bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Lustre and Slurm to process Hadoop workloads and extending to the WLCG
Authors: Traynor Daniel , Froy Terry
Published: September 2019

The Queen Mary University of London Grid site has investigated the use of its Lustre file system to support Hadoop work flows. Lustre is an open source, POSIX compatible, clustered file system often used in high performance computing clusters and is often paired with the Slurm batch system. Hadoop is an open-source software framework for distributed storage and processing of data normally run on dedicated hardware utilising the HDFS file system and Yarn batch system. Hadoop is an important modern tool for data analytics used by a large range of organisation including CERN. By using our existing Lustre file system and Slurm batch system, the need to have dedicated hardware is removed and a single platform only has to be maintained for data storage and processing. The motivation and benefits of using Hadoop with Lustre and Slurm are presented. The installation, benchmarks, limitations and future plans are discussed. We also investigate using the standard WLCG Grid middleware Cream-CE service to provide a Grid enabled Hadoop service.
A prototype for the evolution of ATLAS EventIndex based on Apache Kudu storage
Authors: Baranowski Zbigniew , Canali Luca , Fernandez Casani Alvaro , Gallas Elizabeth J , Garcia Montoro Carlos , González de la Hoz Santiago , Hrivnac Julius , Prokoshin Fedor , Rybkine Grigori , Salt Jose , Sanchez Javier , Barberis Dario
Published: September 2019

The ATLAS EventIndex has been in operation since the beginning of
LHC Run 2 in 2015. Like all software projects, its components have been constantly
evolving and improving in performance. The main data store in Hadoop,
based on MapFiles and HBase, can work for the rest of Run 2 but new solutions
are explored for the future. Kudu offers an interesting environment, with a
mixture of BigData and relational database features, which look promising at
the design level. This environment is used to build a prototype to measure the
scaling capabilities as functions of data input rates, total data volumes and data
query and retrieval rates. In this proceedings we report on the selected data
schemas and on the current performance measurements with the Kudu prototype.
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.
Implementation of Feldman-Cousins corrections and oscillation calculations in the HPC environment for the NOvA Experiment
Authors: Sousa Alexandre , Buchanan Norman , Calvez Steven , Ding Pengfei , Doyle Derek , Himmel Alexander , Holzman Burt , Kowalkowski James , Norman Andrew , Peterka Thomas
Published: September 2019

Analysis of neutrino oscillation data involves a combination of complex fitting procedures and statistical correction techniques that are used to determine the full three-flavor PMNS parameters and constraint contours. These techniques rely on computationally intensive “multi-universe” stochastic modeling. The process of calculating these contours and corrections can dominate final stages of the data analysis and become a bottleneck for examining the ef-fect of systematic variations on the final results. As part of the DOE SciDAC-4 sponsored research program, we present a new implementation of a neutrino oscillation fitting and framework to carry out calculations of Feldman-Cousins corrections. This implementation is specifically designed and optimized to operate on modern High-Performance Computing (HPC) facilities. We present the performance of the system in calculating allowed regions for the NOvA experiment based on 8.9 x 1020 and 6.9 x 1020 protons-on-target (POT) neutrino and antineutrino datasets, and compare the performance of this new implementation run at the NERSC supercomputing facility with that from methods used previously by the NOvA collaboration running on grid computing facilities.
Improvements to the LHCb software performance testing infrastructure using message queues and big data technologies
Authors: Szyman´ski Maciej , Couturier Ben
Published: September 2019

Software is an essential component of High Energy Physics experiments. Due to the fact that it is upgraded on relatively short timescales, software provides flexibility, but at the same time is susceptible to issues introduced during development process, thus mandating systematic testing. We present recent improvements to LHCbPR, the framework implemented at LHCb to measure physics and computational performance of complete applications. This infrastructure is essential for keeping track of the optimisation activities related to the upgrade of computing systems which is crucial to meet the requirements of the LHCb detector upgrade for the next stage of data taking of the LHC. Latest developments in LHCbPR include application of messaging system to trigger the tests right after the corresponding software version is built within LHCb nightly builds infrastructure. We will also report on the investigation of using big data technologies in LHCbPR. We have found that using tools such as Apache Spark and Hadoop Distributed File System may significantly improve the functionality of the framework, providing an interactive exploration of the test results with efficient data filtering and flexible development of reports.
The Event Buffer Management for MT-SNiPER
Authors: Zou Jiaheng , Lin Tao , Li Weidong , Huang Xingtao , Deng Ziyan , Cao Guofu , You Zhengyun
Published: September 2019

SNiPER is a general purpose offline software framework for high energy physics experiment. It provides some features that are attractive to neutrino experiments, such as the event buffer. More than one events are available in the buffer according to a customizable time window, so that it is easy for users to apply events correlation analysis. We also implemented the MT-SNiPER to support multithreading computing based on Intel TBB. In MT-SNiPER, the event loop is split into pieces, and each piece is dispatched to a task. The global buffer, an extension and enhancement to the event buffer, is implemented for MT-SNiPER. The global buffer is available by all threads. It keeps all the events being processed in memory. When there is an available task, a subset of its events is dispatched to that task. There can be overlaps between the subsets in different tasks due to the time window. However, it is ensured that each event is processed only once. In the task side, the subsets of events are locally managed by a normal event buffer. So the global buffer can be transparent to most user algorithms. Within the global buffer, the multithreading computing of MT-SNiPER becomes more practicable.
Conditions DataHandling in the Multithreaded ATLAS Framework
Authors: Leggett Charles , Shapoval Illya , Snyder Scott , Tsulaia Vakho
Published: September 2019

In preparation for Run 3 of the LHC, the ATLAS experiment is migrating its offline software to use a multithreaded framework, which will allow multiple events to be processed simultaneously. This implies that the handling of non-event, time-dependent (conditions) data, such as calibrations and geometry, must also be extended to allow for multiple versions of such data to exist simultaneously. This has now been implemented as part of the new ATLAS framework. The detector geometry is included in this scheme by having sets of time-dependent displacements on top of a static base geometry.
HEPCon – A Cross-Platform Mobile Application for HEP Events
Authors: Vassilev Martin , Vassilev Vassil , Penev Alexander , Vassileva Petya
Published: September 2019

Collaboration in research is essential for saving time and money. The field of high-energy physics (HEP) is no different. The higher level of collaboration the stronger the community. The HEP field encourages organizing various events in format and size such as meetings, workshops and conferences. Making attending a HEP event easier leverages cooperation and dialogue and this is what makes Indico service defacto a community standard. The paper describes HEPCon, a cross-platform mobile application which collects all information available on Indico and makes it available on a portable device. It keeps most of the data locally which speeds up the interaction. HEP-Con uses a shared code base which allows easy multiplatform development and support. There are iOS and Android implementations available for free download. The project is based on C# and we use the Xamarin mobile app technology for building native iOS and Android apps. SQLite database is responsible for retrieving and storing conference data. The app can be used to preview data from past CHEP conferences but the tool is implemented generic enough to support other Indico events.
ATLAS Technical Coordination Expert System
Authors: Asensi Tortajada Ignacio , Rummler André , Salukvadze George , Solans Sánchez Carlos , Reeves Kendall
Published: September 2019

When planning an intervention on a complex experiment like ATLAS, the detailed knowledge of the system under intervention and of the interconnection with all the other systems is mandatory. In order to improve the understanding of the parties involved in an intervention, a rule-based expert system has been developed. On the one hand this helps to recognise dependencies that are not always evident and on the other hand it facilitates communication between experts with different backgrounds by translating between vocabularies of specific domains. To simulate an event this tool combines information from different areas such as detector control (DCS) and safety (DSS) systems, gas, cooling, ventilation, and electricity distribution. The inference engine provides a list of the systems impacted by an intervention even if they are connected at a very low level and belong to different domains. It also predicts the probability of failure for each of the components affected by an intervention. Risk assessment models considered are fault tree analysis and principal component analysis. The user interface is a web-based application that uses graphics and text to provide different views of the detector system adapted to the different user needs and to interpret the data
The core software framework for the LHCb Upgrade
Authors: Bozzi Concezio , Ponce Sébastien , Roiser Stefan
Published: September 2019

The LHCb detector will be upgraded for the LHC Run 3. The new, full software trigger must be able to sustain the 30MHz proton-proton inelastic collision rate. The Gaudi framework currently used in LHCb has been re-engineered in order to enable the efficient usage of vector registers and of multi-and many-core architectures. This contribution presents the critical points that had to be tackled, the current status of the core software framework and an outlook of the work program that will address the challenges of the software trigger.
The ALICE Analysis Framework for LHC Run 3
Authors: Berzano Dario , Deckers Roel , Grigoras¸ Costin , Floris Michele , Hristov Peter , Krzewicki Mikolaj , Zimmermann Markus
Published: September 2019

The ALICE experimentatthe LHC (CERN)iscurrently developinganew software framework designed for Run3: detector and software will havetocope with Pb–Pb collision rates 100 times higher than today, leadingtothe combinationofcore Online-Offline operations intoasingle framework called O2. The analysis code is expectedtorunonafew large Analysis Facilities counting 20k cores and sustaining a 100 GB/s throughput: this requiresaconjoint effort between the definitionofthe data format, the configurationofthe Analysis Facilities and the developmentofthe Analysis Framework. Wepresent the prototypeofanew Analysis Object Data format basedontimeframes and optimized for continuous readout. Such formatisdesigned tobeextensible and transported efficiently over the network. Wealso present the first iterationofthe Analysis Framework, basedonthe O2Data Processing Layer and leveraging message passing acrossatopologyofprocesses. Wewill also illustrate the implementation and benchmarkingofacompatibility layer designedtomitigate the transition from the current event-oriented analysis modeltothe new time-oriented one. Finally,wewill giveastatus reportonthe integrationofthe Analysis Framework and Analysis Facilities for Run3into the current organized analysis model in ALICE.
New Fitting Concept in ATLAS muon tracking for the LHC Run-2
Authors: Leight William , Giraud Pierre-Francois , Kluit Peter , Meyer Jochen , Moyse Edward , Poppleton Alan
Published: September 2019

Muons with high momentum - above 500 GeV - are an important constituent of new physics signatures in many models. Run-2 of the LHC is greatly increasing ATLAS’s sensitivity to such signatures thanks to an ever-larger dataset of such particles, enhanced further by an increase in the center-of-mass energy. The ATLAS Muon Spectrometer chamber alignment contributes significantly to the uncertainty of the reconstruction of these high-momentum objects. The proper treatment of measurements during tracking and the correct propagation of the alignment effects is extremely challenging. Recently, an innovative approach that imposes Gaussian constraints on ensembles of detector hits was implemented. It provides a significant improvement to high-momentum tracking without increasing the CPU budget. Furthermore, it allows for the verification of the expected alignment quality using high-statistics collision data. A detailed discussion of the algorithmic realization is given, the expected performance gains are presented and prospects for further applications of the approach are outlined.
Belle2Lab - An Interactive Tool for a Public Analysis of the Belle II Data
Authors: Pestotnik Rok
Published: September 2019

Several data samples from a Belle II experiment will be available to the public as a part of the experiment outreach activities. A Belle2Lab tool is designed as an interactive graphical user interface to reconstructed particles, offering users basic particle selection tools. The tool is based on a Blockly JavaScript graphical code generator and can be run in an HTML5 capable browser. It allows a description of different particle decays by selecting and combining particles from the data file, easy histogramming tools and a display of the results by using the JSROOT library. During the analysis, the user has the possibility to apply cuts to the selected variables. A pseudo-code generated by the user interface is sent to the execution server which returns the histograms, that can also be interactively fitted. The Belle2Lab is accessible in two ways: hosted on a single public web server or as a part of the virtual appliance which consists of an Ubuntu 16.04 LTS operating system, a data sample, an analysis framework, and a private web server. The public web server can be used for a single access while the virtual appliance is more suited for a use in a classroom.
Using Machine Learning for Precision Measurements
Authors: Bourilkov Dimitri
Published: September 2019

The use of machine learning techniques for classification is well established. They are applied widely to improve the signal-to-noise ratio and the sensitivity of searches for new physics at colliders. In this study I explore the use of machine learning for optimizing the output of high precision experiments by selecting the most sensitive variables to the quantity being measured. The precise determination of the electroweak mixing angle at the Large Hadron Collider using linear or deep neural network regressors is developed as a test case.
HIPSTER
Authors: Bevan Adrian , Charman Thomas , Hays Jonathan
Published: September 2019

HIPSTER (Heavily Ionising Particle Standard Toolkit for Event Recognition) is an open source Python package designed to facilitate the use of TensorFlow in a high energy physics analysis context. The core functionality of the software is presented, with images from the MoEDAL experiment Nuclear Track Detectors (NTDs) serving as an example dataset. Convolutional neural networks are selected as the classification algorithm for this dataset and the process of training a variety of models with different hyper-parameters is detailed. Next the results are shown for the MoEDAL problem demonstrating the rich information output by HIPSTER that enables the user to probe the performance of their model in detail.
RDataFrame: Easy Parallel ROOT Analysis at 100 Threads
Authors: Piparo Danilo , Canal Philippe , Guiraud Enrico , Pla Xavier Valls , Ganis Gerardo , Amadio Guilherme , Naumann Axel , Tejedor Enric
Published: September 2019

The Physics programmes of LHC Run III and HL-LHC challenge the HEP community. The volume of data to be handled is unprecedented at every step of the data processing chain: analysis is no exception. Physicists must be provided with first-class analysis tools which are easy to use, exploit bleeding edge hardware technologies and allow to seamlessly express parallelism. This document discusses the declarative analysis engine of ROOT, RDataFrame, and gives details about how it allows to profitably exploit commodity hardware as well as high-end servers and manycore accelerators thanks to the synergy with the existing parallelised ROOT components. Real-life analyses of LHC experiments’ data expressed in terms of RDataFrame are presented, highlighting the programming model provided to express them in a concise and powerful way. The recent developments which make RDataFrame a lightweight data processing framework are described, such as callbacks and I/O capabilities. Finally, the flexibility of RDataFrame and its ability to read data formats other than ROOT’s are characterised, as an example it is discussed how RDataFrame can directly read and analyse LHCb’s raw data format MDF.
Applications of Machine Learning at BESIII
Authors: Liu Beijiang , Xiong Xian , Hou Guoyi , Song Shiming , Shen Lin
Published: September 2019

BESIII is an experiment at the high precision frontier of hadron physics in τ-charm region. Machine learning techniques have been used to improve the performance of BESIII software. In this proceeding, we present novel approaches with XGBoost for multi-dimensional distribution reweighting, muon identification and cluster reconstruction for CGEM (Cylindrical Gas Electron Multiplier) inner tracker.
Service for parallel applications based on JINR cloud and HybriLIT resources
Authors: Balashov Nikita , Bashashin Maxim , Goncharov Pavel , Kuchumov Ruslan , Kutovskiy Nikolay , Kulikov Kiril , Matveev Mikhail , Nechaevskiy Andrey , Ososkov Gennady , Rahmonov Ilkhom , Ilkhom Rahmonov , Ilkhom Rahmonov , Yuri Shukrinov , Ivan Sokolov , Yuri Shukrinov , Oksana Streltsova , Elena Zemlyanaya
Published: September 2019

Cloud computing has become a routine tool for scientists in many fields. The JINR cloud infrastructure provides JINR users with computational resources to perform various scientific calculations. In order to speed up achievements of scientific results the JINR cloud service for parallel applications has been developed. It consists of several components and implements a flexible and modular architecture which allows to utilize both more applications and various types of resources as computational backends. An example of using the Cloud&HybriLIT resources in scientific computing is the study of superconducting processes in the stacked long Josephson junctions (LJJ). The LJJ systems have undergone intensive research because of the perspective of practical applications in nano-electronics and quantum computing. In this contribution we generalize the experience in application of the Cloud&HybriLIT resources for high performance computing of physical characteristics in the LJJ system.
Optimizing OpenStack Nova for Scientific Workloads
Authors: Moreira Belmiro , Trigazis Spyridon , Tsioutsias Theodoros
Published: September 2019

The CERN OpenStack cloud provides over 300,000 CPU cores to run data processing analyses for the Large Hadron Collider (LHC) experiments. To deliver these services, with high performance and reliable service levels, while at the same time ensuring a continuous high resource utilization has been one of the major challenges for the CERN cloud engineering team. Several optimizations like NUMA-aware scheduling and huge pages, have been deployed to improve scientific workloads performance, but the CERN Cloud team continues to explore new possibilities like preemptible instances and containers on bare-metal. In this paper we will dive into the concept and implementation challenges of preemptible instances and containers on bare-metal for scientific workloads. We will also explore how they can improve scientific workloads throughput and infrastructure resource utilization. We will present the ongoing collaboration with the Square Kilometer Array (SKA) community to develop the necessary upstream enhancement to further improve OpenStack Nova to support large-scale scientific workloads.
The ALICE Analysis Facility Prototype at GSI
Authors: Schwarz Kilian , Fleischer Soeren , Grosso Raffaele , Knedlik Jan , Kollegger Thorsten , Kramp Paul
Published: September 2019

In LHC Run 3 the ALICE Computing Model will change. The Grid Tiers will to a large extend be specialised for a given role. 2/3 of the reconstruction and calibration will be done at the combined online and offline O2 compute facility, 1/3 will be done by the Tier1 centres in the Grid. Additionally all Tier1 centres, as already now, will take care of archiving one copy of the raw data on tape. The Tier2 centres will only do simulation. The AODs will will be collected on specialised Analysis Facilities which shall be capable of processing 10 PB of data within 24 hours. A prototype of such an Analysis Facility has been set up at GSI based on the experiences with the local ALICE Tier2 centre which has been in production since 2002. The main components are a general purpose HPC cluster with a mounted cluster file system enhanced by Grid components like an XRootD based Storage Element and an interface for being able to receive and run dedicated Grid jobs on the Analysis Facility prototype. The necessary I/O speed as well as easy local data access is facilitated by self developed XRootD PlugIns. Performance tests with real life ALICE analysis trains suggest that the target throughput rate can be achieved.
Beyond X.509: token-based authentication and authorization for HEP
Authors: Ceccanti Andrea , Vianello Enrico , Caberletti Marco , Giacomini Francesco
Published: September 2019

X.509 certificates and VOMS have proved to be a secure and reliable solution for authentication and authorization on the Grid, but also showed usability issues and required the development of ad-hoc services and libraries to support VO-based authorization schemes in Grid middleware and experiment computing frameworks. The need to move beyond X.509 certificates is recognized as an important objective in the HEP R&D roadmap for software and computing, to overcome the usability issues of the current AAI and embrace recent advancement in web technologies widely adopted in industry, but also to enable the secure composition of computing and storage resources provisioned across heterogeneous providers in order to meet the computing needs of HL-LHC. A flexible and usable AAI based on modern web technologies is a key enabler of such secure composition and has been a major topic of research of the recently concluded INDIGO-DataCloud project. In this contribution, we present an integrated solution, based on the INDIGO-DataCloud Identity and Access Management service that demonstrates how a next generation, token-based VO-aware AAI can be built in support of HEP computing use cases, while maintaining compatibility with the existing, VOMS-based AAI used by the Grid.
Belle II at the Start of Data Taking
Authors: Kuhr Thomas
Published: September 2019

The Belle II experiment is expected to collect e+e-collision data at a 40 times higher instantaneous luminosity than achieved so far. The high collision rate requires not only an upgrade of the detector, but also of the computing system and the software to handle the data. The first collision data taken during the commissioning runin Spring 2018 provides an excellent opportunity to review the status of the Belle II computing and software and assess its readiness for the physics data taking starting 2019.
Towards a serverless CernVM-FS
Authors: Blomer Jakob , Ganis Gerardo , Mosciatti Simone , Popescu Radu
Published: September 2019

The CernVM File System (CernVM-FS) provides a scalable and reliable software distribution and—to some extent—a data distribution service. It gives POSIX access to more than a billion binary files of experiment application software stacks and operating system containers to end user devices, grids, clouds, and supercomputers. Increasingly, CernVM-FSalso provides access to certain classes of data, such as detector conditions data, genomics reference sets, or gravitational wave detector experiment data. For most of the high- energy physics experiments, an underlying HTTP content distribution infrastructure is jointly provided by universities and research institutes around the world. In this contribution, we will present recent developments and future plans. For future developments, we put a focus on evolving the content distribution infrastructure and at lowering the barrier for publishing into CernVM-FS. Through so-called serverless computing, we envision cloud hosted CernVM-FS repositories without the need to operate dedicated servers or virtual machines. An S3 compatible service in conjunction with a content delivery network takes on data provisioning, replication, and caching. A chainof time-limited and resource-limited functions (so called “lambda function” or “function-as- a-service”) operate on the repository and stage the updates. As a result, any CernVM-FS client should be able to turn intoawriter, possession of suitable keys provided. For repository owners, we aim at providing cost transparency and seamless scalability from very small to very large CernVM-FS installations.
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

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.
Editorial
Authors: Wendl Brigitte , Bantleon Hans-Peter
Published: September 2019

Liebe Kolleginnen und Kollegen,

dieses Heft wurde gemeinsam von Hans-Peter Bantleon und Brigitte Wendl für Sie gestaltet. Es werden verschiedene Themenbereiche angesprochen und Empfehlungen für die tägliche Praxis gegeben.
A Neurologist's View of Lyme Disease and Other Tick-Borne Infections
Authors: Halperin John J.
Published: September 2019

Tick-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

Objectives 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.
Requirements and sensitivity analysis for temporally- and spatially-resolved thermometry using neutron resonance spectroscopy
Authors: Fernández Juan C. , Barnes Cris W. , Mocko Michael J. , Zavorka Lukas
Published: September 2019

Neutron resonance spectroscopy (NRS) has been used extensively to make temperature measurements that are accurate, absolute, and nonperturbative within the interior of material samples under extreme conditions applied quasistatically. Yet NRS has seldom been used in dynamic experiments. There is a compelling incentive to do so because of the significant shortcomings of alternative techniques. An important barrier to adopting dynamic NRS thermometry is the difficulty in fielding it with conventional spallation neutron sources. To enable time-dependent and spatially resolved temperature measurements in dynamic environments, more compact neutron sources that can be used at user facilities in conjunction with other diagnostic probes (such as x-ray light sources) are required. Such sources may be available using ultrafast high-intensity optical lasers. We evaluate such possibilities by determining the sensitivities of the temperature estimate on neutron-beam and diagnostic parameters. Based on that evaluation, requirements are set on a pulsed neutron-source and diagnostics to make a meaningful dynamic temperature measurement. Dynamic thermometry measurements are examined in this context when driven by two alternative fast-neutron sources: the Los Alamos Neutron Scattering Center (LANSCE) proton accelerator driving isotropic spallation neutrons as a baseline and a laser-plasma ion accelerator driving a neutron beam from deuterium breakup. Strategies to close the gap between the required and demonstrated performance of laser-based fast-neutron sources are presented. A short-pulse high-intensity laser with state-of-the-art pulse contrast and an energy of a few hundred Joules would drive a compact neutron source suitable for NRS thermometry that could transform the dynamic study of materials.
2-bit amplitude-modulated coding metasurfaces based on indium tin oxide films
Authors: Luo Jun , Ma Qian , Jing Hongbo , Bai Guodong , Wu Ruiyuan , Bao Lei , Cui Tiejun
Published: September 2019

Metasurfaces exhibit some extraordinary phenomena, resulting in their wide applications in controlling electromagnetic (EM) waves. Recently, the introduction of digital coding metasurfaces has greatly improved the design and broadened the application scope of metasurfaces. However, in most previous studies, the control of EM waves was achieved based on the phase distribution. Here, we present 2-bit amplitude-modulated coding metasurfaces based on optically transparent indium tin oxide films in the microwave frequency regime. The proposed coding metasurfaces are composed of coding unit cells with multiring structures with specific coding sequences, allowing the dramatic control of reflected amplitudes under the normal incidence while keeping other states unchanged. Using this method, almost continuous amplitude modulation can be easily realized with different coding sequences without the need to redesign the structure. The results of simulations and experiments show precise agreement, thereby validating the feasibility of our design. In addition, the optical transparency of the metasurface indicates its promise in a variety of microwave and visible-light applications.
An approach towards the promotion of Kesterite solar cell efficiency: The use of nanostructures
Authors: Courel Maykel
Published: September 2019

In this work, a theoretical study on the application of nanostructures to Cu2ZnSnS4 (CZTS) solar cells under the radiative limit is presented. In particular, the addition of Cu2ZnSn(SSe)4 (CZTSSe) quantum wells to CZTS host material to increase photon absorption with energies lower than the CZTS bandgap, while keeping the advantage of using a wider bandgap material for a host semiconductor to obtain open-circuit voltage values near the ones reported for CZTS solar cells is proposed. The impact of the well number, well thickness, and S/(S + Se) compositional ratio at barriers and wells on solar cell characteristics is studied. It is found that S/(S + Se) compositional ratios of about 0.2 and 1 for wells and host material, respectively, and 50 wells with thicknesses in the range of 20–80 nm are able to promote solar cell efficiency. In particular, an increase in efficiency, short-circuit current density, and open-circuit voltage of 45.8%, 30.5%, and 10.7%, respectively, compared to the optimized device without nanostructures is expected.
Charge-transfer excited states in the donor/acceptor interface from large-scale GW calculations
Authors: Fujita Takatoshi , Noguchi Yoshifumi , Hoshi Takeo
Published: September 2019

Predicting the charge-transfer (CT) excited states across the donor/acceptor (D/A) interface is essential for understanding the charge photogeneration process in an organic solar cell. Here, we present a fragment-based GW implementation that can be applied to a D/A interface structure and thus enables accurate determination of the CT states. The implementation is based on the fragmentation approximation of the polarization function and the combined GW and Coulomb-hole plus screened exchange approximations for self-energies. The fragment-based GW is demonstrated by application to the pentacene/C60 interface structure containing more than 2000 atoms. The CT excitation energies were estimated from the quasiparticle energies and electron–hole screened Coulomb interactions; the computed energies are in reasonable agreement with experimental estimates from the external quantum efficiency measurements. We highlight the impact of the induced polarization effects on the electron–hole energetics. The proposed fragment-based GW method offers a first-principles tool to compute the quasiparticle energies and electronic excitation energies of organic materials.
Realization of high quality silicon nitride deposition at low temperatures
Authors: Surana V. K. , Bhardwaj N. , Rawat A. , Yadav Y. , Ganguly S. , Saha D.
Published: September 2019

This work demonstrates the low temperature thin-film deposition of silicon nitride (SiNx) for III-nitride-based high electron mobility transistors using inductively coupled plasma chemical vapor deposition. It is observed that the nonlinear dependency of the deposition temperature and gas flow rates have a profound impact on the film quality. The process parameter space is scanned and the optimum film quality is achieved, which is verified with physical and electrical characterizations. The best quality film is achieved at a deposition temperature of 380 °C demonstrating near ideal stoichiometry with negligible hydrogen (<5%) and oxygen (<3%) concentrations. In addition, the optimized film is found to have zero pinholes even at a thickness of 10 nm and is uniform over a large area with an rms roughness of 0.58 nm. The deposited films are characterized by atomic force microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The dielectric strength and dielectric constant of these films are determined from current-voltage (I-V) and capacitance-voltage (C-V) characteristics of the metal-insulator-metal structure, respectively. For the best quality film, the values of dielectric strength and dielectric constant are measured to be ∼8 MV/cm and ∼7.5, respectively. A metal-insulator-semiconductor-heterostructure (metal/SiNx/AlGaN/GaN) capacitor is fabricated with the optimized recipe for interface characterization. The density of slow traps is determined from the hysteresis in the C-V curve and found to be 7.38×1010 cm−2. The frequency dependent conductance method is also used to investigate the trap density. The trap state density is found to be 1.67×1012 cm−2 eV−1 at 0.29 eV below conduction band.
Size-dependent mode contributions to the thermal transport of suspended and supported graphene
Authors: Zou Ji-Hang , Xu Xin-Tong , Cao Bing-Yang
Published: September 2019

Graphene is promising for thermal management applications due to its superior thermal conductivity, but the inherent thermal transport mechanism is not fully understood. In this work, we directly extract the mode contributions to the thermal conductivity of free-standing and supported graphene nanoribbons using nonequilibrium molecular dynamics simulations. With the aid of the mode analyses, it is uncovered that the acoustic contribution increases with respect to the characteristic length in suspended graphene, and such a size-dependency is compromised in supported graphene. In addition, the contribution of optical modes could be more than 25% for heat conduction in narrow graphene nanoribbons because of strong boundary scatterings. Furthermore, the LA and TA modes rather than the ZA modes are dominant heat carriers in suspended and supported graphene owing to their large group velocities and long mean free path. Our results are instructive for understanding the mode thermal transport in free and supported graphene.
Optoelectrokinetics-based microfluidic platform for bioapplications: A review of recent advances
Authors: Liang Wenfeng , Liu Lianqing , Zhang Hemin , Wang Yuechao , Li Wen Jung
Published: September 2019

The introduction of optoelectrokinetics (OEK) into lab-on-a-chip systems has facilitated a new cutting-edge technique—the OEK-based micro/nanoscale manipulation, separation, and assembly processes—for the microfluidics community. This technique offers a variety of extraordinary advantages such as programmability, flexibility, high biocompatibility, low-cost mass production, ultralow optical power requirement, reconfigurability, rapidness, and ease of integration with other microfluidic units. This paper reviews the physical mechanisms that govern the manipulation of micro/nano-objects in microfluidic environments as well as applications related to OEK-based micro/nanoscale manipulation—applications that span from single-cell manipulation to single-molecular behavior determination. This paper wraps up with a discussion of the current challenges and future prospects for the OEK-based microfluidics technique. The conclusion is that this technique will allow more opportunities for biomedical and bioengineering researchers to improve lab-on-a-chip technologies and will have far-reaching implications for biorelated researches and applications in the future.
Resolution-of-the-identity approximation for complex-scaled basis functions
Authors: Hernández Vera Mario , Jagau Thomas-C.
Published: September 2019

A resolution-of-the-identity (RI) approximation for two-electron integrals over Gaussian basis functions with a complex-scaled exponent is presented. Such functions are used in non-Hermitian quantum mechanics to represent electronic resonances by L2 integrable wave functions with complex energies. We have implemented this new RI approximation for second-order Møller-Plesset perturbation (MP2) theory as well as for the Coulomb and exchange contributions in Hartree-Fock (HF) theory. We discuss the differences to the standard RI approximation of Hermitian quantum mechanics and demonstrate the utility of the non-Hermitian RI-MP2 and RI-HF methods by computations of the orientation-dependent ionization rates of CO, C6H6, and C10H8 in static electric fields. Our results illustrate that RI-MP2 correctly describes correlation effects in molecular electronic resonances while the computational cost is low enough to allow for investigations of medium-sized molecules.
Photochemistry of HOSO radical in the gas phase
Authors: Trabelsi Tarek , Anglada Josep M. , Ruiz-López Manuel F. , Francisco Joseph S.
Published: September 2019

The photochemistry of HOSO in the near- and deep-UV spectral range has been studied in the gas phase using the multireference configuration interaction MRCI+Q/aug-cc-pV(T+d)Z level of theory. HOSO is found to be a nonplanar radical in its ground electronic state with a torsion angle calculated to be 49.7°. The lowest three doublet electronic states are characterized by a large transition dipole moment and are implicated in the photodissociation of HOSO in the gas phase to generate SO and OH as products. Sulfur dioxide and hydrogen products may also result after UV absorption to reach the first excited state, and this channel competes with the production of OH and SO.
Spatial varying profiling of air PM constituents using paper-based microfluidics
Authors: Jia Yuan , Wu Wenyu , Zheng Jianping , Ni Zhonghua , Sun Hao
Published: September 2019

Accurate and quantitative profiling of air particulate matter (PM) compositions is essential for assessing local pollution information. The method combining mobile aerial sampling using unmanned aerial vehicles (UAVs) and prompt analysis excels in this regard as it allows spatiotemporal mapping of air pollution, especially in the vertical direction. However, applications of the method are still scarce as it is limited by a lack of sampling reliability due to insufficient aerial sampling time and a lack of accurate, portable quantification techniques. In this work, by integrating mobile aerial sampling with in-flight tethered charging and smartphone-based colorimetric analysis in a cost-effective paper microfluidic device, we present a method for quantitative, reliable profiling of spatiotemporal variation in air PM compositions. The method extends aerial sampling time to 12–15 flight hours per deployment, thereby significantly improving sampling reliability while maintaining the maneuverability of the UAVs. Also, smartphone-based colorimetric analysis combined with paper-based microfluidics enables portable, economically efficient analysis and is well-suited for using in low-resource settings. We demonstrated the utility of the method by carrying out a spatiotemporal variation study of air PM trace metal components (Fe, Ni, and Mn) at 4 geographical locations in Fuzhou, China, for a period of 21 days, and the results were in good agreement with results obtained from using a commercial instrument. Beside air PM composition study, this method is universally applicable and holds great potential to be extended to multipollutant analysis, such as prompt detection of airborne viruses, bacteria, and others.