 1 have been identified. These model has been determined as x2 = 80.209, sd = 49 and p = 0.003. The fit indices were as follows: x2/SD = 1.637; RMSEA = 0.073, GFI = 0.90, CFI = 0.94, IFI = 0.95, TLI = 0.92 and NFI = 0.87. The scale has a total Cronbach’s alpha of 0.66. With test–retest analysis, it was determined that it had a good, positive and significant correlation in terms of both the scale and its sub-dimensions. The Turkish form of the form is a valid and reliable tool.
Predicting suitable habitat for the endangered tree Ormosia microphylla in China
Authors: Wei Lijuan , Wang Guohai , Xie Chunping , Gao Zequn , Huang Qinying , Jim C. Y.
Published: May 2024

Climate change has significantly influenced the growth and distribution of plant species, particularly those with a narrow ecological niche. Understanding climate change impacts on the distribution and spatial pattern of endangered species can improve conservation strategies. The MaxEnt model is widely applied to predict species distribution and environmental tolerance based on occurrence data. This study investigated the suitable habitats of the endangered Ormosia microphylla in China and evaluated the importance of bioclimatic factors in shaping its distribution. Occurrence data and environmental variables were gleaned to construct the MaxEnt model, and the resulting suitable habitat maps were evaluated for accuracy. The results showed that the MaxEnt model had an excellent simulation quality (AUC = 0.962). The major environmental factors predicting the current distribution of O. microphylla were the mean diurnal range (bio2) and precipitation of the driest month (bio14). The current core potential distribution areas were concentrated in Guangxi, Fujian, Guizhou, Guangdong, and Hunan provinces in south China, demonstrating significant differences in their distribution areas. Our findings contribute to developing effective conservation and management measures for O. microphylla, addressing the critical need for reliable prediction of unfavorable impacts on the potential suitable habitats of the endangered species.
Topology optimization of the flat steel shear wall based on the volume constraint and strain energy assumptions under the seismic loading conditions
Authors: Chen Xi , Yan Gongxing , Hosseinzadeh Hasan
Published: May 2024

In structural engineering systems, shear walls are two-dimensional vertical elements designed to endure lateral forces acting in-plane, most frequently seismic and wind loads. Shear walls come in a variety of materials and are typically found in high-rise structures. Because steel shear walls are lighter, more ductile, and stronger than other concrete shear walls, they are advised for usage in steel constructions. It is important to remember that the steel shear wall has an infill plate, which can be produced in a variety of forms. The critical zones in flat steel shear walls are the joints and corners where the infill plate and frame meet. The flat infill plate can be modified to improve the strength and weight performance of the steel shear walls. One of these procedures is Topology Optimization (TO) and this method can reduce the weight and also, increase the strength against the cyclic loading sequences. In the current research paper, the TO of the infill steel plate was considered based on the two methods of volume constraint and maximization of strain energy. Four different volumes (i.e., 60%, 70%, 80%, and 90%) were assumed for the mentioned element in the steel shear wall. The obtained results revealed that the topology configuration of CCSSW with 90% volume constraint presented the highest seismic loading performance. The cumulated energy for this type of SSW was around 700 kJ while it was around 600 kJ for other topology optimization configurations.
The consequences of generative AI for online knowledge communities
Authors: Burtch Gordon , Lee Dokyun , Chen Zhichen
Published: May 2024

Generative artificial intelligence technologies, especially large language models (LLMs) like ChatGPT, are revolutionizing information acquisition and content production across a variety of domains. These technologies have a significant potential to impact participation and content production in online knowledge communities. We provide initial evidence of this, analyzing data from Stack Overflow and Reddit developer communities between October 2021 and March 2023, documenting ChatGPT’s influence on user activity in the former. We observe significant declines in both website visits and question volumes at Stack Overflow, particularly around topics where ChatGPT excels. By contrast, activity in Reddit communities shows no evidence of decline, suggesting the importance of social fabric as a buffer against the community-degrading effects of LLMs. Finally, the decline in participation on Stack Overflow is found to be concentrated among newer users, indicating that more junior, less socially embedded users are particularly likely to exit.
Application of citizen science with the nationwide bird census
Authors: Lee Yerim , Do Yuno , Lineman Maurice , Joo Gea-Jae , Jo Hyunbin
Published: May 2024

Citizen science (CS) is the most effective tool for overcoming the limitations of government and/or professional data collection. To compensate for quantitative limitations of the 'Winter Waterbird Census of Korea', we conducted a total of four bird monitoring via CS from 2021 to 2022. To use CS data alongside national data, we studied CS data quality and improvement utilizing (1) digit-based analysis using Benford’s law and (2) comparative analysis with national data. In addition, we performed bird community analysis using CS-specific data, demonstrating the necessity of CS. Neither CS nor the national data adhered to Benford's law. Alpha diversity (number of species and Shannon index) was lower, and total beta diversity was higher for the CS data than national data. Regarding the observed bird community, the number of species per family was similar; however, the number of individuals per family/species differed. We also identified the necessity of CS by confirming the possibility of predicting bird communities using CS-specific data. CS was influenced by various factors, including the perceptions of the survey participants and their level of experience. Therefore, conducting CS after systematic training can facilitate the collection of higher-quality data
Measurement of the reaction enthalpy of CO2 in aqueous solutions with thermographic and gravimetric methods
Authors: Jung-Fittkau Jessica , Diebold Josef , Kruse Andrea , Deigner Hans-Peter , Schmidt Magnus S.
Published: May 2024

In this work, a new concept for the approximate determination of the reaction enthalpy of the reaction between CO2 and monoethanolamine (MEA) in aqueous solution was developed. For this purpose, a CO2 gas stream was flowed into aqueous MEA solutions with different concentrations of 1 wt%, 2.5 wt% and 7.5 wt%. The weight difference ∆T, which is based on the increase in CO2 bound by the MEA over time, was documented using a thermographic camera. The mass difference ∆m, which is also based on the increase in CO2 bound by the MEA over time, was determined using a balance. By determining ∆T and ∆m, an approximate calculation of the reaction enthalpy is possible. The deviation from the values from the data known from the literature was less than 5% in all experiments.
The dynamics of functional brain network segregation in feedback-driven learning
Authors: Wang Xiaoyu , Zwosta Katharina , Hennig Julius , Böhm Ilka , Ehrlich Stefan , Wolfensteller Uta , Ruge Hannes
Published: May 2024

Prior evidence suggests that increasingly efficient task performance in human learning is associated with large scale brain network dynamics. However, the specific nature of this general relationship has remained unclear. Here, we characterize performance improvement during feedback-driven stimulus-response (S-R) learning by learning rate as well as S-R habit strength and test whether and how these two behavioral measures are associated with a functional brain state transition from a more integrated to a more segregated brain state across learning. Capitalizing on two separate fMRI studies using similar but not identical experimental designs, we demonstrate for both studies that a higher learning rate is associated with a more rapid brain network segregation. By contrast, S-R habit strength is not reliably related to changes in brain network segregation. Overall, our current study results highlight the utility of dynamic functional brain state analysis. From a broader perspective taking into account previous study results, our findings align with a framework that conceptualizes brain network segregation as a general feature of processing efficiency not only in feedback-driven learning as in the present study but also in other types of learning and in other task domains.
Greening the physical recycling of HDPE: dissolution precipitation with natural solvents
Authors: Aparício Sofia C. , Castro Pedro M. , Ribeiro Bernardo D. , Marrucho Isabel M.
Published: May 2024

The selective dissolution of HDPE with a green solvent allows its simple and sustainable separation from other polymers, e.g. PET.
RSM optimization of Friedel–Crafts C-acylation of para-fluorophenol over the catalysis of phosphomolybdic acid encapsulated in MIL-53 (Fe) metal organic frameworks
Authors: Nikseresht Ahmad , Mehravar Reza , Mohammadi Masoud
Published: May 2024

In this research, a heterogeneous acid catalyst was synthesized by room temperature encapsulation of phosphomolybdic acid (PMA) in the pores of the MIL-53 (Fe) metal organic framework (MOF) under ultrasonic conditions.
Hydroxypyridinone based chelators: a molecular tool for fluorescence sensing and sensitization
Authors: Singh Shalini , Kumari Neha , Kanungo B. K. , Baral Minati
Published: May 2024

This review describes the chemistry of new HOPO based chelators and their complexes in terms of their use as sensors and sensitizers.
Solvent-free transformation of protic ionic liquids into zwitterions
Authors: Nakazono Yosuke , Inoue Ryota , Sumitani Ryo , Mochida Tomoyuki
Published: May 2024

Protic ionic liquids containing a vinyl-sulfonylamide anion catalytically transformed into zwitterions upon addition of a base under solvent-free conditions.
Local force constants and charges of the nitrosyl ligand in photoinduced NO linkage isomers in a prototypical ruthenium nitrosyl complex
Authors: Mikhailov Artem A. , Gansmüller Axel , Konieczny Krzysztof A. , Pillet Sébastien , Kostin Gennadiy , Klüfers Peter , Woike Theo , Schaniel Dominik
Published: May 2024

Photoinduced NO linkage isomers: total charges on NO are not correlated to the frequency of the NO stretching vibration. Local force constants reveal a significant change in coupling of Ru–N/O and N–O stretching vibrations.
Challenges and opportunities for zeolite-based catalysts in catalytic oxidation of volatile organic compounds
Authors: Zhang Juan , Li Feng , Meng Xiangju , Xiao Feng-Shou
Published: May 2024

Challenges and opportunities for zeolite-based catalysts in catalytic oxidations of volatile organic compounds (VOCs), which have emerged as highly promising materials for the elimination of VOCs due to their unique features.
Controlling the electronic transport through the carbon nanotube junction via the local electronic environment
Authors: Xu Huaguo , Zhao Jianwei , Zhang Liuyue , Liu Lianmei , Cheng Na , He Yuanyuan
Published: May 2024

The nonvertical edges of SWNT-4CH greatly hinder the electronic signature. Removing and replacing edge positions can significantly increase the current. The current through SWNTs is twenty times greater than that through SWNT-4CH.
Th@C2(14)-C86 and Th@C3(18)-C86: two missing C86 isomers stabilized by the encapsulation of thorium
Authors: Qiu Jiawei , Zheng Lihao , Roselló Yannick , Merimi Khaoula , Yao Yang-Rong , Cao Zhengkai , He Zhiwen , Poblet Josep M. , Rodríguez-Fortea Antonio , Chen Ning
Published: May 2024

Two missing C86 isomers, C2(14)-C86 and C3(18)-C86, were successfully stabilized by the encapsulation of thorium.
“Metafining” of nerolidol with a Grubbs-Hoveyda catalyst to generate high-performance sustainable aviation fuels
Authors: Keller C. Luke , Walkling Christopher J. , Zhang Derek D. , Harvey Benjamin G.
Published: May 2024

trans-Nerolidol was converted into high-performance sustainable aviation fuel by a combination of ring-closing olefin metathesis, dehydration, and hydrogenation. The fuels exhibited exceptional gravimetic energy density and low viscosity.
Biomimetic synthesis of single-crystalline anhydrous xanthine nanoplates in an aqueous solution with high reflectivity
Authors: Hou Xiubin , Wang Yingxia , Song Xinbing , Gao Juan , Ma Yurong
Published: May 2024

A synthesis route for bio-inspired rhomboidal xanthine nanoplates similar to biogenic xanthine crystals that exhibit excellent optical properties was reported. The nanoplate crystals are proposed to be anhydrous xanthine with monoclinic symmetry, and the nanoplates mainly expose the (100) plane.
Reduction of dust radial drift by turbulence in protoplanetary disks
Authors: Gerosa Fabiola Antonietta , Bec Jérémie , Méheut Héloïse , Kapoor Anand Utsav
Published: May 2024

Context. Dust particles in protoplanetary disks rotate at velocities exceeding those of the surrounding gas due to a lack of pressure support. Consequently, they experience a headwind from the gas that drives them toward the central star. Radial drift occurs on timescales much shorter than those inferred from disk observations or those required for dust to aggregate and form planets. Additionally, turbulence is often assumed to amplify the radial drift of dust in planet-forming disks when modeled through an effective viscous transport. However, the local interactions between turbulent eddies and particles are known to be significantly more intricate than in a viscous fluid.

Aims. Our objective is to elucidate and characterize the dynamic effects of Keplerian turbulence on the mean radial and azimuthal velocities of dust particles.

Methods. We employed 2D shearing-box incompressible simulations of the gas, which is maintained in a developed turbulent state while rotating at a sub-Keplerian speed. Dust is modeled as Lagrangian particles set at a Keplerian velocity, therefore experiencing a radial force toward the star through drag.

Results. Turbulent eddies are found to reduce the radial drift, while simultaneously enhancing the azimuthal velocities of small particles. This dynamic behavior arises from the modification of dust trajectories due to turbulent eddies.
Galaxies with grains: unraveling dust evolution and extinction curves with hydrodynamical simulations
Authors: Dubois Yohan , Rodríguez Montero Francisco , Guerra Corentin , Trebitsch Maxime , Han San , Beckmann Ricarda , Yi Sukyoung K. , Lewis Joseph , Jang J. K.
Published: May 2024

Dust in galaxies is an important tracer of galaxy properties and their evolution over time. The physical origin of the grain size distribution, the dust chemical composition, and, hence, the associated ultraviolet-to-optical extinctions in diverse galaxies remains elusive. To address this issue, we introduce a model for dust evolution in the RAMSES code for simulations of galaxies with a resolved multiphase interstellar medium. Dust is modelled as a fluid transported with the gas component, and is decomposed into two sizes, 5 nm and 0.1 μm, and two chemical compositions for carbonaceous and silicate grains. This dust model includes the growth of dust by accretion of elements from the gas phase and by the release of dust in stellar ejecta, the destruction by thermal sputtering, supernovae, and astration, and the exchange of dust mass between the two main populations of grain sizes by coagulation and shattering. Using a suite of isolated disc simulations with different masses and metallicities, the simulations can explore the role of these processes in shaping the key properties of dust in galaxies. The simulated Milky Way analogue reproduces the dust-to-metal mass ratio, depletion factors, size distribution and extinction curves of the Milky Way. Galaxies with lower metallicities reproduce the observed decrease in the dust-to-metal mass ratio with metallicity at around a few 0.1 Z⊙. This break in the dust-to-metal ratio corresponds to a galactic gas metallicity threshold that marks the transition from an ejecta-dominated to an accretion-dominated grain growth, and that is different for silicate and carbonaceous grains, with ≃0.1 Z⊙ and ≃0.5 Z⊙ respectively. This leads to more Magellanic Cloud-like extinction curves, i.e. with steeper slopes in the ultraviolet and a weaker bump feature at 2175 Å, in galaxies with lower masses and lower metallicities. Steeper slopes in these galaxies are caused by the combination of the higher efficiency of gas accretion by silicate relative to carbonaceous grains and by the low rates of coagulation that preserves the amount of small silicate grains. Weak bumps are due to the overall inefficient accretion growth of carbonaceous dust at low metallicity, whose growth is mostly supported by the release of large grains in SN ejecta. We also show that the formation of CO molecules is a key component to limit the ability of carbonaceous dust to grow, in particular in low-metallicity gas-rich galaxies.
Mathematical Modeling of Absorption-adsorption Processes for Waste Free Decontamination of Gases from SO2 in a Bubble Tray Column
Authors: Popova-Krumova Petya , Razkazova-Velkova Elena , Boyadjiev Boyan , Boyadjiev Christo
Published: May 2024

Integrated absorption-adsorption for waste free desulfurization of gases from SO2 in a bubble tray column is presented. The method includes physical absorption of SO2 with water and chemical adsorption of HSO3-from the water solution by particles anionite. The two steps method is integrated in one apparatus-a bubble tray column. This method is regenerative and the regeneration is made with solution of ammonium hydroxide. The further step for utilization of the obtained (NH4)2SO3 and (NH4HSO3) is by using HNO3) for production of concentrated SO2 (gas) and NH4NO3 (solution). Convection-diffusion and average concentration models are presented, which are used to describe absorption and adsorption processes. A comparison of the calculated trough the mathematical model and the experimental data is shown.
A Ceph S3 Object Data Store for HEP
Authors: Smith Nick , Jayatilaka Bo , Mason David , Gutsche Oliver , Peisker Alison , Illingworth Robert , Jones Chris
Published: May 2024

In CMS, data access and management is organized around the data tier model: a static definition of what subset of event information is available in a particular dataset, realized as a collection of files. We present a novel data management model that obviates the need for data tiers by exploding files into individual event data product objects. The objects are stored and retrieved through Ceph S3 technology, with a layout designed to minimize data and metadata volume while maximizing data processing parallelism. We demonstrate that this object data format shows promise in reducing total storage requirements while allowing more flexible data access patterns. Performance benchmarks of a prototype data processing framework using this object data format and a test Ceph cluster are presented, showing good scaling behavior in a distributed processing task.
A web workbench system for the Slurm cluster at IHEP
Authors: Du Ran , Shi Jingyan , Jiang Xiaowei , Guo Chaoqi
Published: May 2024

Slurm REST APIs are released since version 20.02. With those REST APIs one can interact with slurmctld and slurmdbd daemons in a REST- ful way. As a result, job submission and cluster status query can be achieved with a web system. To take advantage of Slurm REST APIs, a web workbench system is developed for the Slurm cluster at IHEP. The workbench system con- sists with four subsystems including dashboard, tomato, jasmine and cosmos. The dashboard subsystem is used to display cluster status including nodes and jobs. The tomato subsystem is developed to submit special HTCondor glidein jobs in the Slurm cluster. The jasmine system is used to generate and submit batch jobs based on workload parameters. The cosmos subsystem is an ac- counting system, which not only generates statistical charts but also provides REST APIs to query jobs. This paper presents design and implementation de- tails of the Slurm workbench. With the help of workbench, administrators and researchers can get their work done in an effective way.
An HTTP REST API for Tape-backed Storage
Authors: Afonso João , Caffy Cédric , Patrascoiu Mihai , Leduc Julien , Davis Michael , Murray Steven , Cortes Pablo
Published: May 2024

The goal of the HTTP REST API for Tape project is to provide a simple, minimalistic and uniform interface to manage data transfers between Storage Endpoints (SEs) where the source file is on tape. The project is a collaboration between the developers of WLCG storage systems (EOS+CTA, dCache, StoRM) and data transfer clients (gfal2, FTS).

For some years, HTTP has been growing in popularity as the preferred data transfer protocol between many WLCG SEs. However — unlike other protocols such as XRootD and SRM — HTTP does not include a method to stage files from tape to disk prior to transfer, forcing the use of workarounds such as hybrid protocols (different protocols used for the “stage” and “transfer” parts of the operation). The HTTP REST API offers a simple and consistent solution, by extending the HTTP protocol to include staging operations. It provides clients with a common and consistent API across different storage systems to manage and monitor the disk and tape residency of stored files.

In this contribution, we present the history and motivation of the HTTP REST API project, the specification of version 1 of the API and implementation details in the various storage and data transfer systems. We also describe our experience of its deployment and use for LHC Run-3 operations. We conclude with a discussion of possible future work.
Integration of Rucio Metadata in Belle II
Authors: Serfon Cédric , Panta Anil , Ito Hironori , De Stefano Jr John Steven , Hernández Villanueva Michel , Laycock Paul , Mashinistov Ruslan , Miyake Hideki , Ueda Ikuo
Published: May 2024

Rucio is a Data Management software that has become a de-facto standard in the HEP community and beyond. It allows the management of large volumes of data over their full lifecycle. The Belle II experiment located at KEK (Japan) recently moved to Rucio to manage its data over the coming decade (O(10) PB/year). In addition to its Data Management functionalities, Rucio also provides support for storing generic metadata. Rucio metadata already provides accurate accounting of the data stored all over the sites serving Belle II. Annotating files with generic metadata opens up possibilities for finer-grained metadata query support. We will first introduce some of the new developments aimed at providing good performance that were done to cover Belle II use-cases like bulk insert methods, metadata inheritance, etc. We will then describe the various tests performed to validate Rucio generic metadata at Belle II scale (O(100M) files), detailing the import and performance tests that were made.
Extending Rucio with modern cloud storage support
Authors: Barisits Martin , Barnsley Robert , Barreiro Megino Fernando Harald , Elmsheuser Johannes , Lassnig Mario , Patrascoiu Mihai , Perry James , Serfon Cedric , Vendrell Moya Alba , Wegner Tobias
Published: May 2024

Rucio is a software framework designed to facilitate scientific collaborations in efficiently organising, managing, and accessing extensive volumes of data through customizable policies. The framework enables data distribution across globally distributed locations and heterogeneous data centres, integrating various storage and network technologies into a unified federated entity. Rucio offers advanced features like distributed data recovery and adaptive replication, and it exhibits high scalability, modularity, and extensibility.

Originally developed to meet the requirements of the high-energy physics experiment ATLAS, Rucio has been continuously expanded to support LHC experiments and diverse scientific communities. Recent R&D projects within these communities have evaluated the integration of both private and commercially-provided cloud storage systems, leading to the development of additional functionalities for seamless integration within Rucio. Furthermore, the underlying systems, FTS and GFAL/Davix, have been extended to cater to specific use cases.

This contribution focuses on the technical aspects of this work, particularly the challenges encountered in building a generic interface for self-hosted cloud storage, such as MinIO or CEPH S3 Gateway, and established providers like Google Cloud Storage and Amazon Simple Storage Service. Additionally, the integration of decentralised clouds like SEAL is explored. Key aspects, including authentication and authorisation, direct and remote access, throughput and cost estimation, are highlighted, along with shared experiences in daily operations.
HBase/Phoenix-based Data Collection and Storage for the ATLAS EventIndex
Authors: García Montoro Carlos , Sánchez Javier , Barberis Dario , González de la Hoz Santiago , Salt Jose
Published: May 2024

The ATLAS EventIndex is the global catalogue of all ATLAS real and simulated events. During the LHC long shutdown between Run 2 (20152018) and Run 3 (2022-2025) its components were substantially revised, and a new system was deployed for the start of Run 3 in Spring 2022. The new core storage system is based on HBase tables with a Phoenix interface. It allows faster data ingestion rates and scales better than the old system. This paper describes the data collection, the technical design of the core storage, and the properties that make it fast and efficient, namely the compact and optimized design of the events table, which already holds more than 400 billion entries, and all the auxiliary tables, and the EventIndex Supervisor, in charge of orchestrating the whole data collection, now simplified thanks to the Loaders, the Spark jobs that load the data into the new core system. The extractors, in charge of preparing the pieces of data that the loaders will put into the final back-end, have been updated too. The data migration from HDFS to HBase and Phoenix is also described.
HPC resources for CMS offline computing: An integration and scalability challenge for the Submission Infrastructure
Authors: Pérez-Calero Yzquierdo Antonio , Mascheroni Marco , Kizinevic Edita , Khan Farrukh Aftab , Kim Hyunwoo , Acosta Flechas Maria , Tsipinakis Nikos , Haleem Saqib
Published: May 2024

The computing resource needs of LHC experiments are expected to continue growing significantly during the Run 3 and into the HL-LHC era. The landscape of available resources will also evolve, as High Performance Computing (HPC) and Cloud resources will provide a comparable, or even dominant, fraction of the total compute capacity. The future years present a challenge for the experiments’ resource provisioning models, both in terms of scalability and increasing complexity. The CMS Submission Infrastructure (SI) provisions computing resources for CMS workflows. This infrastructure is built on a set of federated HTCondor pools, currently aggregating 400k CPU cores distributed worldwide and supporting the simultaneous execution of over 200k computing tasks. Incorporating HPC resources into CMS computing represents firstly an integration challenge, as HPC centers are much more diverse compared to Grid sites. Secondly, evolving the present SI, dimensioned to harness the current CMS computing capacity, to reach the resource scales required for the HLLHC phase, while maintaining global flexibility and efficiency, will represent an additional challenge for the SI. To preventively address future potential scalability limits, the SI team regularly runs tests to explore the maximum reach of our infrastructure. In this note, the integration of HPC resources into CMS offline computing is summarized, the potential concerns for the SI derived from the increased scale of operations are described, and the most recent results of scalability test on the CMS SI are reported.
Identifying and Understanding Scientific Network Flows
Authors: Attebury Garhan , Babik Marian , Carder Dale , Chown Tim , Hanushevsky Andrew , Hoeft Bruno , Lake Andrew , Lambert Michael , Letts James , McKee Shawn , Newell Karl , Sullivan Tristan
Published: May 2024

The High-Energy Physics (HEP) and Worldwide LHC Computing Grid (WLCG) communities have faced significant challenges in understanding their global network flows across the world’s research and education (R&E) networks. This article describes the status of the work carried out to tackle this challenge by the Research Technical Networking Working Group (RNTWG) and the Scientific Network Tags (Scitags) initiative, including the evolving framework and tools, as well as our plans to improve network visibility before the next WLCG Network Data Challenge in early 2024. The Scitags initiative is a long-term effort to improve the visibility and management of network traffic for data-intensive sciences. The efforts of the RNTWG and Scitags initiatives have created a set of tools, standards, and proof-of-concept demonstrators that show the feasibility of identifying the owner (community) and purpose (activity) of network traffic anywhere in the network.
Testing framework and monitoring system for the ATLAS EventIndex
Authors: Cherepanova Elizaveta , Gallas Elizabeth J. , Prokoshin Fedor , Villaplana Pérez Miguel
Published: May 2024

The ATLAS EventIndex is a global catalogue of the events collected, processed or generated by the ATLAS experiment. The system was upgraded in advance of LHC Run 3, with a migration of the Run 1 and Run 2 data from HDFS MapFiles to HBase tables with a Phoenix interface. Two frameworks for testing functionality and performance of the new system have been developed. There are two types of tests running. First, the functional test that must check the correct functioning of the import chain. These tests run event picking over a random set of recently imported data to see if the data have been imported correctly, and can be accessed by both the CLI and the PanDA client. The second, the performance test, generates event lookup queries on sets of the EventIndex data and measures the response times. These tests enable studies of the response time dependence on the amount of requested data, and data sample type and size. Both types of tests run regularly on the existing system. The results of the regular tests as well as the statuses of the main EventIndex subsystems (services health, loaders status, filesystem usage, etc.) are sent to InfluxDB in JSON format via HTTP requests and are displayed on Grafana monitoring dashboards. In case (part of) the system misbehaves or becomes unresponsive, alarms are raised by the monitoring system.
Improved HLT Framework for Belle II Experiment
Authors: Itoh Ryosuke , Baur Anselm , Park Seokhee , Nakao Mikihiko , Yamada Satoru , Suzuki Soh Y. , Kunigo Takuto , Levit Dmytro
Published: May 2024

The original Belle II HLT framework was formally upgraded replacing the old IPC based ring buffer with the ZeroMQ data transport to overcome the unexpected IPC locking problem. The new framework has been working stably in the beam run so far, but it lacks the capability to recover the processing fault without stopping the on-going data taking. In addition, the compatibility with the offline framework (basf2) was lost which was maintained in the original. In order to solve these, an improved core processing framework is developed based on original basf2, while keeping the existing ZeroMQ data transport between the servers unchanged. A new core framework zmq-basf2 is developed with a lock-free 1-to-N and N-to-1 data transport using the ZeroMQ IPC socket so that it keeps a 100% compatibility with the original ring-buffer based framework. When a processing fault occurs, the affected faulty event is salvaged from the input buffer and sent directly to the output using the ZeroMQ broadcast. The terminated process is automatically restarted without stopping data taking. This contribution describes the detail of the improved Belle II HLT framework with the result of the performance test in the real Belle II DAQ data flow.
Level-3 Trigger for CLAS12 with Artificial Intelligence
Authors: Tyson Richard , Gavalian Gagik , McKinnon Bryan , Ireland David
Published: May 2024

Fast, efficient and accurate triggers are a critical requirement for modern high energy physics experiments given the increasingly large quantities of data that they produce. The CEBAF Large Acceptance Spectrometer (CLAS12) employs a highly efficient electron trigger to filter the amount of data recorded by requiring at least one electron candidate in each event, at the cost of a low purity in electron identification. However, machine learning algorithms are increasingly employed for classification tasks such as particle identification due to their high accuracy and fast processing times. In this proceeding we present recently published work that showed how a convolutional neural network could be deployed as a Level 3 electron trigger at CLAS12. We demonstrate that this AI trigger would achieve a significant data reduction compared to the conventional CLAS12 electron trigger, whilst preserving a 99.5% electron identification efficiency, at nominal CLAS12 beam currents.
Line Segment Tracking in the High-luminosity LHC
Authors: Chang Philip , Elmer Peter , Gu Yanxi , Krutelyov Vyacheslav , Niendorf Gavin , Reid Michael , Venkat Sathia Narayanan Balaji , Tadel Matevz , Vourliotis Emmanouli , Wang Bei , Wittich Peter , Yagil Avraham
Published: May 2024

The Large Hadron Collider (LHC) will be upgraded to Highluminosity LHC, increasing the number of simultaneous proton-proton collisions (pileup, PU) by several-folds. The harsher PU conditions lead to exponentially increasing combinatorics in charged particle tracking, placing a large demand on the computing resources. The projection on required computing resources exceeds the computing budget with the current algorithms running on single-thread CPUs. Motivated by the rise of heterogeneous computing in high-performance computing centers, we present Line Segment Tracking (LST), a highly parallelizeable algorithm that can run efficiently on GPUs and is being integrated to the CMS experiment central software. The usage of Alpaka framework for the algorithm implementation allows better portability of the code to run on different types of commercial parallel processors allowing flexibility on which processors to purchase for the experiment in the future. To verify a similar computational performance with a native solution, the Alpaka implementation is compared with a CUDA one on a NVIDIA Tesla V100 GPU. The algorithm creates short track segments in parallel, and progressively form higher level objects by linking segments that are consistent with genuine physics track hypothesis. The computing and physics performance are on par with the latest, multi-CPU versions of existing CMS tracking algorithms.
MiniDAQ-3: Providing concurrent independent subdetector data-taking on CMS production DAQ resources
Authors: Amoiridis Vassileios , Behrens Ulf , Bocci Andrea , Branson James , Brummer Philipp , Cano Eric , Cittolin Sergio , Da Silva Almeida Da Quintanilha Joao , Darlea Georgiana-Lavinia , Deldicque Christian , Dobson Marc , Dvorak Antonin , Gigi Dominique , Glege Frank , Gomez-Ceballos Guillelmo , Gorniak Patrycja , Gutić Neven , Hegeman Jeroen , Izquierdo Moreno Guillermo , James Thomas Owen , Karimeh Wassef , Kartalas Miltiadis , Krawczyk Rafał Dominik , Li Wei , Long Kenneth , Meijers Frans , Meschi Emilio , Morović Srećko , Orsini Luciano , Paus Christoph , Petrucci Andrea , Pieri Marco , Rabady Dinyar Sebastian , Racz Attila , Rizopoulos Theodoros , Sakulin Hannes , Schwick Christoph , Šimelevičius Dainius , Tzanis Polyneikis , Vazquez Velez Cristina , Žejdl Petr , Zhang Yousen , Zogatova Dominika
Published: May 2024

The data acquisition (DAQ) of the Compact Muon Solenoid (CMS) experiment at CERN, collects data for events accepted by the Level-1 Trigger from the different detector systems and assembles them in an event builder prior to making them available for further selection in the High Level Trigger, and finally storing the selected events for offline analysis. In addition to the central DAQ providing global acquisition functionality, several separate, so-called “MiniDAQ” setups allow operating independent data acquisition runs using an arbitrary subset of the CMS subdetectors.

During Run 2 of the LHC, MiniDAQ setups were running their event builder and High Level Trigger applications on dedicated resources, separate from those used for the central DAQ. This cleanly separated MiniDAQ setups from the central DAQ system, but also meant limited throughput and a fixed number of possible MiniDAQ setups. In Run 3, MiniDAQ-3 setups share production resources with the new central DAQ system, allowing each setup to operate at the maximum Level-1 rate thanks to the reuse of the resources and network bandwidth. Configuration management tools had to be significantly extended to support the synchronization of the DAQ configurations needed for the various setups.

We report on the new configuration management features and on the first year of operational experience with the new MiniDAQ-3 system.
Overview of the HL-LHC Upgrade for the CMS Level-1 Trigger
Authors: Savard Claire
Published: May 2024

The High-Luminosity LHC will open an unprecedented window on the weak-scale nature of the universe, providing high-precision measurements of the standard model as well as searches for new physics beyond the standard model. Such precision measurements and searches require informationrich datasets with a statistical power that matches the high-luminosity provided by the Phase-2 upgrade of the LHC. Efficiently collecting those datasets will be a challenging task, given the harsh environment of 200 proton-proton interactions per LHC bunch crossing. For this purpose, CMS is designing an efficient data-processing hardware trigger (Level-1) that will include tracking information and high-granularity calorimeter information. Trigger data analysis will be performed through sophisticated algorithms such as particle flow reconstruction, including widespread use of Machine Learning. The current conceptual system design is expected to take full advantage of advances in FPGA and link technologies over the coming years, providing a high-performance, lowlatency computing platform for large throughput and sophisticated data correlation across diverse sources.
The ALICE Data Quality Control
Authors: von Haller Barthélémy , Konopka Piotr
Published: May 2024

ALICE (A Large Ion Collider Experiment) has undertaken a major upgrade during the Long Shutdown 2. The increase in the detector data rates, and in particular the continuous readout of the TPC, led to a hundredfold increase in the input raw data, up to 3.5 TB/s. To cope with it, a new common Online and Offline computing system, called O2, has been developed and put in production.

The online Data Quality Monitoring (DQM) and the offline Quality Assurance (QA) are critical aspects of the data acquisition and reconstruction software chains. The former intends to provide shifters with precise and complete information to quickly identify and overcome problems while the latter aims at selecting good quality data for physics analyses. Both DQM and QA typically involve the gathering of data, its distributed analysis by user-defined algorithms, the merging of the resulting objects and their visualization.

This paper discusses the final architecture and design of the Quality Control (QC), which runs synchronously to data taking and asynchronously on the Worldwide LHC Computing Grid. Following the successful first year of data taking with beam, we will present our experience and the lessons we learned, before and after the LHC restart, when monitoring the data quality in a realworld and challenging environment. We will finally illustrate the wide range of usages people make of this system by presenting a few, carefully picked, use cases.