bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstitution of T follicular helper-humoral immune axis with elimination of hepatitis C virus
Authors: Khanam Arshi , Kottilil Shyamasundaran , Wilson Eleanor
Published: November 2020

Exhaustion of Hepatitis C Virus (HCV)-specific T cells and abnormal B cell function is a hallmark of chronic HCV infection. Direct-acting antiviral (DAA) therapies are effective in achieving sustained virologic response (SVR), however, whether successful DAA treatment reconstitute T follicular helper (TFH)-B cell axis in HCV patients is unclear. Here, we aimed to evaluate the immunological changes in global and HCV-specific CD4 + CXCR5 + TFH, CD4 + CXCR5-T and B cells in 20 HCV patients who achieved SVR with Sofosbuvir and Ledipasvir for 12 weeks and compared with 15 healthy controls (HC). Global and HCV-specific CD4 + CXCR5 + TFH, CD4 + CXCR5-T and CD19 + B cells had significant phenotypic and functional reconstitution post DAA therapy. Reconstitution of effector, central and terminally differentiated memory cell population and increased ICOS and BCL6 expression was seen in HCV patients at SVR12. HCV-specific cytokines were also improved post DAA. Exhausted and regulatory B cells were declined whereas memory B cells were expanded post DAA therapy. Importantly, frequencies of TFH cells were significantly associated with HCV RNA reduction, expansion of memory B and plasmablasts, while negatively associated with exhausted/regulatory B cells. Our results demonstrate that SVR with DAA therapy is effective in the reconstitution of phenotypic and functional abnormalities of TFH-B cell axis.
Response of soil fungal communities to continuous cropping of flue-cured tobacco
Authors: Wang Shengnan , Cheng Jiangke , Li Tong , Liao Yuncheng
Published: November 2020

Fungal communities are considered to be critically important for crop health and soil fertility. However, our knowledge of the response of fungal community structure to the continuous cropping of flue-cured tobacco is limited, and the interaction of soil fungal communities under different cropping systems remains unclear. In this study, we comparatively investigated the fungal abundance, diversity, and community composition in the soils in which continuous cropping of flue-cured tobacco for 3 years (3ys), 5 years (5ys), and cropping for 1 year (CK) using quantitative polymerase chain reaction and high-throughput sequencing technology. The results revealed that continuous cropping of flue-cured tobacco changed the abundance of soil fungi, and caused a significant variation in fungal diversity. In particular, continuous cropping increased the relative abundance of Mortierellales, which can dissolve mineral phosphorus in soil. Unfortunately, continuous cropping also increased the risk of potential pathogens. Moreover, long-term continuous cropping had more complex and stabilize network. This study also indicated that available potassium and available phosphorous were the primary soil factors shifting the fungal community structure. These results suggested that several soil variables may affect fungal community structure. The continuous cropping of flue-cured tobacco significantly increased the abundance and diversity of soil fungal communities.
Design and verify a dual modulated metasurface in terahertz range
Authors: Zhong Min
Published: November 2020

A single peak tunable metasurface absorber is proposed and verified in Terahertz (THz) range. This absorption peak is excited by the localized surface plasma (LSP) and dielectric loss modes at resonance frequency 2.98 THz with 83% of amplitude. Three groups of experiments are performed to verify the sensing properties of samples. In the first groups of experiments, temperature is increasing from T = 300 k to T = 400 k, which leads to the absorption peak enhance from 83% (at 2.98 THz) to 93.7% (at 3.5 THz). In the second groups of experiments, samples are covered by ethanol or chloroform (T = 300 k), this absorption peak is also increased and moved to higher frequencies. When temperature and liquid layer are changed simultaneously, samples achieve more intense resonance behaviors in a smaller temperature scale. Finally, this absorption peak is reduced by increasing pump fluence. This proposed tunable metasurface absorber reveals the feasibility of sensing field.
The expression of circadian clock genes in Daphnia magna diapause
Authors: Schwarzenberger Anke , Chen Luxi , Weiss Linda C.
Published: November 2020

Diapause is a mechanism necessary for survival in arthropods. Often diapause induction and resurrection is light-dependent and therefore dependent on the photoperiod length and on the number of consecutive short-days. In many organisms, including the microcrustaceanDaphnia magna, one functional entity with the capacity to measure seasonal changes in day-length is the circadian clock. There is a long-standing discussion that the circadian clock also controls photoperiod-induced diapause. We tested this hypothesis inD. magna, an organism which goes into a state of suspended animation with the shortening of the photoperiod. We measured gene expression of clock genes in diapause-destined embryos ofD. magnain the initiation, resting and resurrection phases and checked it against gene expression levels of continuously developing embryos. We demonstrate that some genes of the clock are differentially expressed during diapause induction but not during its maintenance. Furthermore, the photoreceptor genecry2and the clock-associated genebrpare highly expressed during induction and early diapause, probably in order to produce excess mRNA to prepare for immediate resurrection. After resurrection, both types of embryos show a similar pattern of gene expression during development. Our study contributes significantly to the understanding of the molecular basis of diapause induction, maintenance and termination.
Chemical compounds with a neuroprotective effect from the seeds of Celosia argentea L.
Authors: Guo Jinggong , Shen Shan , Zhang Xiao , Wang Guoying , Lu Yiqing , Liu Xiping , Wang Shuyun , Li Qin , Cong Yue , Shi Bingyang
Published: November 2020

Compounds isolated from Semen Celosiae are potent inhibitors of neuron injury via inhibition of oxidative stress and apoptosis, and activation of autophagy.
The effect of black tea supplementation on blood pressure: a systematic review and dose–response meta-analysis of randomized controlled trials
Authors: Ma Chang , Zheng Xuehui , Yang Yi , Bu Peili
Published: November 2020

The main goal of this work was to clarify the effects of black tea supplementation on blood pressure by performing a systematic review according to the PRISMA guidelines, followed by a dose–response meta-analysis of randomized controlled trials.
Isoleucine increases muscle mass through promoting myogenesis and intramyocellular fat deposition
Authors: Liu Shuge , Sun Yunmei , Zhao Rui , Wang Yingqian , Zhang Wanrong , Pang Weijun
Published: November 2020

Isoleucine (Ile), as a branched-chain amino acid (BCAA), has a vital role in regulating body weight and muscle protein synthesis.
The formation principle of micro-droplets induced by using optical tweezers
Authors: Zhai Cong , Hu Chunguang , Li Shuai , Ma Yanhua , Zhang Yajing , Guo Tong , Li Hongbin , Hu Xiaotang
Published: November 2020

A novel method of micro-droplet generation induced by using optical tweezers is proposed; the mechanism is verified through experiments and simulation.
Band structure tuning of α-MoO3 by tin intercalation for ultrafast photonic applications
Authors: Lin Jiamei , Chen Hualong , Ma Dingtao , Gong Youning , Li Zhongjun , Li Delong , Song Yufeng , Zhang Feng , Li Jianqing , Wang Hongcheng , Zhang Yupeng , Zhang Han
Published: November 2020

Atomic intercalation is an effective way to enhance the nonlinear optical properties of α-MoO3.
Dual-faced borax mediated synthesis of self-healable hydrogels merging dynamic covalent bonding and micellization
Authors: Li Xiaohui , Mutlu Hatice , Fengler Christian , Wilhelm Manfred , Theato Patrick
Published: November 2020

A facile route towards multifunctional hydrogels was proposed via borax catalyzed thiol-acrylate and borax–diol chemistry. The hydrogels exhibited self-healable ability and anti-fatigue property by merging dynamic boronate ester bonds and micellization in one system.
Facile fabrication of BiOCl nanoplates with high exposure {001} facets for efficient photocatalytic degradation of nitro explosives
Authors: Yan Jing , Jin Bo , Zhao Ping , Peng Rufang
Published: November 2020

BiOCl nanoplates with highly exposed {001} facets displayed excellent photocatalytic activity on the degradation of nitro explosives.
Regioselective benzoylation of unprotected β-glycopyranosides with benzoyl cyanide and an amine catalyst – application to saponin synthesis
Authors: Li Tianlu , Li Tong , Sun Yajing , Yang Yue , Lv Panpan , Wang Fengshan , Lou Hongxiang , Schmidt Richard R. , Peng Peng
Published: November 2020

Regioselective protection of trans-trans triol and tetrol moieties in carbohydrates was achieved with BzCN as the benzoylating agent and amine catalysts. The protocols are useful for the chemical synthesis of oligosaccharides and saponins.
The effect of alcohols as vehicles on the percutaneous absorption and skin retention of ibuprofen modified with l-valine alkyl esters
Authors: Ossowicz Paula , Klebeko Joanna , Janus Ewa , Nowak Anna , Duchnik Wiktoria , Kucharski Łukasz , Klimowicz Adam
Published: November 2020

The effect of various alcohols as vehicles on skin permeability was compared for unmodified ibuprofen (IBU) and ion pairs of ibuprofen with l-valine alkyl esters [ValOR][IBU], in which the alkyl chain R was changed from C1 to C8.
Room temperature synthesis of BiOBr1−xIx thin films with tunable structure and conductivity type for enhanced photoelectric performance
Authors: Jia Huimin , Li Yuxing , Mao Yuanyang , Yu Dufei , He Weiwei , Zheng Zhi
Published: November 2020

The significantly improved photoelectric conversion performance of the BiOBr1−xI0.5x film is due to the more efficient photoinduced carrier separation and transfer, longer carrier lifetime and stronger absorption in the visible light region.
Reactive crystallization: a review
Authors: McDonald Matthew A. , Salami Hossein , Harris Patrick R. , Lagerman Colton E. , Yang Xiaochuan , Bommarius Andreas S. , Grover Martha A. , Rousseau Ronald W.
Published: November 2020

Reactive crystallization is not new, but there has been recent growth in its use as a means of improving performance and sustainability of industrial processes.
C–H functionalization reactions enabled by hydrogen atom transfer to carbon-centered radicals
Authors: Sarkar Sumon , Cheung Kelvin Pak Shing , Gevorgyan Vladimir
Published: November 2020

Intramolecular and intermolecular HAT to C-centered radicals enables selective C–H functionalization of organic molecules.
Method for accurate experimental determination of singlet and triplet exciton diffusion between thermally activated delayed fluorescence molecules
Authors: Jakoby Marius , Heidrich Shahriar , Graf von Reventlow Lorenz , Degitz Carl , Suresh Subeesh Madayanad , Zysman-Colman Eli , Wenzel Wolfgang , Richards Bryce S. , Howard Ian A.
Published: November 2020

A method for measuring triplet diffusion between TADF molecules is presented, and implications of limited triplet diffusion for OLEDs discussed.
Morphologically controlled rapid fabrication of rhodium sulfide (Rh2S3) thin films for superior and robust hydrogen evolution reaction
Authors: Ehsan Muhammad Ali , Adam Alaaldin , Rehman Abdul , Hakeem Abbas Saeed , Isab Anvarhusein A. , Qamar Mohammad
Published: November 2020

Rh2S3 thin film electrodes prepared by a facile and rapid fabrication route exhibit superior HER catalysis performance in acidic media.
Increasing the active sites and intrinsic activity of transition metal chalcogenide electrocatalysts for enhanced water splitting
Authors: Huang Jingbin , Jiang Yan , An Tianyun , Cao Minhua
Published: November 2020

Strategies for enhancing the electrocatalytic activities of transition metal chalcogenides by increasing the number of active sites and intrinsic activity.
Rational design of poly(ethylene oxide) based membranes for sustainable CO2capture
Authors: Zhu Bin , Jiang Xu , He Shanshan , Yang Xiaobin , Long Jun , Zhang Yanqiu , Shao Lu
Published: November 2020

The separation mechanism and material design of advanced PEO membranes for CO2capture have been reviewed in detail and further directions in this field have been provided.
The assembly of a polymer and metal nanoparticle coated glass capillary array for efficient solar desalination
Authors: Fan Yukang , Wang Shuo , Wang Fei , He Jingxian , Tian Zhuoyue , Zhao Huyang , Zhu Zhaoqi , Sun Hanxue , Liang Weidong , Li An
Published: November 2020

A novel solar steam generator was fabricated by via assembling aof PDA and PDN coated glass capillary array (GCA) that possesses superior salt-resistance.
An overlapped electron-cloud model for the contact electrification in piezo-assisted triboelectric nanogeneratorsviacontrol of piezoelectric polarization
Authors: Koay Jason Soon Chye , Gan Wee Chen , Soh Arn Er , Cheong Jian Ye , Aw Kean Chin , Velayutham Thamil Selvi
Published: November 2020

An enhanced contact electrification process in P-TENGs caused by piezoelectric polarization.
The progress on aluminum-based anode materials for lithium-ion batteries
Authors: Wang Haidong , Tan Hengfeng , Luo Xinyuan , Wang Hui , Ma Ting , Lv Miao , Song Xiaolan , Jin Shengming , Chang Xinghua , Li Xingguo
Published: November 2020

This review elaborates on the decay mechanism of aluminum anodes from five different aspects and their modification from four different aspects.
Neural tissue engineering: the influence of scaffold surface topography and extracellular matrix microenvironment
Authors: Yang Chun-Yi , Huang Wei-Yuan , Chen Liang-Hsin , Liang Nai-Wen , Wang Huan-Chih , Lu Jiaju , Wang Xiumei , Wang Tzu-Wei
Published: November 2020

Strategies using surface topography, contact guidance and biomechanical cues in the design of scaffolds as an ECM support for neural tissue engineering.
A PEGylated alternating copolymeric prodrug of sulfur dioxide with glutathione responsiveness for Irinotecan delivery
Authors: Zhang Yu , Zhang Hongyu , He Pan , Yi Xuan , Liu Xinming , Xiao Chunsheng
Published: November 2020

An enhanced anticancer strategy combining the chemotherapy from Irinotecan with the oxidative damage from a sulfur dioxide polymer prodrug is presented.
Blue-emitting butterfly-shaped donor–acceptor-type 1,3,5,9-tetraarylpyrenes: easily available, low-cost conventional fluorophores for high-performance near ultraviolet electroluminescence with CIEy < 0.05
Authors: Ran Huijuan , Zhao Zhen , Duan Xuewei , Xie Fuli , Han Ruijun , Sun Huaming , Hu Jian-Yong
Published: November 2020

Three donor–acceptor (DA)-type pyrene-based blue emitters with good thermal stability and their applications in NUV OLEDs are demonstrated.
Changes in a Daily Phonotrauma Index After Laryngeal Surgery and Voice Therapy: Implications for the Role of Daily Voice Use in the Etiology and Pathophysiology of Phonotraumatic Vocal Hyperfunction
Authors: Van Stan Jarrad H. , Mehta Daryush D. , Ortiz Andrew J. , Burns James A. , Marks Katherine L. , Toles Laura E. , Stadelman-Cohen Tara , Krusemark Carol , Muise Jason , Hron Tiffiny , Zeitels Steven M. , Fox Annie B. , Hillman Robert E.
Published: November 2020

Purpose

This study attempts to gain insights into the role of daily voice use in the etiology and pathophysiology of phonotraumatic vocal hyperfunction (PVH) by applying a logistic regression-based daily phonotrauma index (DPI) to predict group-based improvements in patients with PVH after laryngeal surgery and/or postsurgical voice therapy.

Method

A custom-designed ambulatory voice monitor was used to collect 1 week of pre- and postsurgery data from 27 female patients with PVH; 13 of these patients were also monitored after postsurgical voice therapy. Normative weeklong data were obtained from 27 matched controls. Each week was represented by the DPI, standard deviation of the difference between the first and second harmonic amplitudes (H1–H2).

Results

Compared to pretreatment, the DPI significantly decreased in the patient group after surgery (Cohen's
d
effect size = −0.86) and voice therapy (
d
= −1.06). The patient group DPI only normalized after voice therapy.

Conclusions

The DPI produced the expected pattern of improved ambulatory voice use across laryngeal surgery and postsurgical voice therapy in a group of patients with PVH. The results were interpreted as providing new objective information about the role of daily voice use in the etiology and pathophysiology of PVH. The DPI is viewed as an estimate of potential vocal fold trauma that relies on combining the long-term distributional characteristics of two parameters representing the magnitude of phonatory forces (neck-surface acceleration magnitude) and vocal fold closure dynamics (H1–H2). Further validation of the DPI is needed to better understand its potential clinical use.
ATLAS Level-1 Endcap Muon Trigger for Run 3
Authors: Mizukami Atsushi
Published: November 2020

The Large Hadron Collider is expected to operate with a centre-ofmass energy of 14 TeV and an instantaneous luminosity of 2.0 1034 cm−2s−1 for Run 3 scheduled from 2021 to 2024. In order to cope with the high event rate, an upgrade of the ATLAS trigger system is required. The level-1 endcap muon trigger system identifies muons with high transverse momentum by combining data from fast muon trigger detectors, called Thin Gap Chambers on the Big Wheel. Inner muon detectors (the Small Wheel and the Tile Calorimeter) coincidence was introduced to reduce fake muon contamination. In the ongoing Phase-1 upgrade the present Small Wheel is replaced with the New Small Wheel and additional Resistive Plate Chambers are installed in the inner region of the ATLAS muon spectrometer for the endcap muon trigger. Precision track information from the new detectors can be used as part of the muon trigger logic to enhance the performance significantly. The trigger processor board, Sector Logic, has been upgraded to handle the additional data from the new detectors. The new Sector Logic board has a modern FPGA to make use of Multi-Gigabit transceiver technology, which is used to receive data from the new detectors. The readout system for trigger data has also been re-designed to minimize the use of custom electronics and instead use commercial computers and network switches, by using TCP/IP for the data transfer. The new readout system uses a software-based data-handling. This paper describes the development of the level-1 endcap muon trigger and its readout system for Run 3.
The upgrade and re-validation of the Compact Muon Solenoid Electromagnetic Calorimeter Control and Safety Systems during the Second Long Shutdown of the Large Hadron Collider at CERN
Authors: Jiménez Estupiñán R. , Adzic P. , Auffray E. , Bailleux D. , Di Calafiori D. , Dissertori G. , Djambazov L. , Fay J. , Jovanovic D. , Lustermann W. , Milenovic P. , Tsirou A. , Veljanovic I. , Verdini P. G. , Zelepoukine S.
Published: November 2020

The Electromagnetic Calorimeter (ECAL) is one of the subdetectors of the Compact Muon Solenoid (CMS), a general-purpose particle detector at the CERN Large Hadron Collider (LHC). The CMS ECAL Detector Control System (DCS) and the CMS ECAL Safety System (ESS) have supported the detector operations and ensured the detector’s integrity since the CMS commissioning phase, more than 10 years ago. Over this long period, several changes to both systems were necessary to correct issues, extend functionality and keep them in-line with current hardware technologies and the evolution of software platforms. Due to the constraints imposed on significant changes to a running system, major hardware and software upgrades were therefore deferred to the second LHC Long Shutdown (LS2). This paper presents the architectures of the CMS ECAL control and safety systems, discusses the ongoing and planned upgrades, details implementation processes and validation methods and highlights the expectations for the post-LS2 systems.
Assessment of the ALICE O2 readout servers
Authors: Costa Filippo , Chapeland Sylvain , Alexopoulos Konstantinos , Fuchs Ulric
Published: November 2020

The ALICE experiment at CERN LHC (Large Hadron Collider) is undertaking a major upgrade during LHC Long Shutdown 2 in 2019-2020. The raw data input from the detector will then increase a hundredfold, up to 3.4 TB/s. In order to cope with such a large throughput, a new Online-Offline com-9 puting system, called O2, will be deployed. The FLP servers (First Layer Pro-10 cessor) are the readout nodes hosting the CRU (Common Readout Unit) cards in charge of transferring the data from the detector links to the computer mem-12 ory. The data then flow through a chain of software components until they are shipped over network to the processing nodes. In order to select a suitable plat-14 form for the FLP (First Level Processor), it is essential that the hardware and the software are tested together. Each candidate server is therefore equipped with multiple readout cards (CRU), one InfiniBand 100G Host Channel Adapter, and the O2 readout software suite. A series of tests are then run to ensure the readout system is stable and fulfils the data throughput requirement of 42Gbps (highest data rate in output of the FLP equipped with three CRUs). This paper presents the software and firmware features developed to evaluate and validate different candidates for the FLP servers. In particular we describe the data flow from the CRU firmware generating data, up to the network card where the buffers are sent over the network using RDMA. We also discuss the testing procedure and the results collected on different servers.
Zero-deadtime processing in beta spectroscopy for measurement of the non-zero neutrino mass
Authors: LaRoque Benjamin
Published: November 2020

The Project 8 collaboration seeks to measure, or more tightly bound, the mass of the electron antineutrino by applying a novel spectroscopy technique to precisely measure the tritium beta-decay spectrum. The current system produces a single analog signal, which is digitized and processed in several stages before being saved to local disk storage. Online processing includes two stages, an FPGA connected to the analog to digital converter reduces the data down to the region of interest before shipping over the local network for further processing and storage. A normal CPU-based processing stage applies triggering logic to only save data at times when a signal is present, further reducing the total volume of data which needs to be written to disk or transferred for long-term storage. The next stage of the project will need to process many input channels and will integrate a necessary aggregation and combination step prior to applying the event search and triggering logic. We present the online processing system which has successfully been deployed for the current, singlechannel, phase. We also present the status and design for a many-channel platform.
The CMS Electromagnetic Calorimeter workflow
Authors: Rovelli Chiara
Published: November 2020

The CMS experiment at the LHC features an electromagnetic calorimeter (ECAL) made of lead tungstate scintillating crystals. The ECAL energy response is fundamental for both triggering purposes and offline analysis. Due to the challenging LHC radiation environment, the response of both crystals and photodetectors to particles evolves with time. Therefore continuous monitoring and correction of the ageing effects are crucial. Fast, reliable and efficient workflows are set up to have a first set of corrections computed within 48 hours from data-taking, making use of dedicated data streams and processing. Such corrections, stored in relational databases, are then accessed during the prompt offline reconstruction of the CMS data. Twice a week, the calibrations used in the trigger are also updated in the database and accessed during the data-taking. In this note, the design of the CMS ECAL data handling and processing is reviewed.
Time measurement with the SND electromagnetic calorimeter
Authors: Druzhinin Vladimir , Korol Aleksandr , Melnikova Natalya , Serednyakov Sergey , Surin Ilya
Published: November 2020

The SND is a non-magnetic detector deployed at the VEPP-2000 e+e− collider (BINP, Novosibirsk) for hadronic cross-section measurements in the center of mass energy range below 2 GeV. The important part of the detector is a three-layer hodoscopic electromagnetic calorimeter (EMC) based on NaI(Tl) counters. Until the recent EMC spectrometric channel upgrade, only the measurement of the energy deposition in counters was possible. New EMC signal digitizing electronics based on FADC allow us to obtain also the signal arrival time. The new electronics and supporting software, including digitized signal processing algorithms, are now used for data taking in the ongoing experiment. We discuss the amplitude and time extraction algorithms, the new system performance on experimental events and how this time measurement can be applied to physics analysis.
Ingest pipeline for ASKAP
Authors: Voronkov Maxim
Published: November 2020

The Australian Square Kilometre Array Pathfinder (ASKAP) is a new generation 36-antenna 36-beam interferometer capable of producing about 2.2 Gb/s of raw data. The data are streamed from the observatory directly to the dedicated small cluster at the Pawsey Supercomputing centre. The ingest pipeline is a distributed real time software which runs on this cluster and prepares the data for further (offline) processing by imaging and calibration pipelines. In addition to its main functionality, it turned out to be a valuable tool for various commissioning experiments and allowed us to run an interim system to achieve the first scientific results much earlier than otherwise possible. I will review the architecture of the ingest pipeline, its role in the overall ASKAP design as well as the lessons learned by developing a real-time application in the HPC environment.
ANaN — ANalyse And Navigate: Debugging Compute Clusters with Techniques from Functional Programming and Text Stream Processing
Authors: Adler Alexander , Kebschull Udo
Published: November 2020

Monitoring is an indispensable tool for the operation of any large installation of grid or cluster computing, be it high energy physics or elsewhere. Usually, monitoring is configured to collect a small amount of data, just enough to enable detection of abnormal conditions. Once detected, the abnormal condition is handled by gathering all information from the affected components. This data is processed by querying it in a manner similar to a database.

This contribution shows how the metaphor of a debugger (for software applications) can be transferred to a compute cluster. The concepts of variables, assertions and breakpoints that are used in debugging can be applied to monitoring by defining variables as the quantities recorded by monitoring and breakpoints as invariants formulated via these variables. It is found that embedding fragments of a data extracting and reporting tool such as the UNIX tool awk facilitates concise notations for commonly used variables since tools like awk are designed to process large event streams (in textual representations) with bounded memory. A functional notation similar to both the pipe notation used in the UNIX shell and the point-free style used in functional programming simplify the combination of variables that commonly occur when formulating breakpoints.
Fast Calorimeter Simulation in ATLAS
Authors: Gasiorowski Sean , Gray Heather
Published: November 2020

The ATLAS physics program at the LHC relies on very large samples of simulated events. Most of these samples are produced with Geant4, which provides a highly detailed and accurate simulation of the ATLAS detector. However, this accuracy comes with a high price in CPU, and the sensitivity of many physics analyses is already limited by the available Monte Carlo statistics and will be even more so in the future as datasets grow. To solve this problem, sophisticated fast simulation tools are developed, and they will become the default tools in ATLAS production in Run 3 and beyond. The slowest component is the simulation of the calorimeter showers. Those are replaced by a new parametrised description of the longitudinal and lateral energy deposits, including machine learning approaches, achieving a fast but accurate description. In this talk we will describe the new tool for fast calorimeter simulation that has been developed by ATLAS, review its technical and physics performance, and demonstrate its potential to transform physics analyses.
DD4hep a community driven detector description for HEP
Authors: Gaede Frank , Frank Markus , Petric Marko , Sailer Andre
Published: November 2020

Detector description is an essential component in simulation, reconstruction and analysis of data resulting from particle collisions in high energy physics experiments and for the detector development studies for future experiments. Current detector description implementations of running experiments are mostly specific implementations. DD4hep [1] is an open source toolkit created in 2012 to serve as a generic detector description solution. The main motivation behind DD4hep is to provide the community with an integrated solution for all these stages and address detector description in a broad sense, including the geometry and the materials used in the device, and additional parameters describing e.g. the detection techniques, constants required for alignment and calibration, description of the readout structures and conditions data. In these proceedings, we will give an overview of the project and discuss recent developments in DD4hep as well as showcase adaptions of the framework by LHC and upcoming accelerator projects together with the road map of future developments.
ATLAS Tile Calorimeter Conditions Database architecture and operations in Run 2
Authors: Smirnov Yuri , Chakraborty Dhiman , Solodkov Alexander , Harkusha Siarhei
Published: November 2020

An overview of the Conditions Database (DB) structure for the hadronic Tile Calorimeter (TileCal), one of the sub-systems of the ATLAS detector at LHC, is presented. ATLAS Conditions DB stores the data on the ORACLE backend, and the design and implementation have been developed using the COOL (Conditions Objects for LCG) software package as a common persistency solution for the storage and management of the conditions data. TileCal conditions and calibration data are stored in 4 separate Databases, each with its own schema: TileCal Online and Offline DBs for data, DB for Monte Carlo simulation and Detector Control System (DCS) DB. In order to ensure smooth operation of the TileCal during data taking, experts perform the necessary calibrations, add the changes of detector status and other conditions data, prepare new conditions for data reprocessing and Monte Carlo production campaigns, and upload the new up-to-date information into DB using custom-made software tools. The procedure of TileCal conditions’ preparation, validation, uploading to DBs is described, and some DB-related statistics collected in Run 2 is presented.
GTS – Garfield-based Triple-GEM Simulator
Authors: Farinelli Riccardo
Published: November 2020

Triple-GEM detectors are gaseous devices used in high energy physics to measure the path of the particles which cross them. The characterisation of triple GEM detectors and the estimation of the performance for real data experiments require a complete comprehension of the mechanisms which transform the passage of one particle in the detector into electric signals, and dedicated MonteCarlo simulations are needed. In this work we will describe GTS (Garfield-based Triple-gem Simulator), a MonteCarlo code which has been developed to simulate the detector response to the passage of particles inside triple GEMs. The software takes into account the processes from the primary ionization up to the signal formation, e.g. avalanche multiplication and the effects of the diffusion in the gas volume. It uses a parametrization of the variables of interest meant to reproduce the same detector response (i.e. the charge distribution at the anode) as provided by Garfield++, a well known software that already performs this kind of simulation more detailed and therefore with a high CPU time consumption. In addition to the detector response, the simulation of the APV-25 electronics is implemented and the output is used to reconstruct the particle position with the Charge Centroid (CC) and the microTime Projection Chamber (µTPC) methods. A comparison of the simulated performance and the one collected in testbeams is used to tune the parameters used in GTS. Results in different conditions of incident angle will be shown.
Generative Adversarial Networks for LHCb Fast Simulation
Authors: Ratnikov Fedor
Published: November 2020

LHCb is one of the major experiments operating at the Large Hadron Collider at CERN. The richness of the physics program and the increasing precision of the measurements in LHCb lead to the need of ever larger simulated samples. This need will increase further when the upgraded LHCb detector will start collecting data in the LHC Run 3. Given the computing resources pledged for the production of Monte Carlo simulated events in the next years, the use of fast simulation techniques will be mandatory to cope with the expected dataset size. Generative models, which are nowadays widely used for computer vision and image processing, are being investigated in LHCb to accelerate generation of showers in the calorimeter and high-level responses of Cherenkov detector. We demonstrate that this approach provides high-fidelity results and discuss possible implications of these results. We also present an implementation of this algorithm into LHCb simulation software and validation tests.
Managing the ATLAS Grid through Harvester
Authors: Barreiro Megino Fernando Harald , Alekseev Aleksandr , Berghaus Frank , Cameron David , De Kaushik , Filipcic Andrej , Glushkov Ivan , Lin FaHui , Maeno Tadashi , Magini Nicolò
Published: November 2020

ATLAS Computing Management has identified the migration of all computing resources to Harvester, PanDA’s new workload submission engine, as a critical milestone for LHC Run 3 and 4. This contribution will focus on the Grid migration to Harvester. We have built a redundant architecture based on CERN IT’s common offerings (e.g. Openstack Virtual Machines and Database on Demand) to run the necessary Harvester and HTCondor services, capable of sustaining the load of O(1M) workers on the Grid per day. We have reviewed the ATLAS Grid region by region and moved as much possible away from blind worker submission, where multiple queues (e.g. single core, multi core, high memory) compete for resources on a site. Instead we have migrated towards more intelligent models that use information and priorities from the central PanDA workload management system and stream the right number of workers of each category to a unified queue while keeping late binding to the jobs. We will also describe our enhanced monitoring and analytics framework. Worker and job information is synchronized with minimal delays to a CERN IT provided ElasticSearch repository, where we can interact with dashboards to follow submission progress, discover site issues (e.g. broken Compute Elements) or spot empty workers. The result is a much more efficient usage of the Grid resources with smart, built-in monitoring of resources.
Nordugrid ARC Datastaging and Cache: Efficiency gains on HPC and cloud resources
Authors: Pedersen Maiken , Konya Balazs , Cameron David , Ellert Mattias , Konstantinov Aleksandr , Smirnova Oxana , Wäänänen Anders
Published: November 2020

The Worldwide LHC Computing Grid (WLCG) is today comprised of a range of different types of resources such as cloud centers, large and small HPC centers, volunteer computing as well as the traditional grid resources. The Nordic Tier 1 (NT1) is a WLCG computing infrastructure distributed over the Nordic countries. The NT1 deploys the Nordugrid ARC-CE, which is non-intrusive and lightweight, originally developed to cater for HPC centers where no middleware could be installed on the worker nodes. The NT1 runs ARC in the native Nordugrid mode which contrary to the Pilot mode leaves jobs data transfers up to ARC. ARCs data transfer capabilities together with the ARC Cache are the most important features of ARC.

In this article we will describe the datastaging and cache functionality of the ARC-CE set up as an edge service to an HPC or cloud resource, and show the gain in efficiency this model provides compared to a traditional pilot model, especially for sites with remote storage.
Distributing User Code with the CernVM FileSystem
Authors: Dykstra Dave , Bhat Shreyas , Box Dennis , Kim Hyun Woo , Levshina Tanya
Published: November 2020

The CernVM FileSystem (CVMFS) is widely used in High Throughput Computing to efficiently distributed experiment code. However, the standard CVMFS publishing tools are designed for a small group of people from each experiment to maintain common software, and the tools are not a good fit for publishing software from numerous users in each experiment. As a result, most user code, such as code to do specific physics analyses, is still sent with every job to the place the job is run. That process is relatively inefficient, especially when the user code is large. To overcome these limitations, we have built a CVMFS user code publication system. This publication system enables users to still submit their code with their jobs but the code is distributed and accessed through the standard CVMFS infrastructure. The user code is automatically deleted from CVMFS after a period of no use. Most of the software for the system is available as a single self-contained open source rpm called cvmfs-user-pub and is available for other deployments.
Beyond X.509: Token-based authentication and authorization in practice
Authors: Ceccanti Andrea , Vianello Enrico , Giacomini Francesco
Published: November 2020

One of the key challenges identified by the HEP R&D roadmap for software and computing is the ability to integrate heterogeneous resources in support of the computing needs of HL-LHC. In order to meet this objective, a flexible Authentication and Authorization Infrastructure (AAI) has to be in place, to allow the secure composition of computing and storage resources provisioned across heterogeneous providers (e.g., Grid, private and commercial Clouds, HPC centers). At CHEP 2018, we presented how a flexible AAI based on modern, standard Web technologies (OpenID Connect, OAuth and JSON Web Tokens) and centered on the INDIGO Identity and Access Management (IAM) service could support the transition of the WLCG infrastructure to a token-based AAI. In the meanwhile, INDIGO IAM has been selected by the WLCG Management Board as the solution that will be adopted by LHC experiments, and is also at the core of the AAI envisioned to support the computing needs of the ESCAPE project. In this contribution, which represents a follow up to last-year plenary talk, we describe the work done recently on the IAM service to support WLCG requirements.
Big data solutions for CMS computing monitoring and analytics
Authors: Ariza-Porras Christian , Kuznetsov Valentin , Legger Federica
Published: November 2020

The CMS computing infrastructure is composed of several subsystems that accomplish complex tasks such as workload and data management, transfers, submission of user and centrally managed production requests. Till recently, most subsystems were monitored through custom tools and web applications, and logging information was scattered over several sources and typically accessible only by experts. In the last year, CMS computing fostered the adoption of common big data solutions based on open-source, scalable, and no-SQL tools, such as Hadoop, InfluxDB, and ElasticSearch, available through the CERN IT infrastructure. Such systems allow for the easy deployment of monitoring and accounting applications using visualisation tools such as Kibana and Grafana. Alarms can be raised when anomalous conditions in the monitoring data are met, and the relevant teams are automatically notified. Data sources from different subsystems are used to build complex workflows and predictive analytics (such as data popularity, smart caching, transfer latency), and for performance studies. We describe the full software architecture and data flow, the CMS computing data sources and monitoring applications, and show how the stored data can be used to gain insights into the various subsystems by exploiting scalable solutions based on Spark.
Production Operations Management System (POMS) for Fermilab Experiments
Authors: Mengel Marc , White Stephen , Podstavkov Vladimir , Wiersma Margherita , Mazzacane Anna , Herner Kenneth
Published: November 2020

The Production Operations Management System (POMS) software allows production teams and analysis groups across multiple Fermilab experiments to launch, modify and monitor large scale campaigns of related Monte Carlo or data processing jobs, and currently manages the majority of production computing of experiments at Fermilab.

POMS provides a web service interface that enables automated job submission on distributed resources according to customers’ requests, as well as subsequent monitoring of those submissions as well as recovery of failed submissions, debugging and record keeping.

POMS interfaces with existing HEP data access, processing, movement and monitoring tools at Fermilab, including Jobsub (for job submission), SAM (for data management), and Landscape (for monitoring), and in combination with them handles the creation of intermediate datasets of files for multistage campaigns.

POMS visualizes these campaigns with an interactive GUI interface. An important feature of POMS is a one-to-one connection between the GUI campaign visualizer and a text based representation of the complete campaign configuration. An extensible library of template campaign configurations is available. The templates are user modifiable and map cleanly to and from the GUI description of the campaign.

This paper will discuss the current usage, history, and some technical details of POMS, as well as planned future extensions, particularly interfacing with Rucio as well as SAM for file movement.
A Lightweight Submission Frontend Toolkit HepJob
Authors: JIANG Xiaowei , Du Ran , Shi Jingyan , Zou Jiaheng , Hu Qingbao
Published: November 2020

A typical HEP Computing Center normally runs at least one batch system. As an example, at IHEP (Institute of High Energy Physics, Chinese Academy of Sciences), we’ve used three batch systems: PBS, HTCondor and SLURM. After running PBS as a local batch system for 10 years, we replaced it by HTCondor (for HTC) and SLURM (for HPC). During that period, problems came up on both user and admin sides.

Introduction of the new batch systems implies necessity for users to acquire additional knowledge specific for every batch system, in particular, batch commands. In some cases, users have to use both HTCondor and SLURM in parallel. Furthermore, HTCondor and SLURM provide more functionality, which means more complicated usage mode, compared to the simple PBS commands. On admin side, HTCondor gives more freedom to users, which brings an additional challenge to site administrators. Site administrators have to find the solutions for many problems: preventing users from requesting the resources they are not allowed to use, checking if the required attributes are correct, deciding where requested resources are located (SLURM cluster, the cluster of the virtual machines, the remote sites, etc).

To meet the above requirements, HepJob was designed and developed. HepJob provides a set of simple user commands, for example: hep_sub, hep_q, hep_rm, etc. In the submission process, HepJob checks all the attributes and ensures all attributes are correct; assigns proper resources to users (the user and group info is obtained from the management database); routes jobs to the target site; performs other steps as required.

Users can start with HepJob very easily and administrators can take the necessary management actions in HepJob.
Adapting ATLAS@Home to trusted and semi-trusted resources
Authors: Cameron David , Garonne Vincent , Millar Paul , Sun Shaojun , Wu Wenjing
Published: November 2020

ATLAS@Home is a volunteer computing project which enables members of the public to contribute computing power to run simulations of the ATLAS experiment at CERN’s Large Hadron Collider. The computing resources provided to ATLAS@Home increasingly come not only from traditional volunteers, but also from data centres or office computers at institutes associated to ATLAS. The design of ATLAS@Home was built around not giving out sensitive credentials to volunteers, which means that a sandbox is needed to bridge data transfers between trusted and untrusted domains. As the scale of ATLAS@Home increases, this sandbox becomes a potential data management bottleneck. This paper explores solutions to this problem based on relaxing the constraints of sending credentials to trusted volunteers, allowing direct data transfer to grid storage and avoiding the intermediate sandbox. Fully trusted resources such as grid worker nodes can run with full access to grid storage, whereas semi-trusted resources such as student desktops can be provided with “macaroons”: time-limited access tokens which can only be used for specific files. The steps towards implementing these solutions as well as initial results with real ATLAS simulation tasks are discussed along with the experience gained so far and the next steps in the project.
Evolution of the WLCG Information Infrastructure
Authors: Andreeva Julia , Anisenkov Alexey , Di Girolamo Alessandro , Forti Alessandra , Jones Stephen , Konya Balazs , McNab Andrew , Paparrigopoulos Panos
Published: November 2020

The WLCG project aimed to develop, build, and maintain a global computing facility for storage and analysis of the LHC data. While currently most of the LHC computing resources are being provided by the classical grid sites, over the last years the LHC experiments have been using more and more public clouds and HPCs, and this trend will certainly continue. The heterogeneity of the LHC computing resources is not limited to the procurement mode. It also implies variety of storage solutions and types of computer architecture which represent new challenges for the topology and configuration description of the LHC computing resources. The WLCG Information infrastructure has to evolve in order to meet these challenges and to be flexible enough to follow technology innovation. It should provide a complete and reliable description of all types of the storage and computing resources to ensure their effective use. This implies changes at all levels, starting from the primary information providers, through data publishing, transportation mechanism and central aggregators. This paper describes the proposed changes in the WLCG Information Infrastructure, their implementation and deployment.