bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual multi-alignment theory of parallel-beam CT image reconstruction for rigid objects
Authors: Jun Kyungtaek 
Published: September 2019

AbstractX-ray computed tomography has become an essential technique in various fields, such as biology, archaeology, geoscience, and materials science. Although considerable effort has been given to reconstructing projection image sets from fixed rigid specimens, little attention has been given to the reconstruction of projected images using an alignment method with a rotation axis for objects that are moving during scanning. Therefore, in this study, a mathematical solution for the reconstruction of a projection image set that is obtained from moving objects is presented. In particular, this study presents the reconstruction of a projection image set for two and three objects moving in different directions using the virtual multi-alignment method.
Period-luminosity diagram of long period variables in the Magellanic Clouds
Authors: Lebzelter T. , Trabucchi M. , Mowlavi N. , Wood P. R. , Marigo P. , Pastorelli G. , Lecoeur-Taïbi I. 
Published: September 2019

Context. The period-luminosity diagram (PLD) has proven to be a powerful tool for studying populations of pulsating red giants. Gaia Data Release 2 (DR2) provides a large data set including many long-period variables (LPVs) on which this tool can be applied.
Aims. We investigate the location of LPVs from the Large and Small Magellanic Clouds in the PLD using various optical and infrared luminosity indicators from Gaia and 2MASS, respectively. We thereby distinguish between stars of different masses and surface chemistry.
Methods. The data set taken from the Gaia DR2 catalogue of LPVs allows for a homogeneous study from low- to high-mass LPVs. These sources are divided into sub-populations of asymptotic giant branch (AGB) stars according to their mass and their O- or C-rich nature using the Gaia-2MASS diagram developed by our group. This diagram uses a Wesenheit index WBP, RP based on Wesenheit functions in the Gaia and 2MASS photometric bands. Four different luminosity indicators are used to study the period-luminosity (P–L) relations.
Results. We provide the first observational evidence of a P–L relation offset for both fundamental and 1O pulsators between low- and intermediate-mass O-rich stars, in agreement with published pulsation predictions. Among the luminosity indicators explored, sequence C′ is the narrowest in the P–WBP, RP diagram, and is thus to be preferred over the other PLDs for the determination of distances using LPVs. The majority of massive AGB stars and red supergiants form a smooth extension of sequence C of low- and intermediate-mass AGB stars in the P–WBP, RP diagram, suggesting that they pulsate in the fundamental mode. All results are similar in the two Magellanic Clouds.
Protostellar Outflows at the EarliesT Stages (POETS)
Authors: Moscadelli L. , Sanna A. , Goddi C. , Krishnan V. , Massi F. , Bacciotti F. 
Published: September 2019

Context. Although recent observations and theoretical simulations have pointed out that accretion disks and jets can be essential for the formation of stars with a mass of up to at least 20 M⊙, the processes regulating mass accretion and ejection are still uncertain.
Aims. The goal of the Protostellar Outflows at the EarliesT Stages (POETS) survey is to image the disk-outflow interface on scales of 10–100 au in a statistically significant sample (36) of luminous young stellar objects (YSO), targeting both the molecular and ionized components of the outflows.
Methods. The outflow kinematics is studied at milliarcsecond scales through very long baseline interferometry (VLBI) observations of the 22 GHz water masers, which are ideal test particles to measure the three-dimensional (3D) motion of shocks owing to the interaction of winds and jets with ambient gas. We employed the Jansky Very Large Array (JVLA) at 6, 13, and 22 GHz in the A- and B-Array configurations to determine the spatial structure and the spectral index of the radio continuum emission, and address its nature.
Results. In about half of the targets, the water masers observed at separation ≤1000 au from the YSOs trace either or both of these kinematic structures: (1) a spatially elongated distribution oriented at close angle with the direction of collimation of the maser proper motions (PM), and (2) a linear local standard of rest (LSR) velocity (VLSR) gradient across the YSO position. The kinematic structure (1) is readily interpreted in terms of a protostellar jet, as confirmed in some targets via the comparison with independent observations of the YSO jets, in thermal (continuum and line) emissions, reported in the literature. The kinematic structure (2) is interpreted in terms of a disk-wind (DW) seen almost edge-on on the basis of several pieces of evidence: first, it is invariably directed perpendicular to the YSO jet; second, it agrees in orientation and polarity with the VLSR gradient in thermal emissions (when reported in the literature) identifying the YSO disk at scales of ≤1000 au; third, the PMs of the masers delineating the VLSR gradients hint at flow motions at a speed of 10–20 km s−1 directed at large angles with the disk midplane. In the remaining targets, the maser PMs are not collimated but rather tend to align along two almost perpendicular directions. To explain this peculiar PM distribution, and in light of the observational bias strongly favoring masers moving close to the plane of sky, we propose that, in these sources, the maser emission could originate in DW-jet systems slightly inclined (≤30°) with respect to edge-on. Magneto-centrifugally driven DWs could in general account for the observed velocity patterns of water masers.
Data Handling In The Alice O2 Event Processing
Authors: Richter Matthias , Krzewicki Mikolaj , Eulisse Giulio 
Published: September 2019

The ALICE experiment at the Large Hadron Collider (LHC) at CERN is planned to be operated in a continuous data-taking mode in Run 3. This will allow to inspect data from all Pb-Pb collisions at a rate of 50 kHz, giving access to rare physics signals embedded in a large background.
Based on experience with real-time reconstruction of particle trajectories and event properties in the ALICE High Level Trigger, the ALICE O2 facility is currently designed and developed to support processing of a continuous, triggerless stream of data segmented into entities referred to as timeframes.
Both raw data input into the ALICE O2 system and the actual processing of aggregated timeframes are distributed among multiple processes on a manynode cluster. Process communication is based on the asynchronous message
passing paradigm.
This paper presents the basic concept for identification of data in the distributed system together with prototype implementations and performance measurements.
Implementation Of The Atlas Trigger Within The Multithreaded Athenamt Framework
Authors: Stewart Martin—Haugh 
Published: September 2019

We present an implementation of the ATLAS High Level Trigger (HLT) that provides parallel execution of trigger algorithms within the ATLAS multithreaded software framework, AthenaMT. This development will enable the HLT to meet future challenges from the evolution of computing hardware and upgrades of the Large Hadron Collider (LHC) and ATLAS Detector. During the LHC data-taking period starting in 2021, luminosity will reach up to three times the original design value. In the following data-taking period (2026) upgrades to the ATLAS trigger architecture will increase the HLT input rate by a factor of 4-10, while the luminosity will increase by a further factor of 2-3.
AthenaMT provides a uniform interface for offine and trigger algorithms, facilitating the use of offine code in the HLT. Trigger-specific optimizations provided by the framework include early event rejection and reconstruction within restricted geometrical regions. We report on the current status, including experience of migrating trigger selections to this new framework,and present the next steps towards a full implementation of the redesigned ATLAS trigger.
Data Preparation for NA62
Authors: Laycock Paul 
Published: September 2019

In 2017, NA62 recorded over a petabyte of raw data, collecting around a billion events per day of running. Data are collected in bursts of 3-5 seconds, producing output files of a few gigabytes. A typical run, a sequence of bursts with the same detector configuration and similar experimental conditions, contains 1500 bursts and constitutes the basic unit for offline data processing. A sample of 100 random bursts is used to make timing calibrations of all detectors, after which every burst in the run is reconstructed. Finally the reconstructed events are filtered by physics channel with an average reduction factor of 20, and data quality metrics are calculated.
Initially a bespoke data processing solution was implemented using a simple finite state machine with limited production system functionality. In 2017, the ATLAS Tier-0 team offered the use of their production system, together with the necessary support. Data processing workflows were rewritten with better error-handling and I/O operations were minimised, the reconstruction software was improved and conditions data handling was changed to follow best practices suggested by the HEP Software Foundation conditions database working group. This contribution describes the experience gained in using these tools and methods for data-processing on a petabyte scale experiment.
A scalable and asynchronous detector simulation system based on ALFA
Authors: Wenzel Sandro 
Published: September 2019

In the context of the common online-offline computing infrastructure for Run3 (ALICE-O2), ALICE is reorganizing its detector simulation software to be based on FairRoot, offering a common toolkit to implement simulation based on the Virtual-Monte-Carlo (VMC) scheme. Recently, FairRoot has been augmented by ALFA, a software framework developed in collaboration between ALICE and FAIR, offering portable building blocks to construct message-based and loosely-coupled multiprocessing systems.
We will report here on the implementation of a scalable and asynchronous de-tector simulation system which is based on ALFA. The system offers paral-lelization at the primary-track level, going beyond the usual inter-event parallelism of Geant4-MT, and the possibility to asynchronously and simultaneously process simulation data for the purpose of digitization and clusterization. Core advantages of our implementation are an ideal reduction of the processing time per event as well as a reduction of the memory footprint, allowing us to make significantly better use of opportunistic resources, such as HPC backfills. Moreover, the track-level parallelism opens up the interesting possibility to use different simulation engines (such as Geant4 and Fluka) concurrently, based on simple selection filters on the primary particles. The integration of fast MC processes, such as machine learning kernels running on a dedicated GPU, are a natural extension to the system.
GRACC: GRid ACcounting Collector
Authors: Weitzel Derek , Bockelman Brian , Zvada Marian , Retzke Kevin , Bhat Shreyas 
Published: September 2019

The OSG has long maintained a central accounting system called Gratia. It uses small probes on each computing and storage resource in order to collect resource usage. The probes report to a central collector which stores the usage in a database. The database is then queried to generate reports. As the OSG aged, the size of the database grew very large. It became too large for the database technology to efficiently query to generate detailed reports. The design of a replacement requires data storage that could be queried efficiently to generate multi-year reports. Additionally, it requires flexibilityto add new attributes to the collected data.
In this paper we will describe updates to the GRACC architecture in the last 18 months. GRACC uses modern web technologies that were designed for large data storage, query, and visualization. That includes the open source database Elasticsearch, message broker software RabbitMQ, and Grafana and Kibana as data visualization platforms. It uses multiple agents that perform operations on the data to transform it for easier querying and summarization.
WLCG space accounting in the SRM-less world
Authors: Andreeva Julia , Christidis Dimitrios , Di Girolamo Alessandro , Keeble Oliver 
Published: September 2019

The WLCG computing infrastructure provides distributed storage capacity hosted at the geographically dispersed computing sites. In order to effectively organize storage and processing of the LHC data, the LHC experiments require a reliable and complete overview of the storage capacity in terms of the occupied and free space, the storage shares allocated to different computing activities, and the possibility to detect “dark” data that occupies space while being unknown to the experiment's file catalogue. The task of the WLCG space accounting activity is to provide such an overview and to assist LHC experiments and WLCG operations to manage storage space and to understand future requirements.
Several space accounting solutions which have been developed by the LHC experiments are currently based on Storage Resource Manager (SRM). In the coming years SRM becomes an optional service for sites which do not provide tape storage. Moreover, already now some of the storage implementations do not provide an SRM interface. Therefore, the next generation of the space accounting systems should not be based on SRM. In order to enable possibility for exposing storage topology and space accounting information the Storage Resource Reporting proposal has been agreed between LHC experiments, sites and storage providers. This contribution describes the WLCG storage resource accounting system which is being developed based on Storage Resource Reporting proposal.
Data Mining Techniques for Software Quality Prediction in Open Source Software
Authors: Canaparo Marco , Ronchieri Elisabetta 
Published: September 2019

Software quality monitoring and analysis are among the most productive topics in software engineering research. Their results may be effectively employed by engineers during software development life cycle. Open source software constitutes a valid test case for the assessment of software characteristics. The data mining approach has been proposed in literature to extract software characteristics from software engineering data.
This paper aims at comparing diverse data mining techniques (e.g., derived from machine learning) for developing effective software quality prediction models. To achieve this goal, we tackled various issues, such as the collection of software metrics from open source repositories, the assessment of prediction models to detect software issues and the adoption of statistical methods to evaluate data mining techniques. The results of this study aspire to identify the data mining techniques that perform better amongst all the ones used in this paper for software quality prediction models.
Traiter la dermatite atopique par les probiotiques
Authors: Lopez-Ramirez Noémie , Masse Ingrid 
Published: September 2019

Dans le cadre du module d’enseignement Communication Scientifique et Littérature du Master Biologie Moléculaire et Cellulaire de Lyon, les étudiants des parcours M2 Génopath et Biologie de la Peau se sont formés à l’écriture scientifique sur un sujet libre. Suite à un travail préparatoire avec l’équipe pédagogique, chaque étudiant a rédigé, conseillé par un chercheur, une Nouvelle.
Le parcours M2 Génopath s’adresse aux étudiants scientifiques et médecins et les forme à la recherche fondamentale dans les domaines de la génétique, de la biologie cellulaire et de leurs applications biomédicales. Le parcours M2 Biologie de la Peau est une formation unique en France, et forme des spécialistes de la recherche en biologie cutanée qui s’inséreront dans les services de recherche et développement hospitalier ou de l’industrie dermo-cosmétique et dermo-pharmaceutique.
S100B Serum Level is Independent of Moderate Alcohol Intoxication
Authors: Stollhof Laura Emine , Obertacke Udo , Eschmann David , Proba Sandra , Bühler Miriam , Neumeier Michael , Bludau Frederic 
Published: September 2019

Abstract
Objective In Germany, among patients with minor head injury (MHI), the incidence of coexisting alcohol intoxication is indicated up to 50%. The neurological symptoms of patients with MHI may be caused or altered by alcohol intoxication, this could mislead to further, potential harmful, diagnostic steps or to misinterpretation of the symptoms and to non-execution of necessary treatments. In order to decide which patients need further diagnostics by CCT, S100B has been proposed as a potential selection criterion. On the other hand, studies have hypothesized that alcohol intoxication may lead to elevated S100B serum levels. Therefore, the present study aims to investigate the relationship between the blood ethyl alcohol concentration and the S100B serum concentration in an experimental setting in young human adult volunteers.
Methods In a cohort of 58 healthy volunteers, serum S100B concentration and blood ethyl alcohol concentration were measured before and after liberately drinking alcohol. The study was approved by the local Ethics Committee of the Medical Faculty Mannheim (Ethics Committee II, AZ 2012-272 N-MA). Instantaneous analysis of the samples was carried out using state-of-the art automated measuring systems. (Analyzer Cobas e411, Roche and Analyzer Dimension Vista 1500, Siemens).
Results After drinking, alcohol levels ranged from 0,23 to 1,92 g/l. The S100B value ranged from to 0,021 to 0,115 µg/l after alcohol consumption (S100B standard value < 0,11 µg/l). By calculating the Pearson correlation of empirical correlation after drinking alcohol with r = 0.01181, a correlation between serum S100B concentration and ethyl alcohol concentration is not probable. The S100B concentrations were independent on the alcohol intake in low to medium alcohol levels.
Conclusion A relevant alcohol blood concentration (~ 1 g/l), in otherwise healthy volunteers, does not affect the serum concentration of S100B. S100B may be a useful brain injury marker in low to moderate drunken patients.
A Neurologist's View of Lyme Disease and Other Tick-Borne Infections
Authors: Halperin John J. 
Published: September 2019

AbstractTick-borne infections—including tick-borne encephalitis viruses, represented in the United States by rare infections with Powassan and deer tick viruses, and more often Lyme disease—are of increasing importance to neurologists. Lyme neuroborreliosis (LNB) causes all or part of a triad including meningitis, radiculoneuritis, and cranial neuritis. Rarely, parenchymal brain and spinal cord involvement occur, with focal findings on examination and magnetic resonance imaging (MRI). LNB diagnosis requires plausible exposure, objective evidence of nervous system involvement, and, generally, positive two-tier serology. Central nervous system (CNS) LNB is almost always accompanied by abnormal cerebrospinal fluid (CSF) (cells, protein), often with intrathecal antibody production, which is determined by concentration-adjusted comparison of serum and CSF antibody. Measuring CSF antibody in isolation and nucleic acid-based testing of CSF are not useful in LNB and should be avoided. LNB treatment is highly effective with a 2- to 3-week course of antibiotics. Increasing evidence suggests that LNB not involving the CNS parenchyma can be treated successfully with oral doxycycline.
Adenoid Cystic Carcinoma of the Skull Base: Response to Radiation Therapy and Outcomes in a Retrospective Case Series
Authors: Gadkaree Shekhar K. , Parikh Anuraag S. , Rodarte Alejandro I. , Lehmann Ashton , Gray Stacey T. , Lin Derrick T. 
Published: September 2019

AbstractObjectives The main purpose of this article is to examine a single-center cohort of patients with nasopharyngeal adenoid cystic carcinoma (ACC) for pathologic features, skull base invasion, overall survival, and disease-free survival, with a focus on response to proton beam radiation therapy.Design, Setting, and Participants Single-center institutional cancer registry was used to retrospectively identify and analyze outcomes for 12 patients treated for ACC of the nasopharynx from 2000 to 2016.Main Outcomes and Measures Primary outcomes included 5-year overall survival and locoregional control. Statistical analysis was performed using STATA 12.0 (STATACorp, College Station, Texas, United States). Spearman's rank order correlation was used for ordinal, monotonic variables with p-values <0.05 considered statistically significant. Survival analysis was performed by Kaplan–Meier method; comparison between groups was performed using log-rank test.Results Twelve patients with ACC of the nasopharynx were included. All patients presented with advanced disease and were treated with primary radiation therapy, typically proton beam therapy. Only two underwent a surgical attempt at resection. A majority of cases had a cribriform growth pattern. The 5-year survival was 75% and rate of locoregional control rate at 5 years was 50%, comparable to other ACC cohort studies that included earlier stage tumors in various subsites that were surgically resected.Conclusions Although ACC is traditionally noted to be radioresistant, ACC of the nasopharynx was responsive to radiotherapy in our cohort, despite advanced stage and skull base invasion. Reasons for this improved survival are unclear and suggest the need for further pathologic and genetic characterization of nasopharyngeal ACC.
Fishing down then up the food web of an invaded lake
Authors: Dunlop Erin S. , Goto Daisuke , Jackson Donald A. 
Published: September 2019

Significance
Fishing down the food web occurs in oceans when the mean trophic level (MTL) of the fisheries’ catch declines over time. Such a trend arises if fisheries successively deplete higher-trophic level species like top predators, moving on to harvest species closer to the base of the food web such as small fish and invertebrates. Freshwater fisheries have not shown these trends. We analyzed 148 y of catch records for an exploited lake, revealing that MTL declined during years dominated by commercial fishing but increased during the contemporary phase of recreational fishing. Recently, MTL was altered by invasive species and stocking. Thus, while MTL declined historically in this lake, the switch to recreational fishing and other factors altered the trajectory.
Virtual cycling effort is dependent on power update rate
Authors: Lazzari C. D. , Diefenthaeler F. , Marques J. L. B. 
Published: September 2019

AbstractCycling ergometer protocols are commonly integrated with a virtual reality environment (VRE), especially because of its static position that also allows multiple exercise experiments. Concerning VRE scenarios, visually delayed situations like the ones produced at excessive low update rates can also affect the sense of presence and physiological responses. However, the main interface between the subject and a cycling VRE is the power applied over the crank, and there are only a few experiments to evaluate the effect of delayed situations on this particular interface. Thus, this work aims to investigate the effects of the power update rate (PUR) over the subject's performance on an avatar‐based simulator during a drafting task. A custom cycling VRE was built, and 21 male recreational cyclists (175.9 ± 7.5 cm; 76.5 ± 13.9 kg) were tested at six different PUR levels from 100 to 3000 ms. As a result, PUR affects performance scores (virtual distance, efficiency, and heart rate, p < 0.01) at the given VRE conditions. The case‐by‐case analysis of the groups reveals that higher update rates always lead to a statistical equivalent or superior performance. Nevertheless, no parameter shows any group difference between 500 ms and lower PUR. These results suggest that virtual cycling protocols should consider PUR and other delay‐related mechanisms as possible intervening factors over physiological responses and performance scores.