bluuebunny/crossref_metadata_2025 huggingface dataset:
Sim@P1: Using Cloudscheduler for offline processing on the ATLAS HLT farm
Authors: Berghaus Frank , Brasolin Franco , Casteels Kevin , Driemel Colson , Ebert Marcus , Leavatt-Brown Colin , Lee Chris , Love Peter , Paterson Michael , Scannicchio Diana , Seuster Rolf , Sobie Randall , Weiss-Gibbons Tahya
Published: September 2019

The Simulation at Point1 (Sim@P1) project was established in 2013 to take advantage of the Trigger and Data Acquisition High Level Trigger (HLT) farm of the ATLAS experiment at the LHC. The HLT farm is a significant compute resource, which is critical to ATLAS during data taking. This large compute resource is used to generate and process simulation data for the experiment when ATLAS is not recording data. The Sim@P1 system uses virtual machines, deployed by OpenStack, in order to isolate the resources from the ATLAS technical and control network. During the upcoming long shutdown in 2019 (LS2), the HLT farm including the Sim@P1 infrastructure will be upgraded. A previous paper on the project emphasized the need for “simple, reliable, and efficient tools” to quickly switch between data acquisition operation and offline processing. In this contribution we assess various options for updating and simplifying the provisional tools. Cloudscheduler is a tool for provisioning cloud resources for batch computing that has been managing cloud resources in HEP offline computing since 2012. We present the argument for choosing Cloudscheduler, and describe technical details regarding optimal utilization of the Sim@P1 re-sources.
Evaluating Kubernetes as an orchestrator of the Event Filter computing farm of the Trigger and Data Acquisition system of the ATLAS experiment at the Large Hadron Collider
Authors: Avolio Giuseppe , Cadeddu Mattia , Hauser Reiner
Published: September 2019

The ATLAS experiment at the LHC relies on a complex and distributed Trigger and Data Acquisition (TDAQ) system to gather and select particle collision data. The Event Filter (EF) component of the TDAQ system is responsible for executing advanced selection algorithms, reducing the data rate to a level suitable for recording to permanent storage. The EF functionality is provided by a computing farm made up of thousands of commodity servers, each executing one or more processes. Moving the EF farm management towards a solution based on software containers is one of the main themes of the ATLAS TDAQ Phase-II upgrades in the area of the online software; it would make it possible to open new possibilities for fault tolerance, reliability and scalability. This paper presents the results of an evaluation of Kubernetes as a possible orchestrator of the ATLAS TDAQ EF computing farm. Kubernetes is a system for advanced management of containerized applications in large clusters. This paper will first highlight some of the technical solutions adopted to run the offline version of today’s EF software in a Docker container. Then it will focus on some scaling performance measurements executed with a cluster of 1000 CPU cores. In particular, this paper will report about the way Kubernetes scales in deploying containers as a function of the cluster size and show how a proper tuning of the Query per Second (QPS) Kubernetes parameter set can improve the scaling of applications in terms of running replicas. Finally, an assessment will be given about the possibility to use Kubernetes as an orchestrator of the EF computing farm in LHC’s Run 4.
Experience in using public Cloud for Belle II experiment within HNSciCloud Project
Authors: Pardi Silvio , Michelino Davide
Published: September 2019

The current level of flexibility reached by Cloud serviceproviders enables Physicists to take advantage of extra resources to extend the distributed computing infrastructure supporting High Energy Physics Experiments. However, the discussion about the optimal use of such kind of resources is currently ongoing. Moreover, because each Cloud provider offers its interfaces, API sets, and different service levels, the integration in the computing model of an experiment requires a specific work for each provider. In this paper, we summarize the experience matured in the usage of Cloud res urces offered by different providers within the Europeanproject Helix Nebula Science Cloud for Belle II experiment. The goal of the user-case was to run Montecarlo Production jobs properly on Virtual Machines created dynamically. To do that, we defined the golden image, based on CENTOS; we then set up the basic environment, the internal and external network, and local DNS services. For each cloud, we implemented a cache server based on Squid, while the orchestrator has been entralized on a single server located in the INFN-Napoli infrastructure. Finally, we integrated the available resources in the Belle II production framework based on DIRAC, using VCYCLE as Virtual Machine Life Cycle Manager. After a tuning activity that required the optimization of severalaspects included Image distribution and Network configuration, we wer able to run production jobs over the different Cloud with success.
Monitoring virtual machines and containers with VacMon
Authors: McNab Andrew
Published: September 2019

At the start of 2017, GridPP deployed VacMon, a new monitoring system suitable for recording and visualising the usage of virtual machines and containers at multiple sites. The system uses short JSON messages transmitted by logical machine lifecycle managers such as Vac and Vcycle. These are directed to a VacMon logging service which records the messages in an Elasticsearch database. The records can be viewed graphically using the VacMon web portal, with selections based on time ranges, virtual organisations, sites, subclusters within sites, or individual hypervisors.
Monitoring System of the AMS Science Operation Centre
Authors: Zhang Wenchao , Shan Baosong , Choutko Vitali , Egorov Alexander , Eline Alexandre
Published: September 2019

The Alpha Magnetic Spectrometer (AMS) is a high energy physics experiment installed and operating on board of the International Space Station (ISS) from May 2011 and expected to last through year 2024 and beyond. The Science Operation Centre (SOC) is in charge of the offline computing for the AMS experiment, including flight data production, Monte-Carlo simulation, data management, data backup, etc. This paper introduces the design and implementation for the new monitoring system of AMS SOC, from the monitoring data collection at the backend, to the visualisation at the frontend.
Design and development of vulnerability management portal for DMZ admins powered by DBPowder
Authors: Murakami Tadashi
Published: September 2019

It is difficult to promote cyber security measures in research institutes, especially in DMZ networks that allow connections from outside network. This difficulty mainly arises from two types of variety. One is the various requirements of servers operated by each research group. The other is the divergent skill level among server administrators. Unified manners rarely fit managing those servers. One of the solutions to overcome the above mentioned difficulties is vulnerability management. To overcome these challenges, There are two possible approaches. One of the options is to offer a simple and powerful vulnerability management service to the administrators of the DMZ hosts (DMZ admins). The other is to facilitate flexibility and efficiency in the development process of the service. To achieve these requirements, we designed and developed a vulnerability management portal site for DMZ admins, named DMZ User’s Portal. This paper describes the design of DMZ User’s Portal and the development process using a development framework, named DBPowder. Using the DMZ User’s Portal, each DMZ admin can perform a vulnerability scan on his/her own servers with ease. In other words, this delegates security vulnerability discovery and responsibility to individual DMZ admins that improve security awareness for them. Then, each DMZ admin can grasp and manage the security by himself/herself. The 13-year result from vulnerability scans show that the status of security in the KEK-DMZ has been kept in good conditions. Also, we are developing DBPowder object-relational mapping (ORM) framework to improve the flexibility and efficiency in the development process of DMZ User’s Portal.
SGSI project at CNAF
Authors: Chierici Andrea , de Girolamo Donato , Guizzunti Guido , Longo Stefano , Maron Gaetano , Martelli Barbara , Vistoli Cristina , Zani Stefano , Castellani Gastone , Giampieri Enrico
Published: September 2019

The Italian Tier1 center is mainly focused on LHC and physics experiments in general. Recently we tried to widen our area of activity and established a collaboration with the University of Bologna to set-up an area inside our computing center for hosting experiments with high demands of security and privacy requirements on stored data. The first experiment we are going to host is Harmony, a project part of IMI’s Big Data for Better Outcomes programme (IMI stands for Innovative Medicines Initiative). In order to be able to accept this kind of data we had to make a subset of our computing center compliant with the ISO 27001 regulation. In this article we will describe the SGSI project (Sistema Gestione Sicurezza Informazioni, Information Security Management System) with details of all the processes we have been through in order to become ISO 27001 compliant, with a particular focus on the separation of the project dedicated resources from all the others hosted in the center. We will also describe the software solutions adopted to allow this project to accept in the future any experiment or collaboration in need for this kind of security procedures.
IT Service Management at CERN: Data Centre and Service monitoring and status
Authors: Martín Clavo David , Cremel Nicole , Delamare Catherine , Garcia Cuervo Jorge , Moller Mats , Salter Wayne , Toteva Zhechka
Published: September 2019

The Information Technology department at CERN has been using ITIL Service Management methodologies [1] and ServiceNow since early 2011. In recent years, several developments have been accomplished regarding the data centre and service monitoring, as well as service status reporting. The CERN Service Portal, built on top of ServiceNow, hosts the CERN Service Status Board, which informs end users and supporters of ongoing service incidents, planned interventions and service changes. The Service Portal also includes the Service Availability Dashboard, which displays the technical status of CERN computing services. Finally, ServiceNow has been integrated with the data centre monitoring infrastructure, via GNI (General Notification Infrastructure) in order to implement event management and generate incidents from hardware, network, operating system and application alarms. We detail how these developments have been implemented, and how they help supporters monitor and solve issues and keep users informed of service status. Also, we highlight which lessons have been learnt after the implementation. Finally, possible future improvements are discussed.
Integrated automation for configuration management and operations in the ATLAS online computing farm
Authors: Amirkhanov Artem , Ballestrero Sergio , Brasolin Franco , du Plessis Haydn , Lee Christopher Jon , Mitrogeorgos Konstantinos , Pernigotti Marco , Sanchez Pineda Arturo , Scannicchio Diana Alessandra , Twomey Matthew Shaun
Published: September 2019

The online farm of the ATLAS experiment at the LHC, consisting of nearly 4000 PCs with various characteristics, provides configuration and control of the detector and performs the collection, processing, selection, and conveyance of event data from the front-end electronics to mass storage. Different aspects of the farm management are already accessible via several tools. The status and health of each node are monitored by a system based on Icinga 2 and Ganglia. PuppetDB gathers centrally all the status information from Puppet, the configuration management tool used to ensure configuration consistency of every node. The in-house Configuration Database (ConfDB) controls DHCP and PXE, while also integrating external information sources. In these proceedings we present our roadmap for integrating these and other data sources and systems, and building a higher level of abstraction on top of this foundation. An automation and orchestration tool will be able to use these systems and replace lengthy manual procedures, some of which also require interactions with other systems and teams, e.g. for the repair of a faulty node. Finally, an inventory and tracking system will complement the available data sources, keep track of node history, and improve the evaluation of long-term lifecycle management and purchase strategies.
Concurrent Adaptive Load Balancing at CERN
Authors: Canilho Paulo , Reguero Ignacio , Saiz Pablo
Published: September 2019

CERN is using an increasing number of DNS based load balanced aliases (currently over 700). This article explains the Go based concurrent implementation of the Load Balancing Service, both the client (lbclient) and the server (lbd). The article describes how it is being progressively deployed using Puppet and how concurrency greatly improves scalability, ultimately allowing a single master-slave couple of Openstack virtual machines to server all the aliases. It explains the new implementation of the lbclient, which, among other things, allows to incorporate Collectd metrics to determine the status of the node and takes advantage of the Go language concurrency features to reduce the real time needed for checking the status of the node. The article explains that the LBD server acts as an arbiter getting feedback on load and health from the backend nodes using snmp (Simple Network Management Protocol) to decide which IP addresses the LB alias will present. While this architecture has been used since long at CERN for DNS based aliases, the LBD code is generic enough to drive other load balancers. A proof of concept using HAProxy to provide adaptive responses to load and health monitoring has been implemented.
The DAQ systems of the DUNE Prototypes at CERN/
Authors: Hennessy Karol
Published: September 2019

DUNE is a long baseline neutrino experiment due to take data in 2025. Two prototypes of the DUNE far detector were built to assess candidate technologies and methods in advance of the DUNE detector build. Here are described the data acquisition (DAQ) systems for both of its prototypes, Proto-DUNE single-phase (SP) and ProtoDUNE dual-phase (DP). The ProtoDUNEs also break records as the largest beam test experiments yet constructed, and are the fundamental elements of CERN’s Neutrino Platform. This renders each ProtoDUNE an experiment in its own right and the design and construction have been chosen to meet this scale. Due to the aggressive timescale, off-the-shelf electronics have been chosen to meet the demands of the experiments where possible. The ProtoDUNE-SP cryostat comprises two primary sub-detectors - a single phase liquid Argon TPC and a companion Photon Detector. The TPC has two candidate readout solutions under test in ProtoDUNE-SP – RCE (ATCAbased)
and FELIX (PCIe-based). Fermilab’s artDAQ is used as the dataflow software for the single phase experiment. ProtoDUNE-DP will read out the dual-phase liquid argon detector using a microTCA solution. The timing, triggering, and compression schemes are described for both experiments, along with mechanisms for sending data offline to permanent data storage in CERN’s EOS infrastructure. This paper describes the design and implementation of the TDAQ systems as well as first measurements of their performance.
The obsolescence of Information and Information Systems CERN Digital Memory project
Authors: Le Meur Jean-Yves , Tarocco Nicola
Published: September 2019

In 2016 was started the CERN Digital Memory project with the main goal of preventing loss of historical content produced by the organisation. The first step of the project was targeted to address the risk of deterioration of the most vulnerable materials, mostly the multimedia assets created in analogue formats from 1954 to the late 1990’s, like still and moving images kept on magnetic carriers. In parallel was studied today’s best practices to guarantee a long life to digital content, either born digital or resulting from a digitization process. If traditional archives and libraries have grown up during centuries establishing recognized standards to deal with the preservation of printed content, the field of digital archiving is in its infancy.

This paper shortly exposes the challenges when migrating hundreds of thousands of audio, slides, negatives, videotapes or films from the analogue to the digital era. It will then describe how a Digital Memory platform is being built, conform to the principles of the ISO-16363 digital object management norm that defines trustworthy digital repositories. Finally, as all information repository managers are faced with the necessary migration of underlying systems and the obsolescence of the information itself, the talk will explain how a digital archiving platform focusing only on content preservation could be of direct interest for most of the live systems.
LHC Computing: past, present and future
Authors: Charpentier Philippe
Published: September 2019

Although the LHC experiments have been designed and prepared since 1984, the challenge of LHC computing was only tackled seriously much later, at the end of the ‘90s. This was the time at which the Grid paradigm wasemerging, and LHC computing had great hopes that most of its challenges would be solved by this new paradigm. The path to having functional and efficient distributed computing systems was in the end much more complex than anticipated. However, most obstacles were overcome, thanks to the introductionof new paradigms and a lot of manpower investment from the experiments and from the supporting IT units (for middleware development and infrastructuresetup). This contribution is briefly outlining some of the biggest hopes and disillusions of these past 20 years, and gives a brief outlook to the coming trends.
An original unified approach for the description of phase transformations in steel during cooling: first application to binary Fe–C
Authors: Bouaziz Olivier
Published: September 2019

Exploiting Landau’s theory of phase transformations, defining an original order parameter and using the phenomenological transformation temperatures, it is reported that it is possible to describe in a global approach the conditions for the formation of each constituent (ferrite, bainite, martensite) from austenite during cooling in steel. It allowed to propose a new rigorous classification of the different thermodynamic conditions controlling each phase transformation. In a second step, the approach predicts naturally the effect of cooling rate on the bainite start temperature. Finally, perspectives are assessed to extend the approach in order to take into account the effect of an external field such as applied stress.
Brandenburger Netzwerk Gesunde Kinder: Frühe Prävention zeigt Wirkung
Authors: Ellsäßer Gabriele , Karpinski Hendrik , Schmok Annett , Gladitz Johannes , Hüseman Dieter
Published: September 2019

Hintergrund und Ziel der Studie Das Brandenburger Netzwerk Gesunde Kinder (NGK) ist ein durch geschulte Ehrenamtliche getragenes landesweites Gesundheitsförderprogramm für Familien mit Kindern von 0 bis 3 Jahren. Ziel der Studie ist auf der Basis der Schuleingangsuntersuchung (SEU) zu untersuchen, ob das NGK sich positiv auf die Gesundheit der Kinder auswirkt.

Methode In einer retrospektiven epidemiologischen Analyse der SEU, Schuljahr 2016/2017 (Netzwerkkinder/NK: 1152, Nicht-Netzwerkkinder/N-NK: 20 954) wird deskriptiv statistisch untersucht, ob es soziodemografische und gesundheitliche Unterschiede zwischen den Subgruppen NK und N-NK gibt. In einer logistischen Regressionsanalyse wird die Stärke des Einflusses des NGK bezogen auf gesundheitliche Zielgrößen und bei Adjustierung (wie soziale Lage und Region) berechnet.

Ergebnisse Eltern mit niedrigem und mittlerem Sozialstatus sowie Alleinerziehende nahmen häufiger im NGK (p<0,001) teil. NK verglichen zu N-NK brachten das U-Heft (94,3 / 91,5%, p<0,001) und den Impfausweis (95,7 / 91,7%, p<0,001) häufiger zur SEU mit. Eine höhere Quote der 1. Tetanus-, Diphtherie-, Pertussis-Auffrischimpfung wurde nach Netzwerkbegleitung festgestellt. Im adjustierten Modell zeigten NK geringere Quoten bei unvollständiger U2–U6 (OR 0,347 [95%-Konfidenzintervall: 0,192–0,627, p<0,001]), Impflücken (OR 0,621 [95%-KI: 0,508–0,758, p<0,000]) und höhere bei „optimal versorgt“ (OR 1,355 [95%-KI: 1,175–1,562, p<0,001]).

Schlussfolgerung Gesundheitlich profitierten die im Netzwerk begleiteten Kinder.
Tips to Ensure Optimal Ring Apposition of the Ovation Stent Graft in Challenging Necks of Abdominal Aortic Aneurysms
Authors: Georgakarakos Efstratios , Koutsoumpelis Andreas , Tasopoulou Kalliopi-Maria , Georgiadis George S.
Published: September 2019

The Ovation stent graft has been recently introduced for endovascular repair of abdominal aortic aneurysms. Its sealing mechanism is based on a pair of polymer-filled inflatable rings. Based on our experience, we describe useful tips to optimize the use of Ovation in thrombosed or severely angulated necks.
Masson's Hemangioma Mimicking As Leaking Aortic Pseudoaneurysm: An Extremely Rare Presentation
Authors: Yadav Mayank , Popli Khushwant , Bisoi Akshay Kumar , Chouhan Sandeep
Published: September 2019

Intravascular papillary endothelial hyperplasia or Masson's tumor is a rare reactive disease of vascular origin characterized by exuberant proliferation of endothelial cells. Its importance lies in its ability to mimic a variety of diseases, both benign and malignant. Here, we present a unique case of Masson's tumor arising from the abdominal supraceliac aorta in a 32-year-old man initially misdiagnosed as leaking aortic pseudoaneurysm.
Rapid Diagnosis and Treatment of Patients with Acute Type A Aortic Dissection and Malperfusion Syndrome May Normalize Survival to that of Patients with Uncomplicated Type A Aortic Dissection
Authors: Bin Mahmood Syed Usman , Mori Makoto , Luo Jiajun , Zhang Yawei , Safdar Basmah , Ulrich Andrew , Geirsson Arnar , Elefteriades John A. , Mangi Abeel A.
Published: September 2019

Objectives Malperfusion syndrome in the setting of acute Type A dissection (ATAD) is typically associated with poor prognosis. We evaluated the contemporary outcomes of patients with ATAD presenting with and without malperfusion syndrome who underwent aortic surgery.

Methods We performed a single-center, retrospective review of 103 consecutive patients that underwent surgery for ATAD. The cohort was dichotomized by patients with and without malperfusion syndromes. Multivariate and bivariate analyses were performed to evaluate association between the presence of malperfusion syndrome and operative outcomes.

Results A total of 29 (28.1%) patients presented with malperfusion syndrome. The 30-day mortality for patients presenting with and without malperfusion was 13.7 and 9.4%, respectively (p = 0.49). Patients with malperfusion syndrome had a shorter mean admission-to-incision interval of 4.3 ± 2.5 hours compared with 6.3 ± 4.6 hours for those without malperfusion (p = 0.02). Difference in 30-day mortality for patients with and without malperfusion syndrome was found to be nonsignificant on multivariate regression analysis (odds ratio: 1.53; 95% confidence interval: 0.40–5.82, p = 0.49).

Conclusions This series demonstrated that there was nonsignificant difference in early- or midterm outcomes for patients with and without malperfusion syndrome. Patients with malperfusion were taken to the operating room more rapidly than those without, which offers a potential explanation for the comparable outcome of the malperfusion cohort.
Fluoroquinolones and Aortic Diseases: Is There a Connection
Authors: Carino Davide , Zafar Mohammad A. , Singh Mrinal , Ziganshin Bulat A. , Elefteriades John A.
Published: September 2019

Fluoroquinolones (FQs) are one of the most commonly prescribed classes of antibiotics. Their high tissue distribution and broad-spectrum antibacterial coverage make their use very attractive in numerous infectious diseases. Although generally well tolerated, FQs have been associated with different adverse effects including dysglycemia and arrhythmias. FQs have been also associated with a series of adverse effects related to collagen degradation, such as Achilles tendon rupture and retinal detachment. Recently, an association between consumption of FQs and increased risk of aortic aneurysm and dissection has been proposed. This article reviews the pathogenesis of thoracic aortic diseases, the molecular mechanism of FQ-associated collagen toxicity, and the possible contribution of FQs to aortic diseases.
A Randomized Crossover Comparison of Airway Sealing with the Laryngeal Mask Airway Ambu AuraFlex at Three Intracuff Pressures in Pediatric Laparoscopic Surgery
Authors: Liu Xiang , Tan Xiaona , Zhang Qi , Qiao Li , Shi Lei
Published: September 2019

Objective An adequate intracuff pressure is important to ensure sufficient sealing function when using supraglottic airway devices to protect the airway from secretions and achieve adequate positive pressure ventilation. The aim of this study is to analyze a feasible and effective alternative Ambu AuraFlex intracuff pressure in child's laparoscopic surgery.

Study Design Seventy-two children were included in this study. After insertion of the laryngeal mask airway AuraFlex, oropharyngeal leak pressure (OLP) was measured at intracuff pressures of 10, 30, and 60-cmH2O according to one of six sequences produced on the basis of 3 × 6 Williams crossover design. During the intraoperative period, AuraFlex was maintained using the last intracuff pressure of the allocated sequence. Oropharyngeal leak pressure, peak airway pressure, the fiberoptic view, mucosal change, and complications were assessed at three intracuff pressures.

Results The OLP at the intracuff pressure of 10 cmH2O was significantly lower than that of 30 cmH2O (2# 18.1 ± 1.5 vs. 19.5 ± 1.4 cmH2O, p = 0.001; 2.5# 17.7 ± 1.2 vs. 20.2 ± 1.4, p = 0.001) and 60 cmH2O (2# 18.1 ± 1.5 vs. 20.0 ± 1.3 cmH2O, p = 0.002; 2.5# 17.7 ± 1.2 vs. 20.8 ± 1.1, p = 0.003). Compared with the peak airway pressure in pre-and postpneumoperitoneum, the OLP was significantly higher. Subgroup analysis showed no differences in mucosal change and complications.

Conclusion Intracuff pressures of 30 may be sufficient for the Ambu AuraFlex in child's laparoscopic surgery, and there may be no added benefit of an intracuff pressure of 60 cmH2O, as oropharyngeal leak pressures were similar.
Spatiotemporal patterns of US drought awareness
Authors: Kim Sungyoon , Shao Wanyun , Kam Jonghun
Published: September 2019

Drought is a creeping climatological phenomenon with persistent precipitation deficits. Unlike rapid onset natural hazards such as floods and wildfires, the intangible and gradual characteristics of drought cause a lack of social response during the onset. The level of awareness of a local drought increases rapidly through mass media reports and online information searching activities when the drought reaches its peak severity. This high level of local drought awareness drives concerns for water shortage and support for water policy. However, spatiotemporal patterns of national-scale drought awareness have never been studied due to constraints imposed by time-consuming and costly survey data collection and surveys’ limited sample sizes. Here, we present the national-scale study to reveal the spatiotemporal patterns of drought awareness over the contiguous United States (CONUS) using Google Trends data and Principal Component Analysis (PCA). Results show that the first two PC modes can explain 48% (38% for PC1 and 10% for PC2) of the total variance of state-level drought awareness. We find that the PC1 mode relates to a national pattern of drought awareness across the CONUS. The spatiotemporal patterns further imply that residents in the Northeastern US region are the most aware of the emergence of drought, regardless of the geographic location of the occurrence. The results illustrate how big data, such as search query and social media data, can help develop an effective and efficient plan for drought mitigation in the future.
A collaboratively derived international research agenda on legislative science advice
Authors: Akerlof Karen , Tyler Chris , Foxen Sarah Elizabeth , Heath Erin , Gual Soler Marga , Allegra Alessandro , Cloyd Emily T. , Hird John A. , Nelson Selena M. , Nguyen Christina T. , Gonnella Cameryn J. , Berigan Liam A. , Abeledo Carlos R. , Al-Yakoub Tamara Adel , Andoh Harris Francis , dos Santos Boeira Laura , van Boheemen Pieter , Cairney Paul , Cook-Deegan Robert , Costigan Gavin , Dhimal Meghnath , Di Marco Martín Hernán , Dube Donatus , Egbetokun Abiodun , El Kharraz Jauad , Galindo Liliana Estrada , Ferguson Mark W. J. , Franco José , Graves Zach , Hayter Emily , Hernández-Mondragón Alma Cristal , Hobbs Abbi D. , Holden Kerry L. , IJsselmuiden Carel , Jegede Ayodele Samuel , Krstic Snezana B. , Mbonyintwali Jean-Marie , Mengesha Sisay Derso , Michalek Tomas , Nagano Hiroshi , Nentwich Michael , Nouri Ali , Ntale Peter Dithan , Ogundele Olusegun M. , Omenma Jude Tochukwu , Pau Louis-François , Peha Jon M. , Prescott Elizabeth M. , Ramos-Vielba Irene , Roberts Raimundo , Sandifer Paul A. , Saner Marc Albert , Sanganyado Edmond , Sanni Maruf , Santillán Orlando , Stine Deborah D. , Straf Miron L. , Tangney Peter , Washbourne Carla-Leanne , Winderickx Wim , Yarime Masaru
Published: September 2019

The quantity and complexity of scientific and technological information provided to policymakers have been on the rise for decades. Yet little is known about how to provide science advice to legislatures, even though scientific information is widely acknowledged as valuable for decision-making in many policy domains. We asked academics, science advisers, and policymakers from both developed and developing nations to identify, review and refine, and then rank the most pressing research questions on legislative science advice (LSA). Experts generally agree that the state of evidence is poor, especially regarding developing and lower-middle income countries. Many fundamental questions about science advice processes remain unanswered and are of great interest: whether legislative use of scientific evidence improves the implementation and outcome of social programs and policies; under what conditions legislators and staff seek out scientific information or use what is presented to them; and how different communication channels affect informational trust and use. Environment and health are the highest priority policy domains for the field. The context-specific nature of many of the submitted questions—whether to policy issues, institutions, or locations—suggests one of the significant challenges is aggregating generalizable evidence on LSA practices. Understanding these research needs represents a first step in advancing a global agenda for LSA research.
Spectral energy transfer in a viscoelastic homogeneous isotropic turbulence
Authors: Fathali Mani , Khoei Saber
Published: September 2019

Energy dynamics in elastoinertial turbulence is investigated by performing different direct numerical simulations of stationary, homogeneous isotropic turbulence for the range of Weissenberg numbers 0 ≤ Wi ≤ 9. Viscoelastic effects are described by the finite extensibility nonlinear elastic-Peterlin model. It is found that the presence of the polymer additives can nontrivially modify the kinetic energy dynamics by suppressing the rate of the kinetic energy transfer and altering the locality nature of this energy transfer. Spectral representation of the elastic field revealed that the elastic energy is also transferred locally through different elastic degrees of freedom via a dominantly forward energy cascade. Moreover, the elastic energy spectrum can display a power-law behavior, k−m, with the possibility of different scaling exponents depending on the Wi number. It is observed that the energy exchange between macro- and microstructures is a two-directional process: there is a dominant energy transfer from the solvent large-scale structures to the polymers alongside a weak energy transfer from polymers to the solvent small-scale structures. This energy exchange consists of three different fluxes. Two of these fluxes equally transfer a small fraction of the kinetic energy into the mean and fluctuating elastic fields. However, the main energy conversion takes place between fluctuating kinetic and elastic fields through a completely nonlocal energy transfer process.
Low swirl premixed methane-air flame dynamics under acoustic excitations
Authors: Shahsavari M. , Farshchi M. , Chakravarthy S. R. , Chakraborty A. , Aravind I. B. , Wang B.
Published: September 2019

In this study, simultaneous particle image velocimetry and planar laser induced fluorescence of hydroxyl radical, chemiluminescence imaging, and hot-wire measurements are utilized to study reacting low swirl flow dynamics under low to high amplitude acoustic excitations. Results show that a temporal weak recirculation zone exists downstream of the flame, which is enlarged in size under acoustic excitations. Investigations show that temporal behaviors of this recirculation zone play a significant role in flame movements and instabilities. As the acoustic wave amplitude increases, the flame lift-off distance changes drastically, resulting in flame instabilities (flashback and blowout) during the excitations. Prior to the flame blowout, although the flame lift-off distance responds periodically to the acoustic perturbations, heat release fluctuations display an aperiodic response. Flame dynamics are further studied by calculated power spectra of acoustic velocity and heat release fluctuations and reconstructed phase portraits of heat release fluctuations. Investigations show that increasing the forcing amplitude results in more deterministic features in the flame dynamics and amplification of the higher harmonic modes in the heat release fluctuations. However, such regular patterns become scattered prior to the flame blowout due to the existence of nonlinearities induced by high amplitude excitations. It is speculated that flame blowout can be a symptom of such nonlinearities. The Rayleigh index is measured to study thermoacoustic couplings. At low amplitude excitations, various coupling patterns occur at the flame. However, such complex patterns are replaced by simple coherent patterns, when the flame is excited by high amplitude acoustic perturbations.
High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures
Authors: Sanchez Juan C. , Carrillo Melissa , Pandey Suraj , Noda Moraima , Aldama Luis , Feliz Denisse , Claesson Elin , Wahlgren Weixiao Yuan , Tracy Gregory , Duong Phu , Nugent Angela C. , Field Andrew , Šrajer Vukica , Kupitz Christopher , Iwata So , Nango Eriko , Tanaka Rie , Tanaka Tomoyuki , Fangjia Luo , Tono Kensuke , Owada Shigeki , Westenhoff Sebastian , Schmidt Marius , Stojković Emina A.
Published: September 2019

Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca (SaBphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.
New method allows for improved ion images of neurons and skin cells
Authors: Gasparini Allison
Published: September 2019

Using a graphene cover and air plasma treatment, researchers greatly improved ion images in time-of-flight secondary ion mass spectrometry.
Uncovering early response to drought by proteomic, physiological and biochemical changes in the almond × peach rootstock ‘Garnem'
Authors: Bielsa Beatriz , Sanz María Á. , Rubio-Cabetas María J.
Published: September 2019

Drought affects growth and metabolism in plants. To investigate the changes in root protein function involved in the early response to drought stress, a proteomic analysis in combination to a physiological and biochemical analysis was performed in plants of ‘Garnem’, an almond × peach hybrid rootstock, subjected to short-term drought stress. Abscisic acid (ABA) accumulation levels increased during the drought exposure, which induced stomatal closure, and thus, minimised water losses. These effects were reflected in stomatal conductance and leaf water potential levels. However, ‘Garnem’ was able to balance water content and maintain an osmotic adjustment in cell membranes, suggesting a dehydration avoidance strategy. The proteomic analysis revealed significant abundance changes in 29 and 24 spots after 2 and 24 h of drought stress respectively. Out of these, 15 proteins were identified by LC-ESI-MS/MS. The abundance changes of these proteins suggest the influence in drought-responsive mechanisms present in ‘Garnem’, allowing its adaptation to drought conditions. Overall, our study improves existing knowledge on the root proteomic changes in the early response to drought. This will lead to a better understanding of dehydration avoidance and tolerance strategies, and finally, help in new drought-tolerance breeding approaches.
Proliferation-competent Tcf1+ CD8 T cells in dysfunctional populations are CD4 T cell help independent
Authors: Kanev Kristiyan , Wu Ming , Drews Antar , Roelli Patrick , Wurmser Christine , von Hösslin Madlaina , Zehn Dietmar
Published: September 2019

T cell maintenance in chronic infection and cancer follows a hierarchical order. Short-lived effector CD8 T cells are constitutively replaced from a proliferation-competent Tcf1-expressing progenitor population. This occurs spontaneously at low levels and increases in magnitude upon blocking PD-1 signaling. We explore how CD4 T cell help controls transition and survival of the progenitors and their progeny by utilizing single-cell RNA sequencing. Unexpectedly, absence of CD4 help caused reductions in cell numbers only among terminally differentiated cells while proliferation-competent progenitor cells remained unaffected with regard to their numbers and their overall phenotype. In fact, upon restoration of a functional CD4 compartment, the progenitors began to regenerate the effector CD8 T cells. Thus, unlike memory T cells for which secondary expansion requires CD4 T cell help, this is not a necessity for proliferation-competent progenitor cells in dysfunctional populations. Our data therefore reveals that proliferation-competent cells in dysfunctional populations show a previously unrecognized uncoupling of CD4 T cell help that is otherwise required by conventional memory T cells.
Unstable chromosome rearrangements in
Staphylococcus aureus
cause phenotype switching associated with persistent infections
Authors: Guérillot Romain , Kostoulias Xenia , Donovan Liam , Li Lucy , Carter Glen P. , Hachani Abderrahman , Vandelannoote Koen , Giulieri Stefano , Monk Ian R. , Kunimoto Mayu , Starrs Lora , Burgio Gaétan , Seemann Torsten , Peleg Anton Y. , Stinear Timothy P. , Howden Benjamin P.
Published: September 2019

Staphylococcus aureus
small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active antibiotic treatment. The molecular basis for this clinically important phenomenon is poorly understood, hampered by the instability of the SCV phenotype. Here we investigated the genetic basis for an unstable
S. aureus
SCV that arose spontaneously while studying rifampicin resistance. This SCV showed no nucleotide differences across its genome compared with a normal-colony variant (NCV) revertant, yet the SCV presented the hallmarks of
S. aureus
linked to persistent infection: down-regulation of virulence genes and reduced hemolysis and neutrophil chemotaxis, while exhibiting increased survival in blood and ability to invade host cells. Further genome analysis revealed chromosome structural variation uniquely associated with the SCV. These variations included an asymmetric inversion across half of the
S. aureus
chromosome via recombination between type I restriction modification system (T1RMS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC). Phenotypic reversion to the wild-type–like NCV state correlated with reversal of the chromosomal inversion (CI) and with prophage stabilization. Further analysis of 29 complete
S. aureus
genomes showed strong signatures of recombination between
hsdMS
genes, suggesting that analogous CI has repeatedly occurred during
S. aureus
evolution. Using qPCR and long-read amplicon deep sequencing, we detected subpopulations with T1RMS rearrangements causing CIs and prophage activation across major
S. aureus
lineages. Here, we have discovered a previously unrecognized and widespread mechanism of reversible genomic instability in
S. aureus
associated with SCV generation and persistent infections.
Conversion of Sox2-dependent Merkel cell carcinoma to a differentiated neuron-like phenotype by T antigen inhibition
Authors: Harold Alexis , Amako Yutaka , Hachisuka Junichi , Bai Yulong , Li Meng Yen , Kubat Linda , Gravemeyer Jan , Franks Jonathan , Gibbs Julia R. , Park Hyun Jung , Ezhkova Elena , Becker Jürgen C. , Shuda Masahiro
Published: September 2019

Viral cancers show oncogene addiction to viral oncoproteins, which are required for survival and proliferation of the dedifferentiated cancer cell. Human Merkel cell carcinomas (MCCs) that harbor a clonally integrated Merkel cell polyomavirus (MCV) genome have low mutation burden and require viral T antigen expression for tumor growth. Here, we showed that MCV
+
MCC cells cocultured with keratinocytes undergo neuron-like differentiation with neurite outgrowth, secretory vesicle accumulation, and the generation of sodium-dependent action potentials, hallmarks of a neuronal cell lineage. Cocultured keratinocytes are essential for induction of the neuronal phenotype. Keratinocyte-conditioned medium was insufficient to induce this phenotype. Single-cell RNA sequencing revealed that T antigen knockdown inhibited cell cycle gene expression and reduced expression of key Merkel cell lineage/MCC marker genes, including
HES6
,
SOX2
,
ATOH1
, and
KRT20
. Of these, T antigen knockdown directly inhibited Sox2 and Atoh1 expression. MCV large T up-regulated Sox2 through its retinoblastoma protein-inhibition domain, which in turn activated Atoh1 expression. The knockdown of Sox2 in MCV
+
MCCs mimicked T antigen knockdown by inducing MCC cell growth arrest and neuron-like differentiation. These results show Sox2-dependent conversion of an undifferentiated, aggressive cancer cell to a differentiated neuron-like phenotype and suggest that the ontology of MCC arises from a neuronal cell precursor.
Optical deformation of single aerosol particles
Authors: Rafferty Aidan , Gorkowski Kyle , Zuend Andreas , Preston Thomas C.
Published: September 2019

Significance

Optical tweezers have enabled an array of high-precision spectroscopic investigations into the physicochemical properties of atmospheric aerosol particles. The electromagnetic stress from the optical tweezers should deform the trapped particle, but this has previously been disregarded as a negligible effect. We demonstrate that nanometer-scale optical deformations on micron-sized aerosol particles are not always insignificant and can actually be measured using whispering gallery mode splitting. Interpretation of the optical spectrum of the deformed droplet is in itself fascinating as the proper explanation answers fundamental questions concerning optical trapping and how light interacts with matter, which we describe in detail. Furthermore, we present a methodology for contactless tensiometry measurements of single subpicoliter volume aqueous aerosol particles under both stable and metastable conditions.
Significance testing of the Altaic family
Authors: Ceolin Andrea
Published: September 2019

Historical linguists have been debating for decades about whether the classical comparative method provides sufficient evidence to consider Altaic languages as part of a single genetic unity, like Indo-European and Uralic, or whether the implicit statistical robustness behind regular sound correspondences is lacking in the case of Altaic. In this paper, I run a significance test on Swadesh-lists representing Turkish, Mongolian and Manchu to see if there are regular patterns of phonetic similarities or correspondences among word-initial phonemes in the basic vocabulary that cannot be expected to have arisen by chance. The methodology draws onOswalt (1970),Ringe (1992),Baxter & Manaster Ramer (2000)and Kessler (2001,2007). The results only partially point towards an Altaic family: Mongolian and Manchu show significant sound correspondences, while Turkish and Mongolian show some marginally significant phonological similarity, that might however be the consequence of areal contact. Crucially, Turkish and Manchu do not test positively under any condition.1
Borrowing from an unrelated language in support of intragenetic tendencies
Authors: Maisak Timur
Published: September 2019

Udi is a Nakh-Daghestanian (Lezgic) language spoken in northern Azerbaijan, which has undergone many contact-induced changes due to the influence of unrelated languages of the eastern Caucasus (Indo-European, Turkic). A recent change is the borrowing of the conditional enclitic=safrom Azerbaijani (Turkic). In Udi, this marker can combine with finite indicative tenses, resulting in a series of derived ‘realis’ conditional mood forms. The clitic is also used to create an indefiniteness marker, which derives indefinite pronouns from interrogative ones. Prior to the borrowing of the Azerbaijani morpheme there was no comparable marker in Udi available to fulfil these functions, while other Lezgic languages employ their own native grammatical means for the same functions (conditional clitics or auxiliaries). The acquisition of the borrowed clitic has thus made Udi more and not less structurally isomorphic with respect to the other languages of the Lezgic branch. This paper develops a description of functions related to the domain of conditional mood on various stages of the history of Udi, and suggests a diachronic scenario for the borrowing of the Azerbaijani marker=sa.