bluuebunny/crossref_metadata_2025_split huggingface dataset:
EOS architectural evolution and strategic development directions
Authors: Bitzes Georgios , Luchetti Fabio , Manzi Andrea , Patrascoiu Mihai , Peters Andreas Joachim , Simon Michal Kamil , Sindrilaru Elvin Alin 
Published: November 2020

EOS [1] is the main storage system at CERN providing hundreds of PB of capacity to both physics experiments and also regular users of the CERN infrastructure. Since its first deployment in 2010, EOS has evolved and adapted to the challenges posed by ever-increasing requirements for storage capacity, user-friendly POSIX-like interactive experience and new paradigms like collaborative applications along with sync and share capabilities.
Overcoming these challenges at various levels of the software stack meant coming up with a new architecture for the namespace subsystem, completely redesigning the EOS FUSE module and adapting the rest of the components like draining, LRU engine, file system consistency check and others, to ensure a stable and predictable performance. In this paper we detail the issues that triggered all these changes along with the software design choices that we made.
In the last part of the paper, we move our focus to the areas that need immediate improvements in order to ensure a seamless experience for the end-user along with increased over-all availability of the service. Some of these changes have far-reaching effects and are aimed at simplifying both the deployment model but more importantly the operational load when dealing with (non/)transient errors in a system managing thousands of disks.
Third-party transfers in WLCG using HTTP
Authors: Bockelman Brian , Ceccanti Andrea , Furano Fabrizio , Millar Paul , Litvintsev Dmitry , Forti Alessandra 
Published: November 2020

Since its earliest days, the Worldwide LHC Computational Grid (WLCG) has relied on GridFTP to transfer data between sites. The announcement that Globus is dropping support of its open source Globus Toolkit (GT), which forms the basis for several FTP client and servers, has created an opportunity to reevaluate the use of FTP. HTTP-TPC, an extension to HTTP compatible with WebDAV, has arisen as a strong contender for an alternative approach.
In this paper, we describe the HTTP-TPC protocol itself, along with the current status of its support in different implementations, and the interoperability testing done within the WLCG DOMA working group’s TPC activity. This protocol also provides the first real use-case for token-based authorisation for this community. We will demonstrate the benefits of such authorisation by showing how it allows HTTP-TPC to support new technologies (such as OAuth, OpenID Connect, Macaroons and SciTokens) without changing the protocol. We will also discuss the next steps for HTTP-TPC and the plans to use the protocol for WLCG transfers.
Analysis Tools for the VyPR Performance Analysis Framework for Python
Authors: Dawes Joshua Heneage , Han Marta , Reger Giles , Franzoni Giovanni , Pfeiffer Andreas 
Published: November 2020

VyPR (http://pyvypr.github.io/home/) is a framework being developed with the aim of automating as much as possible the performance analysis of Python programs. To achieve this, it uses an analysis-by-specification approach; developers specify the performance requirements of their programs (without any modifications of the source code) and such requirements are checked at runtime. VyPR then provides tools which allow developers to perform detailed analyses of the performance of their code. Such analyses can include determining the common paths taken to reach badly performing parts of code, deciding whether a single path through code led to variations in time taken by future observations, and more.
This paper describes the developments that have taken place in the past year on VyPR’s analysis tools to yield a Python shell-based analysis library, and a web-based application. It concludes by demonstrating the use of the analysis tools on the CMS Experiment’s Conditions Upload service.
Optimizing Provisioning of LCG Software Stacks with Kubernetes
Authors: Bachmann Richard , Ganis Gerardo , Konstantinov Dmitri , Razumov Ivan , Heinz Johannes Martin 
Published: November 2020

The building, testing and deployment of coherent large software stacks is very challenging, in particular when they consist of the diverse set of packages required by the LHC*** experiments, the CERN Beams department and data analysis services such as SWAN. These software stacks comprise a large number of packages (Monte Carlo generators, machine learning tools, Python modules, HEP**** specific software), all available for several compilers, operating systems and hardware architectures. Along with several releases per year, development builds are provided each night to allow for quick updates and testing of development versions of packages such as ROOT, Geant4, etc. It also provides the possibility to test new compilers and new configurations.
Timely provisioning of these development and release stacks requires a large amount of computing resources. A dedicated infrastructure, based on the Jenkins continuous integration system, has been developed to this purpose. Resources are taken from the CERN OpenStack cloud; Puppet configurations are used to control the environment on virtual machines, which are either used directly as resource nodes or as hosts for Docker containers. Containers are used more and more to optimize the usage of our resources and ensure a consistent build environment while providing quick access to new Linux flavours and specific configurations.
In order to add build resources on demand more easily, we investigated the integration of a CERN provided Kubernetes cluster into the existing infrastructure. In this contribution we present the status of this prototype, focusing on the new challenges faced, such as the integration of these ephemeral build nodes into CERN’s IT infrastructure, job priority control, and debugging of job failures.
Raythena: a vertically integrated scheduler for ATLAS applications on heterogeneous distributed resources
Authors: Muškinja Miha , Calafiura Paolo , Leggett Charles , Shapoval Illya , Tsulaia Vakho 
Published: November 2020

The ATLAS experiment has successfully integrated HighPerformance Computing resources (HPCs) in its production system. Unlike the current generation of HPC systems, and the LHC computing grid, the next generation of supercomputers is expected to be extremely heterogeneous in nature: different systems will have radically different architectures, and most of them will provide partitions optimized for different kinds of workloads. In this work we explore the applicability of concepts and tools realized in Ray (the high-performance distributed execution framework targeting large-scale machine learning applications) to ATLAS event throughput optimization on heterogeneous distributed resources, ranging from traditional grid clusters to Exascale computers. We present a prototype of Raythena, a Ray-based implementation of the ATLAS Event Service (AES), a fine-grained event processing workflow aimed at improving the efficiency of ATLAS workflows on opportunistic resources, specifically HPCs. The AES is implemented as an event processing task farm that distributes packets of events to several worker processes running on multiple nodes. Each worker in the task farm runs an event-processing application (Athena) as a daemon. The whole system is orchestrated by Ray, which assigns work in a distributed, possibly heterogeneous, environment.
For all its flexibility, the AES implementation is currently comprised of multiple separate layers that communicate through ad-hoc command-line and filebased interfaces. The goal of Raythena is to integrate these layers through a feature-rich, efficient application framework. Besides increasing usability and robustness, a vertically integrated scheduler will enable us to explore advanced concepts such as dynamically shaping of workflows to exploit currently available resources, particularly on heterogeneous systems.
Large Elasticsearch cluster management
Authors: Saiz Pablo , Schwickerath Ulrich 
Published: November 2020

The Centralised Elasticsearch Service at CERN runs the infrastructure to provide Elasticsearch clusters for more than 100 different use cases.
This contribution presents how the infrastructure is managed, covering the resource distribution, instance creation, cluster monitoring and user support. The contribution will present the components that have been identified as critical in order to share resources and minimise the amount of clusters and machines needed to run the service. In particular, all the automation for the instance configuration, including index template management, backups and visualisation settings, will be explained in detail.
Increasing interoperability for research clouds: CS3APIs for connecting sync&share storage, applications and science environments
Authors: González Labrador Hugo , Mościcki Jakub T. , Lamanna Massimo , Pace Alberto 
Published: November 2020

Cloud Services for Synchronization and Sharing (CS3) [14] have become increasing popular in the European Education and Research landscape in the last years. Services such as CERNBox, SWITCHdrive, SURFdrive, PSNCBox, Sciebo, CloudStor and many more have become indispensable in everyday work for scientists, engineers, educators and other users in public research and education sector.
CS3 services are currently too fragmented and lack interoperability. To fix this problem and interconnect storage-, applicationand research services a set of interoperable interfaces, CS3APIs [10], has been developed.
CS3APIs enable creation of easily-accessible and integrated science environments, facilitating cross-institutional research activities and avoiding fragmented silos based on ad-hoc solutions.
In this paper we introduce the CS3APIs and its reference implementation, Reva [16].
The Acts project: track reconstruction software for HL-LHC and beyond
Authors: Gessinger Paul , Grasland Hadrien , Gray Heather , Kiehn Moritz , Klimpel Fabian , Langenberg Robert , Salzburger Andreas , Schlag Bastian , Zhang Jin , Ai Xiaocong 
Published: November 2020

The reconstruction of trajectories of the charged particles in the tracking detectors of high energy physics (HEP) experiments is one of the most difficult and complex tasks of event reconstruction at particle colliders. As pattern recognition algorithms exhibit combinatorial scaling to high track multiplicities, they become the largest contributor to the CPU consumption within event reconstruction, particularly at current and future hadron colliders such as the LHC, HL-LHC and FCC-hh. Current algorithms provide an extremely high standard of physics and computing performance and have been tested on billions of simulated and recorded data events. However, most algorithms date back to more than 20 years ago and maintaining them has become increasingly challenging. In addition, they are challenging to adapt to modern programming paradigms and parallel architectures.
Acts is based on the well-tested and highly functioning components of LHC track reconstruction algorithms, implemented with modern software concepts and inherently designed for parallel architectures. Multithreading becomes increasingly important to balance the memory usage per CPU core. However, a fully multithreaded event processing framework blurs the clear border between events, which has in the past often been used as a clearly defined validity boundary for event conditions. Acts is equipped with a full contextual conditions concept that allows to run concurrent track reconstruction even in case of multiple detector alignments, conditions or varying magnetic field being processed at the same time. It provides an experiment and, in particular, framework-independent software toolkit and light-weight, highly optimised event data model for track reconstruction. Particular care is given to thread safety and data locality. It is designed as a toolbox that allows to implement and extend widely known pattern recognition algorithms, and in addition suitable for algorithm templating and R&D. Acts has been used as the fast simulation engine for the Tracking Machine Learning (TrackML) Challenge, and will provide reference implementation of several submitted solution programs of the two phases of the challenge.
Schwangerschaft nach sequenzieller Leber-Nieren-Transplantation bei Hyperoxalurie Typ I: Was ist daran anders als sonst?
Authors: Schwarz Anke , Günter Hans Heinrich , Haller Hermann 
Published: November 2020

ZusammenfassungSchwangerschaft nach Nierentransplantation ist immer ein Risiko sowohl für Mutter und Kind als auch für das Nierentransplantat. Wir beschreiben den Fall einer jungen Frau mit primärer Hyperoxalurie Typ 1 und dadurch bedingtem terminalem Nierenversagen durch Nephrokalzinose. Sie hatte als 10-jähriges Kind eine Lebertransplantation durch Fremdspende erhalten zur Behebung des Enzymdefektes in der Leber sowie 2 Monate später eine Nierentransplantation durch Nierenspende der Mutter. Die Immunsuppression erfolgte durch Cyclosporin, Mycophenolatmofetil und Prednisolon. Das Lebertransplantat hatte 3 Abstoßungen, jeweils behandelt mit Steroidboli. Das Nierentransplantat zeigte eine langsame Funktionsverschlechterung über die Jahre, Entwicklung einer Proteinurie von 1 Gramm Protein pro 1 Gramm Kreatinin sowie eine mittelschwere Hypertonie. Trotzdem hatte die Frau einen persistierenden dringenden Kinderwunsch und setzte sich damit durch. Der Artikel beschreibt die speziellen Probleme dieses Falles: (1) das allgemeine Problem, Patienten mit Hyperoxalurie Typ 1 überhaupt zu transplantieren; (2) das spezielle Problem der Schwangerschaft dieser 31-jährigen Frau mit genetisch bedingter Nierenerkrankung und vorangehender Transplantation von 2 soliden Organen vor 18 Jahren; (3) die mit einem immunologisch instabilen Lebertransplantat und einem Nierentransplantat einhergehende langsam progrediente Funktionsverschlechterung und ansteigende Proteinurie. Die generellen Richtlinien für eine Schwangerschaft nach Nierentransplantation werden aufgezeigt im Vergleich zu dem hier beschriebenen Fall einer Schwangerschaft, bei der fast alle Parameter außerhalb der Richtlinien liegen bei persistierend starkem Kinderwunsch dieser Frau.
Gibt es eine neue Kopfspeicheldrüse? – Eher nicht!
Authors: Guntinas-Lichius Orlando , Ihrler Stephan , Freesmeyer Martin , Gühne Falk , Kluge Regine , Bräuer Lars , Iro Heinrich , Paulsen Friedrich , Dietz Andreas , Bechmann Ingo 
Published: November 2020

ZusammenfassungIm Oktober 2020 vermeldeten die Laienpresse, aber auch einige medizinische Journale und Internetseiten, die angebliche Entdeckung einer neuen Speicheldrüse im Nasenrachen ausgehend von Positronen-Emissions-Tomografie-Computertomografie-Untersuchungen mit Liganden für das Prostata-spezifische Membranantigen (PSMA-PET/CT). Als interdisziplinäre Gruppe aus den Fachbereichen Anatomie, Pathologie, Nuklearmedizin und HNO-Heilkunde kommen wir zu der Ansicht, dass hier eine Anhäufung von kleinen Speicheldrüsen beschrieben wird. Kleine Speicheldrüsen im Nasenrachen und peritubar sind mindestens seit 1866 bekannt und immer wieder in der Literatur und in Lehrbüchern beschrieben. Das PSMA-PET/CT könnte aber geeignet sein, bei einer Bestrahlungsplanung funktionell relevante Anhäufungen von Schleimhautspeicheldrüsen, wie beispielsweise im Bereich des Nasenrachens, besser darzustellen und zu schonen. Dies sollte in klinischen Studien geprüft werden.
Management of patients after failed peroral endoscopic myotomy: a multicenter study
Authors: Ichkhanian Yervant , Assis Daniella , Familiari Pietro , Ujiki Michael , Su Baily , Khan Sarah R. , Pioche Mathieu , Draganov Peter V. , Cho Joo young , Eleftheriadis Nikolas , Barret Maximilien , Haji Amyn , Velanovich Vic , Tantau Marcel , Marks Jeffrey M. , Bapaye Amol , Sedarat Alireza , Albeniz Eduardo , Bechara Robert , Kumta Nikhil A. , Costamagna Guido , Perbtani Yaseen B. , Patel Mehul , Sippey Megan , Korrapati Sravan K. , Jain Rishabh , Estremera Fermín , El Zein Mohamad H. , Brewer Gutierrez Olaya I. , Khashab Mouen A. 
Published: November 2020

Abstract
Background Although peroral endoscopic myotomy (POEM) is highly effective for the management of achalasia, clinical failures may occur. The optimal management of patients who fail POEM is not well known. This study aimed to compare the outcomes of different management strategies in patients who had failed POEM.
Methods This was an international multicenter retrospective study at 16 tertiary centers between January 2012 and November 2019. All patients who underwent POEM and experienced persistent or recurrent symptoms (Eckardt score > 3) were included. The primary outcome was to compare the rates of clinical success (Eckardt score ≤ 3) between different management strategies.
Results 99 patients (50 men [50.5 %]; mean age 51.4 [standard deviation (SD) 16.2]) experienced clinical failure during the study period, with a mean (SD) Eckardt score of 5.4 (0.3). A total of 29 patients (32.2 %) were managed conservatively and 70 (71 %) underwent retreatment (repeat POEM 33 [33 %], pneumatic dilation 30 [30 %], and laparoscopic Heller myotomy (LHM) 7 [7.1 %]). During a median follow-up of 10 (interquartile range 3 – 20) months, clinical success was highest in patients who underwent repeat POEM (25 /33 [76 %]; mean [SD] Eckardt score 2.1 [2.1]), followed by pneumatic dilation (18/30 [60 %]; Eckardt score 2.8 [2.3]), and LHM (2/7 [29 %]; Eckardt score 4 [1.8]; P = 0.12). A total of 11 patients in the conservative group (37.9 %; mean Eckardt score 4 [1.8]) achieved clinical success.
Conclusion This study comprehensively assessed an international cohort of patients who underwent management of failed POEM. Repeat POEM and pneumatic dilation achieved acceptable clinical success, with excellent safety profiles.
2-Carbamimidoylbenzoic Acid as a New Effective and Available Precursor for the Synthesis of Substituted 2-(Pyrimidin-2-yl)benzoic Acids
Authors: Hordiyenko Olga V. , Tkachuk Volodymyr A. , Shishkanu Vyacheslav O. , Tkachuk Tetiana M. , Shishkina Svitlana V. 
Published: November 2020

AbstractA new approach to the synthesis of 2-(pyrimidin-2-yl)benzoic acids based on the ring contraction of the 2-carbamimidoylbenzoic acid [(2-amidinobenzoic) acid] with 1,3-dicarbonyl compounds and their synthetic equivalents has been developed. The intramolecular condensation of the obtained acids with 1,3-dielectrophiles proceeds with the formation of the 4,6-dihydropyrimido[2,1-a]isoindole-4,6-dione system, the pyrrolidone ring of which is easily opened under the action of weak nucleophiles. The reaction of 2-amidinobenzoic acid with chromones, which have an aryloxy group at 3-position does not stop at the step of pyrimidine ring formation and undergoes further spontaneous cyclization into 2-(benzo[4,5]furo[3,2-d]pyrimidin-2-yl)benzoic acids.
Synthesis of Tryptamines through a Novel Brønsted Acid Mediated Tandem Reaction Initiated by α-Iminol Rearrangement of Transient 2-Substituted 2-Hydroxycyclobutylimines
Authors: Frongia Angelo , Serusi Lorenzo , Cuccu Federico , Secci Francesco , Aitken David J. 
Published: November 2020

AbstractA novel Brønsted acid promoted condensation reaction between a primary aniline and 2-hydroxycyclobutanone provides access to diverse tryptamine derivatives in moderate to good yields. The proposed mechanism involves an α-iminol rearrangement, ring expansion, ring closure, and a depart-and-return rearrangement process.
Imaging Diagnosis of Adenomyosis
Authors: O'Shea Aileen , Figueiredo Gabrielle , Lee Susanna I. 
Published: November 2020

AbstractUterine adenomyosis can be diagnosed on ultrasonography (US) and magnetic resonance imaging (MRI) with a high degree of accuracy. Adenomyosis is a myometrial process that can appear as diffuse or focal on imaging. Diffuse adenomyosis typically causes uterine enlargement, while focal adenomyosis can mimic other myometrial lesions, such as leiomyomas. Imaging features frequently seen on US include a heterogenous thickened myometrium and myometrial cysts. On MRI, widening of the junctional zone, whether focal or diffuse, and the presence of myometrial cysts, either simple or hemorrhagic, support the diagnosis of adenomyosis. Despite these characteristic imaging appearances, there are several gynecologic pathologies which can mimic adenomyosis and it is important to be vigilant of these when interpreting cross-sectional imaging exams. The decision to evaluate patients with US or MRI is contingent on multiple factors, including availability of the necessary technology and expertise for the latter. However, MRI appears to offer greater specificity and positive predictive value for the diagnosis of adenomyosis.
European Pediatric Surgeon' Association Survey on the Management of Short-Bowel Syndrome
Authors: Dariel Anne , Faure Alice , Martinez Leopoldo , Morini Francesco , Pini Prato Alessio , Friedmacher Florian , Coste Marie-Edith 
Published: November 2020

AbstractIntroduction The aim of this study was to assess the management of short-bowel syndrome (SBS) at the time of primary surgery, and the strategies used to facilitate enteral autonomy depending on the institutional expertise.Materials and Methods An online questionnaire was sent in 2019 to members of The European Pediatric Surgeons' Association.Results Among the 65 responding members (26 countries, 85% from university hospitals), 57% manage less than three new patients with SBS per year (group A), and 43% at least three patients (group B). The cut-off of three patients treated yearly used in our study was defined after statistical analysis of different cut-offs. A multidisciplinary intestinal rehabilitation program is significantly more frequent in group B than in group A (85 and 53%, respectively; p = 0.009). Considering the primary surgical management of multiple intestinal atresia and congenital ultra-short bowel with jejunal atresia, primary surgical strategies to optimize bowel length are more often used in group B than group A (p = 0.09 and p = 0.04, respectively). A minimum of one intestinal lengthening procedure every 2 to 3 years is significantly more frequent in group B than group A (95 and 45%, respectively; p = 0.0013). Among the strategies used to promote intestinal adaptation, group B (35%) uses significantly more often glucagon-like peptide 2 analogs than group A (10%) (p = 0.02).Conclusion Based on our survey, a minimum number of SBS patients treated yearly is required to manage this challenging disease according to up-to-date medical and surgical strategies. However, whatever their level of expertise is in managing SBS, most of pediatric surgeons are involved in the primary surgery. Medical education programs about SBS should be more largely available to pediatric surgeons.
A novel and reliable interlayer exchange coupled nanomagnetic universal logic gate design
Authors: Mattela Venkat , Debroy Sanghamitra , Sivasubramani Santhosh , Acharyya Amit 
Published: November 2020

Abstract
In this paper, we propose an interlayer exchange coupling (IEC) based 3D universal NAND/NOR gate design methodology for the reliable and robust implementation of nanomagnetic logic design as compared to the state-of-the art architectures. Owing to stronger coupling scheme as compared to the conventional dipole coupling, the random flip of the states of the nanomagnets (i.e. the soft error) is reduced resulting in greater scalability and better data retention at the deep sub-micron level. Results obtained from Object Oriented Micromagnetic Framework micromagnetic simulation show even at a Curie temperature of the nanomagnets coupled through IEC, the logic function works properly as opposed to dipole coupled nanomagnets which fails at 5 K when scaled down to sub 50 nm. Contemplating the fabrication challenges, the robustness of the IEC design was studied for structural defects, positional misalignment, shape, and size variations. This proposed 3D universal gate design methodology benefits from the miniaturization of nanomagnets as well as reduces the effect of thermally induced errors resulting in opening up a new perspective for nanomagnet based design in magneto-logic devices.