bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling Obesity and Metabolic Diseases by Hydrodynamic Delivery of a Fusion Gene of Exendin-4 and α1 Antitrypsin
Authors: Gao Mingming , Liu Dexi
Published: September 2019

Obesity and associated metabolic comorbidities represent a growing public health problem. In this study, we demonstrate the use of a newly created fusion gene of exendin-4 and α1-antitrypsin to control obesity and obesity-associated metabolic disorders including insulin resistance, fatty liver and hyperglycemia. The fusion gene encodes a protein with exendin-4 peptide placed at the N-terminus of human α-1 antitrypsin, and is named EAT. Hydrodynamic transfer of the EAT gene to mice prevents high-fat diet-induced obesity, insulin resistance and fatty liver development. In diet-induced obese mice, expression of EAT gene induces weight loss, improves glucose homeostasis, and attenuates hepatic steatosis. In ob/ob mice, EAT gene transfer suppresses body weight gain, maintains metabolic homeostasis, and completely blocks fatty liver development. Six-month overexpression of the EAT fusion gene in healthy mice does not lead to any detectable toxicity. Mechanistic study reveals that the resulting metabolic benefits are achieved by a reduced food take and down-regulation of transcription of pivotal genes responsible for lipogenesis and lipid droplet formation in the liver and chronic inflammation in visceral fat. These results validate the feasibility of gene therapy in preventing and restoring metabolic homeostasis under diverse pathologic conditions, and provide evidence in support of a new strategy to control obesity and related metabolic diseases.
Identification and characterization of SEC24D as a susceptibility gene for hepatitis B virus infection
Authors: Jiang Xianzhong , Zhang Bin , Zhao Junsheng , Xu Yi , Han Haijun , Su Kunkai , Tao Jingjing , Fan Rongli , Zhao Xinyi , Li Lanjuan , Li Ming D.
Published: September 2019

Single nucleotide polymorphisms (SNPs) and genes associated with susceptibility to hepatitis B virus (HBV) infection that have been identified by genome-wide association studies explain only a limited portion of the known heritability, indicating more genetic variants remain to be discovered. In this study, we adopted a new research strategy to identify more susceptibility genes and variants for HBV infection. We first performed genetic association analysis of 300 sib-pairs and 3,087 case-control samples, which revealed that 36 SNPs located in 31 genes showed nominal associations with HBV infection in both samples. Of these genes, we selected SEC24D for further molecular analysis according to the following two main lines of evidence. First, a time course analysis of the expression profiles from HBV-infected primary human hepatocytes (PHH) demonstrated that SEC24D expression increased markedly as time passed after HBV infection (P = 4.0 × 10−4). Second, SNP rs76459466 in SEC24D was adversely associated with HBV risk (ORmeta = 0.82; Pmeta = 0.002), which again indicated that SEC24D represents a novel susceptibility gene for HBV infection. Moreover, SEC24D appeared to be protective against HBV infection in vitro. Consistently, we found that SEC24D expression was significantly enhanced in non-infected liver tissues (P = 0.002). We conclude that SEC24D is a novel candidate gene linked to susceptibility to HBV infection.
Photolysis of dimethoxynitrobenzyl-“caged” acids yields fluorescent products
Authors: Vorob’ev Aleksey Yu. , Dranova Tatyana Yu. , Moskalensky Alexander E.
Published: September 2019

Carboxylic acids conjugated with 4,5-dimethoxy-2-nitrobenzyl photoremovable protecting group are well known and widely used for biological studies. In this paper, we study the photolysis of likewise “caged” acetic, caprylic and arachidonic acids. Unexpectedly, we observed huge growth of fluorescence emission at ~430 nm during photolysis. Following further UV irradiation, a product with fluorescence at longer wavelength was formed (470 nm excitation / ~500–600 nm emission). While it may be used to monitor the “uncaging”, these fluorescent products may interfere with widespread dyes such as fluorescein in biomedical experiments. This effect might be negligible if the photolysis products dissolve in the medium. On the other hand, we observed that arachidonic and caprylic acids derivatives self-organize in emulsion droplets in water environment due to long lipophilic chains. Illumination of droplets by UV rapidly induces orange fluorescence excited by 488 nm light. This fluorescence turn-on was fast (~0.1 s) and apparently caused by the accumulation of water-insoluble fluorescent residuals inside droplets. These self-organized lipophilic structures with fluorescence turn-on capability may be of interest for biomedical and other application. We have identified and hypothesized some compounds which may be responsible for the observed fluorescense.
Atomic-scale viscoplasticity mechanisms revealed in high ductility metallic glass films
Authors: Idrissi Hosni , Ghidelli Matteo , Béché Armand , Turner Stuart , Gravier Sébastien , Blandin Jean-Jacques , Raskin Jean-Pierre , Schryvers Dominique , Pardoen Thomas
Published: September 2019

The fundamental plasticity mechanisms in thin freestanding Zr65Ni35 metallic glass films are investigated in order to unravel the origin of an outstanding strength/ductility balance. The deformation process is homogenous until fracture with no evidence of catastrophic shear banding. The creep/relaxation behaviour of the films was characterized by on-chip tensile testing, revealing an activation volume in the range 100–200 Å3. Advanced high-resolution transmission electron microscopy imaging and spectroscopy exhibit a very fine glassy nanostructure with well-defined dense Ni-rich clusters embedded in Zr-rich clusters of lower atomic density and a ~2–3 nm characteristic length scale. Nanobeam electron diffraction analysis reveals that the accumulation of plastic deformation at room-temperature correlates with monotonously increasing disruption of the local atomic order. These results provide experimental evidences of the dynamics of shear transformation zones activation in metallic glasses. The impact of the nanoscale structural heterogeneities on the mechanical properties including the rate dependent behaviour is discussed, shedding new light on the governing plasticity mechanisms in metallic glasses with initially heterogeneous atomic arrangement.
Low-frequency perfect sound absorption achieved by a modulus-near-zero metamaterial
Authors: Shao Chen , Long Houyou , Cheng Ying , Liu Xiaojun
Published: September 2019

We have analytically proposed a mechanism for achieving a perfect absorber by a modulus-near-zero (MNZ) metamaterial with a properly decorated imaginary part, in which the perfect absorption (PA) is derived from the proved destructive interference. Based on the analysis, an ultrathin acoustic metamaterial supporting monopolar resonance at 157 Hz (with a wavelength about 28 times of the metamaterial thickness) has been devised to construct an absorber for low-frequency sound. The imaginary part of its effective modulus can be easily tuned by attentively controlling the dissipative loss to achieve PA. Moreover, we have also conducted the experimental measurement in impedance tube, and the result is of great consistency with that of analytical and simulated ones. Our work provides a feasible approach to realize PA (>99%) at low frequency with a deep-wavelength dimension which may promote acoustic metamaterials to practical engineering applications in noise control.
Surface plasmon resonance immunosensor for label-free detection of BIRC5 biomarker in spontaneously occurring canine mammary tumours
Authors: Jena Subas Chandra , Shrivastava Sameer , Saxena Sonal , Kumar Naveen , Maiti Swapan Kumar , Mishra Bishnu Prasad , Singh Raj Kumar
Published: September 2019

We report detection of Baculoviral inhibitor of apoptosis repeat containing-5 (BIRC5) protein biomarker in dog serum by label-free surface plasmon resonance (SPR) immunosensor. Initially, overexpression of BIRC5 in canine mammary tumour (CMT) tissues was confirmed by real-time PCR. Recombinant BIRC5 was produced and protein specific antibodies developed in guinea pig specifically reacted with native protein in immunohistochemistry and immunocytochemistry. SPR immunosensor was developed by fabricating anti-BIRC5 antibodies on gold sensor disc. The equilibrium dissociation constant, (KD = kd/ka) was 12.1 × 10−12 M; which indicates that antibodies are of high affinity with sensitivity in picomolar range. The SPR assay could detect as low as 6.25 pg/ml of BIRC5 protein in a calibration experiment (r2 = 0.9964). On testing real clinical samples, 95% specificity and 73.33% sensitivity were recorded. The average amount of serum BIRC5 in dogs with CMT was 110.02 ± 9.77 pg/ml; whereas, in non-cancerous disease conditions, 44.79 ± 4.28 pg/ml and in healthy dog sera 30.28 ± 2.99 pg/ml protein was detected. The SPR immunosensor for detection of BIRC5 in dog sera is reported for the first time and this may find prognostic and diagnostic applications in management of CMT. In future, ‘on-site’ sensors can be developed using this technique for near-patient testing.
A Band-Pass Filter Based on Half-Mode Substrate Integrated Waveguide and Spoof Surface Plasmon Polaritons
Authors: Zhao Lei , Li Yuan , Chen Zhao-Min , Liang Xin-Hua , Wang Jun , Shen Xiaopeng , Zhang Qingfeng
Published: September 2019

In this paper, a band-pass filter based on half-mode substrate integrated waveguide (HMSIW) and double-layer spoof surface plasmon polaritons (SSPPs) consisting of two corrugated metal strips is proposed, which can realize band-pass transmission by etching periodic grooves at the top and bottom metal layers of the HMSIW. Moreover, the influences of important parameters on the performance of the proposed band-pass filter are analyzed by parametric study. By changing the key parameters, the low and high cut-off frequency can be controlled independently. The corresponding equivalent circuit of the proposed band-pass filter is put forward to explain the physical mechanism. Compared with the previous structures, this structure features smaller size, wider bandwidth and lower loss. Simulated results show that the proposed band-pass filter achieves a bandwidth (for |S11| < −10 dB and |S21| > −0.8 dB) of about 69.77% (15.6–32.1 GHz). The measured results have good agreements with the simulated ones, which verify that the proposed band-pass filter has good performances and potential applications at the microwave frequencies.
Microdistribution and quantification of the boron neutron capture therapy drug BPA in primary cell cultures of human glioblastoma tumour by NanoSIMS
Authors: Aldossari Samar , McMahon Greg , Lockyer Nicholas P. , Moore Katie L.
Published: September 2019

The ability of secondary ion mass spectrometry (SIMS) to provide high sensitivity imaging of elements and small-medium mass molecules in biological tissues and cells, makes it a very powerful tool for drug distribution studies.
A simple and sensitive fluorescence assay for biothiol and acetylcholinesterase activity detection based on a HSA–AuNCs@Cu2+ complex
Authors: Ge Jia , Qi Zhangyu , Zhang Liangliang
Published: September 2019

A simple and sensitive fluorescent turn-on method for the detection of biothiols and acetylcholinesterase activity was developed based on a HSA–AuNC@Cu2+ complex.
A supramolecular hydrogel with monitorable macro/microscopic shape memory performance
Authors: Wang Wu , Lai Hua , Cheng Zhongjun , Fan Zhimin , Zhang Haiyang , Wang Jinfeng , Yu Songji , Liu Yuyan
Published: September 2019

A supramolecular shape memory hydrogel with monitorable macro/microscopic shape memory performance was prepared through a combination of pH-responsive fluorescent carbon nanoparticles, polyvinyl alcohol and cross-linked polyacrylamide.
Versatile solid forms of boscalid: insight into the crystal structures and phase transformations
Authors: Li Zhonghua , Jia Lina , Shi Peng , Jiang Shuang , Gong Junbo , Wu Songgu
Published: September 2019

The crystal structures of six solid forms of boscalid were reported for the first time and the transformation relationship between different phases was explored in detail.
Molecular dynamics involving proton exchange of a protic ionic liquid–water mixture studied by NMR spectroscopy
Authors: Hasani Mohammad , Nordstierna Lars , Martinelli Anna
Published: September 2019

Detailed characterisation of proton dynamics in proton conducting electrolytes is crucial in the design of improved ones. We focus on proton exchange and its effect on the proton's translational diffusion in search for desirable anomalies.
Allosteric modulation of the sarcoplasmic reticulum Ca2+ATPase by thapsigarginviadecoupling of functional motions
Authors: Saleh Noureldin , Wang Yong , Nissen Poul , Lindorff-Larsen Kresten
Published: September 2019

Thapsigargin binding to the Ca2+-ATPase SERCA induces a conformational change in the transmembrane regions without regulation of the cytoplasmic domains, and causes a conformational change in the cytoplasmic domains uncoupled from nucleotide binding.
Correction: Hydrophobic silane coating films for the inhibition of water ingress into the nanometer pore of calcium silicate hydrate gels
Authors: Yu Jiao , Li Shaochun , Hou Dongshuai , Jin Zuquan , Liu Qing-feng
Published: September 2019

Correction for ‘Hydrophobic silane coating films for the inhibition of water ingress into the nanometer pore of calcium silicate hydrate gels’ by Jiao Yu et al., Phys. Chem. Chem. Phys., 2019, DOI: 10.1039/c9cp03266e.
Environmentally benign process for selective recovery of valuable metals from spent lithium-ion batteries by using conventional sulfation roasting
Authors: Lin Jiao , Liu Chunwei , Cao Hongbin , Chen Renjie , Yang Yongxia , Li Li , Sun Zhi
Published: September 2019

Recycling of spent lithium-ion batteries (LIBs) has attracted intensive attention owing to their potential environmental risk and the importance of the supply of critical metals.
Capacitive behaviour of nanocrystalline octacalcium phosphate (OCP) (Ca8H2(PO4)6·5H2O) as an electrode material for supercapacitors: biosupercaps
Authors: Tuncer Mustafa , Bakan Feray , Gocmez Hasan , Erdem Emre
Published: September 2019

Observing capacitive behavior in an OCP material is quite exciting and may enable or enhance future medical applications, such as biocompatible energy storage and harvesting microdevices.
A rhodium-catalyzed three-component reaction of arylisocyanides, trifluorodiazoethane, and activated methylene isocyanides or azomethine ylides: an efficient synthesis of trifluoroethyl-substituted imidazoles
Authors: Yu Yang , Zhang Yan , Wang Zhuo , Liang Yong-Xin , Zhao Yu-Long
Published: September 2019

A novel method for the synthesis of trifluoroethyl-substituted imidazoles is reported via a rhodium-catalyzed three-component reaction of isocyanides, 2,2,2-trifluorodiazoethane and activated methylene isocyanides or azomethine ylides.
Calcium-induced dissociation of CIB1 from ASK1 regulates agonist-induced activation of the p38 MAPK pathway in platelets
Authors: Patel Pravin , Naik Meghna U. , Golla Kalyan , Shaik Noor F. , Naik Ulhas P.
Published: September 2019

Apoptosis signal-regulating kinase 1 (ASK1) is a mitogen-activated protein kinase kinase kinase (MAPKKK) that regulates activation of the c-Jun N-terminal kinase (JNK)- and p38-stress response pathways leading to apoptosis in nucleated cells. We have previously shown that ASK1 is expressed in platelets and regulates agonist-induced platelet activation and thrombosis. However, the mechanism by which platelet agonists cause activation of ASK1 is unknown. Here, we show that in platelets agonist-induced activation of p38 is exclusively dependent on ASK1. Both thrombin and collagen were able to activate ASK1/p38. Activation of ASK1/p38 was strongly dependent on thromboxane A2 (TxA2) and ADP. Agonist-induced ASK1 activation is blocked by inhibition of phospholipase C (PLC) β/γ activity or by chelating intracellular Ca2+. Furthermore, treatment of platelets with thapsigargin or Ca2+ ionophore robustly induced ASK1/p38 activation. In addition, calcium and integrin-binding protein 1 (CIB1), a Ca2+-dependent negative regulator of ASK1, associates with ASK1 in resting platelets and is dissociated upon platelet activation by thrombin. Dissociation of CIB1 corresponds with ASK1 binding to tumor necrosis factor (TNF) receptor associated factor 6 (TRAF6) and the autophosphorylation of ASK1 Thr838 within the catalytic domain results in full activation of ASK1. Furthermore, genetic ablation of Cib1 in mice augments agonist-induced Ask1/p38 activation. Together our results suggest that in resting platelets ASK1 is bound to CIB1 at low Ca2+ concentrations. Agonist-induced platelet activation causes an increase in intracellular Ca2+ concentration that leads to the dissociation of CIB1 from ASK1, allowing for proper dimerization through ASK1 N-terminal coiled-coil (NCC) domains.
Front-End Electronics Control and Monitoring for the LHCb Upgrade
Authors: Barbosa Joao , Alessio Federico , Cardoso Luis , Gaspar Clara , Durante Paolo
Published: September 2019

The LHCb experiment, one of the four operating in the LHC, will be enduring a major upgrade of its electronics during the third long shutdown period of the particle accelerator. One of the main objectives of the upgrade effort is to implement a 40MHz readout of collision data. For this purpose, the Front-End electronics will make extensive use of a radiation resistant chipset, the Gigabit Transceiver (GBT), for readout as well as for slow control, monitoring and synchronization. At LHCb, the tools to operate the front-end electronics are developed by a central team and distributed to the users. This contribution describes the architecture of the system that implements the slow control and monitoring of all Front-End electronics using the GBT chipset, namely the GBTx and GBT-SCA. The system is implemented in 3 layers starting with an FPGA based electronic board that interfaces the GBT chipset directly through optical fibers. The second layer is composed by a PCIe driver and a number of processes to operate these boards. The user operates the system in the third layer which is the WinCC OA SCADA that is interfaced with the Front-Ends via a message broker called DIM. The requirements of the system as well as the design and integration of each layer are discussed in detail. The results of the firmware implementation in hardware and operational tests are shown and the overall performance of the system is discussed.
Kalman Filter track reconstruction on FPGAs for acceleration of the High Level Trigger of the CMS experiment at the HL-LHC
Authors: Summers Sioni , Rose Andrew
Published: September 2019

Track reconstruction at the CMS experiment uses the Combinatorial Kalman Filter. The algorithm computation time scales exponentially with pileup, which will pose a problem for the High Level Trigger at the High Luminosity LHC. FPGAs, which are already used extensively in hardware triggers, are becoming more widely used for compute acceleration. With a combination of high performance, energy efficiency, and predictable and low latency, FPGA accelerators are an interesting technology for high energy physics. Here, progress towards porting of the CMS track reconstruction to Maxeler Technologies’ Dataflow Engines is shown, programmed with their high level language MaxJ. The performance is compared to CPUs, and further steps to optimise for the architecture are presented.
The ATLAS Muon Trigger
Authors: Hayashida Shota
Published: September 2019

Events containing muons in the final state are important for many physics analyses performed by the ATLAS experiment at the Large Hadron Collider. To collect such events, an efficient and well-understood muon trigger is required. The ATLAS muon trigger consists of a hardware-based and a software-based subsystem. In order to cope with the high luminosity and pileup conditions in Run 2, several improvements have been implemented to suppress the trigger rate while maintaining a high efficiency. Recent improvements include addition of layers in the coincidence of the muon spectrometer and optimisation of a muon trigger isolation requirement, among others. An overview of the algorithms deployed by the ATLAS muon trigger and its performance in 2018 data taking is presented.
DAQBroker - A general purpose instrument monitoring framework
Authors: Dias António , Amorim António , Tomé António , Almeida João
Published: September 2019

The current scientific environment has experimentalists and system administrators allocating large amounts of time for data access, parsing and gathering as well as instrument management. This is a growing challenge since there is an increasing number of large collaborations with significant amount of instrument resources, remote instrumentation sites and continuously improved and upgraded scientific instruments. DAQBroker is a new software framework adopted by the CLOUD experiment at CERN. This framework was designed to monitor CLOUD’s network of various architectures and operating systems and collect data from any instrument while also providing simple data access to any user. Data can be stored in one or several local or remote databases running on any of the most popular relational databases (MySQL, PostgreSQL, Oracle). It also provides the necessary tools for creating and editing the meta data associated with different instruments, perform data manipulation and generate events based on instrument measurements, regardless of the user’s know-how of individual instruments. This submission will present an overview of each of DAQBroker’s components as well as provide preliminary performance results of the application running on high and low performance machines.
Quantum Associative Memory in Hep Track Pattern Recognition
Authors: Shapoval Illya , Calafiura Paolo
Published: September 2019

We have entered the Noisy Intermediate-Scale Quantum Era. A plethora of quantum processor prototypes allow evaluation of potential of the Quantum Computing paradigm in applications to pressing computational problems of the future. Growing data input rates and detector resolution foreseen in High-Energy LHC (2030s) experiments expose the often high time and/or space complexity of classical algorithms. Quantum algorithms can potentially become the lower-complexity alternatives in such cases. In this work we discuss the potential of Quantum Associative Memory (QuAM) in the context of LHC data triggering. We examine the practical limits of storage capacity, as well as store and recall errorless efficiency, from the viewpoints of the state-of-the-art IBM quantum processors and LHC real-time charged track pattern recognition requirements. We present a software prototype implementation of the QuAM protocols and analyze the topological limitations for porting the simplest QuAM instances to the public IBM 5Q and 14Q cloud-based superconducting chips.
The design of a distributed key-value store for petascale hot storage in data acquisition systems
Authors: Cicalese Danilo , Jereczek Grzegorz , Le Goff Fabrice , Lehmann Miotto Giovanna , Love Jeremy , Maciejewski Maciej , Mommsen Remigius K , Radtke Jakub , Schmiegel Jakub , Szychowska Malgorzata
Published: September 2019

Data acquisition systems for high energy physics experiments readout terabytes of data per second from a large number of electronic components. They are thus inherently distributed systems and require fast online data selection, otherwise requirements for permanent storage would be enormous. Still, incoming data need to be buffered while waiting for this selection to happen. Each minute of an experiment can produce hundreds of terabytes that cannot be lost before a selection decision is made. In this context, we present the design of DAQDB (Data Acquisition Database) — a distributed key-value store for high-bandwidth, generic data storage in event-driven systems. DAQDB offers not only high-capacity and low-latency buffer for fast data selection, but also opens a new approach in high-bandwidth data acquisition by decoupling the lifetime of the data analysis processes from the changing event rate due to the duty cycle of the data source. This is achievable by the option to extend its capacity even up to hundreds of petabytes to store hours of an experiment’s data. Our initial performance evaluation shows that DAQDB is a promising alternative to generic database solutions for the high luminosity upgrades of the LHC at CERN.
Operational experience with the new CMS DAQ-Expert
Authors: Andre Jean-Marc , Behrens Ulf , Branson James , Brummer Philipp , Cittolin Sergio , da Silva Gomes Diego , Darlea Georgiana-Lavinia , Deldicque Christian , Demiragli Zeynep , Dobson Marc , Doualot Nicolas , Erhan Samim , Fulcher Jonathan Richard , Gigi Dominique , Gladki Maciej , Glege Frank , Gomez-Ceballos Guillelmo , Hegeman Jeroen , Holzner Andre , Lettrich Michael , Mecionis Audrius , Meijers Frans , Meschi Emilio , Mommsen Remigius K , Morovic Srecko , O´Dell Vivian , Orsini Luciano , Papakrivopoulos Ioannis , Paus Christoph , Petrucci Andrea , Pieri Marco , Rabady Dinyar , Racz Attila , Rapsevicius Valdas , Reis Thomas , Sakulin Hannes , Schwick Christoph , Simelevicius Dainius , Stankevicius Mantas , Vazquez Velez Cristina , Vougioukas Michail , Wernet Christian , Zejdl Petr
Published: September 2019

The data acquisition (DAQ) system of the Compact Muon Solenoid (CMS) at CERN reads out the detector at the level-1 trigger accept rate of 100 kHz, assembles events with a bandwidth of 200 GB/s, provides these events to the high level-trigger running on a farm of about 30k cores and records the accepted events. Comprising custom-built and cutting edge commercial hardware and several 1000 instances of software applications, the DAQ system is complex in itself and failures cannot be completely excluded. Moreover, problems in the readout of the detectors,in the first level trigger system or in the high level trigger may provoke anomalous behaviour of the DAQ systemwhich sometimes cannot easily be differentiated from a problem in the DAQ system itself. In order to achieve high data taking efficiency with operators from the entire collaboration and without relying too heavily on the on-call experts, an expert system, the DAQ-Expert, has been developed that can pinpoint the source of most failures and give advice to the shift crew on how to recover in the quickest way. The DAQ-Expert constantly analyzes monitoring data from the DAQ system and the high level trigger by making use of logic modules written in Java that encapsulate the expert knowledge about potential operational problems. The results of the reasoning are presented to the operator in a web-based dashboard, may trigger sound alerts in the control room and are archived for post-mortem analysis - presented in a web-based timeline browser. We present the design of the DAQ-Expert and report on the operational experience since 2017, when it was first put into production.
Triggering On Hadronic Signatures In The Atlas Experiment-Developments For 2017 And 2018
Authors: Gouveia Emanuel
Published: September 2019

Hadronic signatures are critical to the ATLAS physics program, and are used extensively for both the StandardModel measurements and searches for new physics. These signatures include generic quark and gluon jets, as well
as jets originating from b-quarks or the decay of massive particles (such as electroweak bosons or top quarks). Additionally, missing transverse momentum from non-interacting particles provides an interesting probe in the search for new physics beyond the Standard Model. Developing trigger selections that target these events is a hugechallenge at the LHC due to the enormous rates associated with hadronic signatures. This challenge is exacerbated by the amount of pile-up activity, which continues to grow. In order to address these challenges, several new techniques were developed to significantly improve the potential of the 2017 dataset. An overview of how we triggeron hadronic signatures at the ATLAS experiment is presented, outlining the challenges of hadronic object triggering and describing the improvements performed over the course of the Run 2 LHC data-taking program. The performance in Run 2 data is shown, including demonstrations of the new techniques being used in 2017. We also discuss further critical developments implemented for the rest of Run 2 and their performance in early 2018 data.
Event reconstruction of free-streaming data for the RICH detector in the CBM experiment
Authors: Adamczewski-Musch J. , Akishin P. , Becker K.–H. , Bendarouach J. , Deveaux C. , Dürr M. , Eschke J. , Förtsch J. , Heep J. , Höhne C. , Ivanishchev D. , Kampert K.–H. , Kochenda L. , Kravtsov P. , Kres I. , Lebedev S. , Lebedeva E. , Linev S. , Mahmoud T. , Malaev M. , Michel J. , Miftakhov N. , Niebur W. , Otto J.–H. , Ovcharenko E. , Patel V. , Pauly C. , Pfeifer D. , Riabov Y. , Roshchin E. , Samsonov V. , Tarasenkova O. , Traxler M. , Tyts D. , Vznuzdaev M. , Weber A.A. , Zumbruch P.
Published: September 2019

The Compressed Baryonic Matter (CBM) experiment is a dedicated heavy ion collision experiment at the FAIR facility. It will be one of the first HEP experiments which works in a triggerless mode: data received in the DAQ
from the detectors will not be associated with events by a hardware trigger anymore. All raw data within a giventime period will be collected continuously in containers, so-called time-slices. The task of the reconstruction algorithms is to create events out of this raw data stream. In this contribution, the optimization of the reconstruction software in the RICH detector to the free-streaming data flow is presented. The implementation of ring reconstruction algorithms which use time measurements of the hits as an additional parameter is discussed.
A Web-based control and monitoring system for DAQ applications
Authors: Anisenkov Alexey , Zhadan Daniil , Logashenko Ivan
Published: September 2019

A comprehensive and efficient environment and data
monitoring system is a vital part of any HEP experiment. In this paper we describe the software web-based framework which is currently used by the CMD-3 Collaboration at the VEPP-2000 Collider and partially by the Muon g-2 experiment at Fermilab to monitor the status of data acquisition and the quality of data taken by the experiments. The system is designed to meet typical requirements and cover various use-cases of DAQ applications, starting from the central configuration, slow control data monitoring, data quality monitoring, user-oriented visualization, control of the hardware and DAQ processes, etc. Being an intermediate middleware between the front-end electronics and the DAQ applications the system is focused to provide a high-level coherent view for shifters and experts for robust operations. In particular, it is used to integrate various experiment dependent monitoring modules and tools into a unified Web oriented portal with appropriate access control policy. The paper describes the design and overall architecture of the system, recent developments and the most important aspects of the framework implementation.
Gpu-Based Online Track Reconstruction for the Alice Tpc in Run 3 With Continuous Read-Out
Authors: Rohr David , Gorbunov Sergey , Ole Marten Schmidt , Shahoyan Ruben
Published: September 2019

In LHC Run 3, ALICE will increase the data taking rate significantly to 50 kHz continuous read-out of minimum bias Pb—Pb collisions. The reconstruction strategy of the online-offline computing upgrade foresees a first synchronous online reconstruction stage during data taking enabling detector calibration and data compression, and a posterior calibrated asynchronous reconstruction stage. Many new challenges arise, among them continuous TPC read-out, more overlapping collisions, no a priori knowledge of the primary vertex and of location-dependent calibration in the synchronous phase, identification of low-momentum looping tracks, and sophisticated raw data compression. The tracking algorithm for the Time Projection Chamber (TPC) will be based on a Cellular Automaton and the Kalman filter. The reconstruction shall run online, processing 50 times more collisions per second than today, while yielding results comparable to current offline reconstruction. Our TPC track finding leverages the potential of hardware accelerators via the OpenCL and CUDA APIs in a shared source code for CPUs and GPUs for both reconstruction stages. We give an overview of the status of Run 3 tracking including performance on processors and GPUs and achieved compression ratios.
AlphaTwirl
Authors: Sakuma Tai
Published: September 2019

AlphaTwirl is a Python library that summarizes large event data into multivariate categorical data, which can be regarded as generalizations of histograms. The output can be imported as data frames in R and pandas. With their rich set of data wrangling tools, users can develop flexible and configurable analysis code. The multivariate categorical data loaded as data frames are readily visualized by graphic tools available in R and Python. AlphaTwirl can process event data concurrently with multiple cores or batch systems. Users can extend and customize nearly any functionality of AlphaTwirl with reusable code. AlphaTwirl is released under the BSD license.
Parallelized and Vectorized Tracking Using Kalman Filters with CMS Detector Geometry and Events
Authors: Cerati Giuseppe , Elmer Peter , Gravelle Brian , Kortelainen Matti , Krutelyov Vyacheslav , Lantz Steven , Lefebvre Matthieu , Masciovecchio Mario , McDermott Kevin , Norris Boyana , Reinsvold Hall Allison , Riley Daniel , Tadel Matevž , Wittich Peter , Würthwein Frank , Yagil Avi
Published: September 2019

The High-Luminosity Large Hadron Collider at CERN will be characterized by greater pileup of events and higher occupancy, making the track reconstruction even more computationally demanding. Existing algorithms at the LHC are based on Kalman filter techniques with proven excellent physics performance under a variety of conditions. Starting in 2014, we have been developing Kalman-filter-based methods for track finding and fitting adapted for many-core SIMD processors that are becoming dominant in high-performance systems.

This paper summarizes the latest extensions to our software that allow it to run on the realistic CMS-2017 tracker geometry using CMSSW-generated events, including pileup. The reconstructed tracks can be validated against either the CMSSW simulation that generated the detector hits, or the CMSSW reconstruction of the tracks. In general, the code’s computational performance has continued to improve while the above capabilities were being added. We demonstrate that the present Kalman filter implementation is able to reconstruct events with comparable physics performance to CMSSW, while providing generally better computational performance. Further plans for advancing the software are discussed.
The Data Quality Monitoring Software for the CMS experiment at the LHC: past, present and future
Authors: Azzolini Virginia , Broen van Besien , Bugelskis Dmitrijus , Hreus Tomas , Maeshima Kaori , Javier Fernandez Menendez , Norkus Antanas , James Fraser Patrick , Rovere Marco , Andre Schneider Marcel
Published: September 2019

The Data Quality Monitoring software is a central tool in the CMS experiment. It is used in the following key environments: (i) Online, for real-time detector monitoring; (ii) Offline, for the prompt-offline-feedback and final fine-grained data quality analysis and certification; (iii) Validation of all the reconstruction software production releases; (iv) Validation in Monte Carlo productions. Though the basic structure of the Run1 DQM system remains the same for Run2, between the Run1 and Run2 periods, the DQM system underwent substantial upgrades in many areas, not only to adapt to the surrounding infrastructure changes, but also to provide improvements to meet the growing needs of the collaboration with an emphasis on more sophisticated methods for evaluating data quality. We need to cope with the higher-energy and -luminosity proton-proton collision data, as well as the data from various special runs, such as Heavy Ion runs. In this contribution, we will describe the current DQM software, structure and workflow in the different environments. We then discuss the performance and our experiences with the DQM system in Run2. The main technical challenges which we have encountered and the solutions adopted during Run2 will also be discussed, including efficient use of memory in multithreading environments. Finally, we present the prospect of a future DQM upgrade with emphasis on functionality and long-term robustness for LHC Run3.
AREUS: A Software Framework for ATLAS Readout Electronics Upgrade Simulation
Authors: Madysa Nico
Published: September 2019

The design of readout electronics for the LAr calorimeters of the ATLAS detector to be operated at the future High-Luminosity LHC (HL-LHC) requires a detailed simulation of the full readout chain in order to find optimal solutions for the analog and digital processing of the detector signals. Due to the long duration of the LAr calorimeter pulses relative to the LHC bunch crossing time, out-of-time signal pileup needs to be taken into account. For this purpose, the simulation framework AREUS has been developed. It models analog-to-digital conversion, gain selection, and digital signal processing at bit precision, including digitization noise and detailed electronics effects. Trigger and object reconstruction algorithms are taken into account in the optimization process. The software implementation of AREUS, the concepts of its main functional blocks, as well as optimization considerations will be presented. Various approaches to introduce parallelism into AREUS will be compared against each other.
Status of the parallelized JUNO simulation software
Authors: Lin Tao , Zou Jiaheng , Li Weidong , Deng Ziyan , Cao Guofu , Huang Xingtao , You Zhengyun
Published: September 2019

The Jiangmen Underground Neutrino Observatory (JUNO) is a multi-purpose neutrino experiment. It consists of a central detector, a water pool and a tracker placed on top. The central detector, which is used for neutrino detection, consists of a 20 kt liquid scintillator target and about 18,000 20-inch photomultiplier tubes (PMTs) to detect scintillation photons. Simulation software is an important part of the JUNO offline software. To speed up the simulation, a parallelized simulation framework has been developed based on the SNiPER framework and Geant4 version 10. The SNiPER task components are in charge of the event loop, which can run in sequential mode, Intel TBB mode and other modes. Based on SNiPER, the simulation framework and its underlying parallel libraries have been decoupled. However, parallelized simulation of correlated events is a challenge. In order to keep the correct event order, a component called global buffer is developed in SNiPER. In this paper, an overview of the parallelized JUNO simulation framework is presented. The global buffer is used in the parallelized event correlation simulation. An event generator produces events with timestamps in sequential mode. These events are put into the global buffer and processed by the detector simulation algorithms in different tasks. After simulation, the events are saved into ROOT files with a ROOT I/O service running in a dedicated thread. Finally, the software performance is presented.
Multi-threaded Output in CMS using ROOT
Authors: Riley Daniel , Jones Christopher
Published: September 2019

CMS has worked aggressively to make use of multi-core architectures, routinely running 4- to 8-core production jobs in 2017. The primary impediment to efficiently scaling beyond 8 cores has been our ROOT-based output module, which has been necessarily single threaded. In this paper we explore the changes made to the CMS framework and our ROOT output module to overcome the previous scaling limits, using two new ROOT features: the TBufferMerger asynchronous file merger, and Implicit Multi-Threading. We examine the architecture of the new parallel output module, the specific accommodations and modifications that were made to ensure compatibility with the CMS framework scheduler, and the performance characteristics of the new output module.
Measurement and simulation of the background in the CMS muon detectors
Authors: Calabria Cesare
Published: September 2019

The study of the different backgrounds which the muon detectors of the CMS experiment are exposed to, is fundamental to assess the system longevity and project its performance to the conditions expected for HL-LHC. In this respect, an accurate modelling of the backgrounds in simulation is of prime importance as many studies rely on simulation-based predictions while these future conditions have never been experienced in reality. This paper will present the state of the art of the work carried out to understand backgrounds observed with data collected during the LHC runs, as well as at the CERN high-intensity gamma irradiation facility. Furthermore, the effort made to improve the accuracy of FLUKA and GEANT4 based simulations of background will be thoroughly described.
Belle II Track Reconstruction and Results from first Collisions
Authors: Hauth Thomas
Published: September 2019

In April 2018, e+e- collisions of the SuperKEKB B-Factory have been recorded by the Belle II detector in Tsukuba (Japan) for the first time. The new accelerator and detector represent a major upgrade from the previous Belle experiment and will achieve a 40 times higher instantaneous luminosity. Special considerations and challenges arise for track reconstruction at Belle II due to multiple factors. This high luminosity configuration of the collider increases the beam-induced background by many factors compared to Belle and a new track reconstruction software has been developed from scratch to achieve an excellent physics performance in this busy environment. Even though on average only eleven signal tracks are present in one event, all of them need to be reconstructed down to a transverse momentum of 50 MeV and no fake tracks should be present in the event. Many analyses at Belle II rely on the advantage that the initial state in B-factories is well known and a clean event reconstruction is possible if no tracks are left after assigning all tracks to particle hypotheses. This contribution will introduce the concepts and algorithms of the Belle II tracking software. Special emphasis will be put on the mitigation techniques developed to perform track reconstruction in high-occupancy events. First results from the data-taking with the Belle II detector will be presented.
Simulation of a Fast Timing Micro-Pattern Gaseous Detector for TOF-PET and future accelerators
Authors: Radogna Raffaella , Verwilligen Piet , Maggi Marcello
Published: September 2019

Simulation is a powerful tool for designing new detectors and guide the construction of new prototypes. Advances in photolithography and micro-electronics led to the development of a new family of devices named Micro-Pattern Gas Detectors (MPGDs) [1], with main features: flexible geometry; high rate capability (> MHz/cm2); excellent spatial resolution ( 100µ m); good time resolution (5-10 ns); and reduced radiation length. A new detector layout, named Fast Timing MPGD (FTM), has been recently proposed [2] that would combine both the high spatial resolution and high rate capability of the MPGDs, while improving the time resolution with nearly two orders of magnitude to ~100ps. However charged particle timing with gaseous detector time resolution below 100 ps has been established with another detection scheme [3], this approach might not be able to sustain high particle rates. This contribution investigates the use of the FTM technology for an innovative TOF-PET imaging detector and emphases the importance of full detector simulation to guide the design of the detector geometry and performance.
Conditions and Alignment Extensions of the DD4hep Detector Description Toolkit
Authors: Frank Markus , Gaede Frank , Petric Marko , Sailer Andre
Published: September 2019

The detector description is an essential component to analyze data resulting from particle collisions in high energy physics experiments. The interpretation of data from particle collisions typically requires auxiliary data which describe in detail the state of the experiment. These accompanying data include alignment parameters, parameters describing the electronics as well as calibration- and environmental constants. We present a mechanism to manage such data in multiple simultaneous versions depending on their validity. The detector conditions data are made available to the physics algorithms through a number of transient objects grouped to collections. Such a collection represents a coherent slice of all conditions data necessary to process one or several events depending on the valid interval of the slice being the intersection of the individual conditions.

A multi-threaded application may hold several such collections in parallel depending on the time-stamps of the events currently processed. Once prepared, these collections are read-only and can easily be shared between threads with minimal requirements for locking and hence minimal overhead. We deliberately restrained ourselves from providing a persistent data solution, which in the past were fields of expertise of the experiments, but rather provided the necessary hooks to populate the conditions cache. We will present the use-cases that have driven the development, the main design choices and details of the implementation.
Background sensitivity studies for GEM based detectors using a Geant4 simulation
Authors: Vai Ilaria
Published: September 2019

Triple-GEM detectors were selected by the CMS Collaboration for instrumenting the high η region of the muon system. This region is characterized by a huge radiation background, mainly composed by neutrons and photons. In this context, a discharge probability test was performed in 2017 at the CHARM facility at CERN, to study the operation of the detector in an environment similar to the one of the CMS muon system. A Geant4 simulation was developed in parallel to the actual test, in order to evaluate the behaviour of the detector. This paper will present this simulation, from the detector geometry implementation to the results obtained in terms of sensitivity and energy deposited into the gas gaps.