bluuebunny/crossref_metadata_2025 huggingface dataset:
BAT.jl Upgrading the Bayesian Analysis Toolkit
Authors: Caldwell Allen , Grunwald Cornelius , Hafych Vasyl , Kröninger Kevin , La Cagnina Salvatore , Schulz Oliver , Shtembari Lolian
Published: November 2020

In all but the simplest cases, performing data analysis based on Bayesian reasoning requires the use of advanced algorithms. The Bayesian Analysis Toolkit (BAT) provides a collection of algorithms and methods that facilitate the application of Bayesian statistics to user-defined problems of arbitrary complexity. With BAT.jl, we present a modern rewrite of BAT in the Julia programming language. Through the use of a modular software design that is capable of running parallel and distributed, and by extending the tool with new sampling and integration algorithms, BAT.jl is a high-performance framework for Bayesian inference, meeting the requirements of modern data analysis.
CERN Analysis Preservation and Reuse Framework: FAIR research data services for LHC experiments
Authors: Fokianos Pamfilos , Feger Sebastian , Koutsakis Ilias , Lavasa Artemis , Maciulaitis Rokas , Naim Kamran , Okraska Jan , Papadopoulos Antonios , Rodríguez Diego , Šimko Tibor , Trzcinska Anna , Tsanaktsidis Ioannis , van de Sandt Stephanie
Published: November 2020

In this paper we present the CERN Analysis Preservation service as a FAIR (Findable, Accessible, Interoperable and Reusable) research data preservation repository platform for LHC experiments. The CERN Analysis Preservation repository allows LHC collaborations to deposit and share the structured information about analyses as well as to capture the individual data assets associated to the analysis. We describe the typical data ingestion pipelines, through which an individual physicist can preserve and share their final n-tuples, ROOT macros, Jupyter notebooks, or even their full analysis workflow code and any intermediate datasets of interest for preservation within the restricted context of experimental collaboration. We discuss the importance of annotating the deposited content with high-level structured information about physics concepts in order to promote information discovery and knowledge sharing inside the collaboration. Finally, we describe techniques used to facilitate the reusability of preserved data assets by capturing and re-executing reproducible recipes and computational workflows using the REANA Reusable Analysis platform.
Directly calculating the glue component of the nucleon in lattice QCD: QCDSF–UKQCD–CSSM Collaborations
Authors: Howson T. L. , Horsley R. , Kamleh W. , Nakamura Y. , Perlt H. , Rakow P. E. L. , Schierholz G. , Stüben H. , Young R. D. , Zanotti J. M.
Published: November 2020

We are investigating the direct determination and non-perturbative renormalisation of gluon matrix elements. Such quantities are sensitive to ultra– violet fluctuations, and are in general statistically noisy. To obtain statistically significant results, we extend an earlier application of the Feynman–Hellmann theorem to gluonic matrix elements to calculate a renormalisation factor in theRI – MOMscheme, in the quenched case. This work demonstrates that the Feynman–Hellmann method is capable of providing a feasible option for calculating gluon quantities.
Signal versus Background Interference in H+ → tb for MSSM Benchmark Scenarios
Authors: Arhrib Abdesslam , Azevedo Duarte , Benbrik Rachid , Harouiz Hicham , Moretti Stefano , Patrick Riley , Santos Rui
Published: November 2020

In this talk an investigation into the interference effects between the process pp→t̄bH+ followed by the decay H+→tb̄ and the background process pp → tt̄bb̄ is presented. The level of interference in parts of the parameter space is shown to be high and as such it may spoil the results of typical analyses which treat signal and background as independent. This is shown for two benchmarks of the MSSM.
Monitoring and Analytics at INFN Tier-1: the next step
Authors: Viola Fabio , Martelli Barbara , Michelotto Diego , Fattibene Enrico , Falabella Antonio , Dal Pra Stefano , Morganti Lucia , Dell’Agnello Luca , Bonacorsi Daniele , Rossi Tisbeni Simone
Published: November 2020

In modern data centres an effective and efficient monitoring system is a critical asset, yet a continuous concern for administrators. Since its birth, INFN Tier-1 data centre, hosted at CNAF, has used various monitoring tools all replaced, a few years ago, by a system common to all CNAF departments (based on Sensu, Influxdb, Grafana). Given the complexity of the inter-dependencies of the several services running at the data centre and the foreseen large increase of resources in the near future, a more powerful and versatile monitoring system is needed. This new monitoring system should be able to automatically correlate log files and metrics coming from heterogeneous sources and devices (including services, hardware and infrastructure) thus providing us with a suitable framework to implement a solution for the predictive analysis of the status of the whole environment. In particular, the possibility to correlate IT infrastructure monitoring information with the logs of running applications is of great relevance in order to be able to quickly find application failure root cause. At the same time, a modern, flexible and user-friendly analytics solution is needed in order to enable users, IT engineers and IT managers to extract valuable information from the different sources of collected data in a timely fashion. In this paper, a prototype of such a system, installed at the INFN Tier-1, is described with an assessment of the state and an evaluation of the resources needed for a fully production system. Technologies adopted, amount of foreseen data, target KPIs and production design are illustrated.
Evolution of the CloudVeneto.it private cloud to support research and innovation
Authors: Andreetto Paolo , Costa Fulvia , Crescente Alberto , Fantinel Sergio , Fanzago Federica , Mazzon Paolo Emilio , Menguzzato Matteo , Sella Gianpietro , Sgaravatto Massimo , Traldi Sergio , Verlato Marco , Zanetti Marco , Zangrando Lisa
Published: November 2020

CloudVeneto.it was initially funded and deployed by INFN in 2014 for serving the computational and storage demands of INFN research projects mainly related to HEP and Nuclear Physics. It is an OpenStack-based scientific cloud with resources spread across two different sites connected with a high speed optical link: INFN Padova Unit and the INFN Legnaro National Laboratories. The infrastructure has grown throughout the years with additional funds from ten University of Padova departments, and nowadays supports a broader range of scientific and engineering disciplines. Its hardware resources provide around 2500 computational cores and 360 TB of storage to about 250 users working for more than 70 projects. In the last months we enhanced the cloud platform in two ways: 1) by integrating a number of heterogeneous GPU cards to address the special needs of user communities whose computations involve machine learning training; 2) by enabling the users to simply deploy on-demand Kubernetes clusters for Big Data Analytics applications taking advantage of the operator framework. In particular, the Kubernetes operators for Apache Kafka and Spark platforms were integrated to address real-time data ingestion and streaming processing on the cloud. This article describes the technical details of these two solutions and their integration with the cloud infrastructure.
The SIMPLE Framework for deploying containerized grid services
Authors: Sharma Mayank , Silva Junior Eraldo , Iliev Vasilev Boris , Litmaath Maarten , Santana Renato
Published: November 2020

The Worldwide LHC Computing Grid (WLCG) currently has about 170 sites. In order to support WLCG workloads, each site has to deploy and maintain a number of possibly complex grid services. Quite often, site managers require assistance of WLCG experts, for example when new software versions need to be deployed. Modern configuration management (e.g. Puppet, Ansible), container orchestration (e.g. Docker Swarm, Kubernetes) and containerization technologies (e.g. Docker, Podman) can help make such activities more lightweight by means of packaging sensible configurations of grid services and providing simple mechanisms to distribute and deploy them across the infrastructure available at a site. This article describes the SIMPLE project: a Solution for Installation, Management and Provisioning of Lightweight Elements. The SIMPLE framework leverages modern infrastructure management tools to deploy containerized grid services, such as popular compute elements (e.g. HTCondor, ARC), batch systems (e.g. HTCondor, Slurm), worker nodes, etc. Its architecture follows principles of sustainability, scalability and extensibility. We describe how system administrators can use the framework, as well as the first results, featuring the migration of computing resources to HTCondor at 2 sites. We conclude with an outlook on further developments.
Abstracting container technologies and transfer mechanisms in the Scalable CyberInfrastructure for Artificial Intelligence and Likelihood Free Inference (SCAILFIN) project
Authors: Hurtado Anampa Kenyi , Kankel Cody , Hildreth Mike , Brenner Paul , Johnson Irena , Hampton Scott , Simko Tibor
Published: November 2020

High Performance Computing (HPC) facilities provide vast computational power and storage, but generally work on fixed environments designed to address the most common software needs locally, making it challenging for users to bring their own software. To overcome this issue, most HPC facilities have added support for HPC friendly container technologies such as Shifter, Singularity, or Charliecloud. These different container technologies are all compatible with the more popular Docker containers, however the implementation and use of said containers is different for each HPC friendly container technology. These usage differences can make it difficult for an end user to easily submit and utilize different HPC sites without making adjustments to their workflows and software. This issue is exacerbated when attempting to utilize workflow management software between different sites with differing container technologies.

The SCAILFIN project aims to develop and deploy artificial intelligence (AI) and likelihood-free inference (LFI) techniques and software using scalable cyberinfrastructure (CI) that span multiple sites. The project has extended the CERN-based REANA framework, a platform designed to enable analysis reusability, and reproducibility while supporting different workflow engine languages, in order to support submission to different HPC facilities. The work presented here focuses on the development of an abstraction layer that allows the support of different container technologies and different transfer protocols for files and directories between the HPC facility and the REANA cluster edge service from the user’s workflow application.
Using Kubernetes as an ATLAS computing site
Authors: Barreiro Megino Fernando Harald , Albert Jeffrey Ryan , Berghaus Frank , De Kaushik , Lin FaHui , MacDonell Danika , Maeno Tadashi , Da Rocha Ricardo Brito , Seuster Rolf , Taylor Ryan Paul , Yang Ming-Jyuan
Published: November 2020

In recent years containerization has revolutionized cloud environments, providing a secure, lightweight, standardized way to package and execute software. Solutions such as Kubernetes enable orchestration of containers in a cluster, including for the purpose of job scheduling. Kubernetes is becoming a de facto standard, available at all major cloud computing providers, and is gaining increased attention from some WLCG sites. In particular, CERN IT has integrated Kubernetes into their cloud infrastructure by providing an interface to instantly create Kubernetes clusters, and the University of Victoria is pursuing an infrastructure-as-code approach to deploying Kubernetes as a flexible and resilient platform for running services and delivering resources.

The ATLAS experiment at the LHC has partnered with CERN IT and the University of Victoria to explore and demonstrate the feasibility of running an ATLAS computing site directly on Kubernetes, replacing all grid computing services. We have interfaced ATLAS’ workload submission engine PanDA with Kubernetes, to directly submit and monitor the status of containerized jobs. We describe the integration and deployment details, and focus on the lessons learned from running a wide variety of ATLAS production payloads on Kubernetes using clusters of several thousand cores at CERN and the Tier 2 computing site in Victoria.
Lightweight dynamic integration of opportunistic resources
Authors: Fischer Max , Kuehn Eileen , Giffels Manuel , Schnepf Matthias Jochen , Petzold Andreas , Heiss Andreas
Published: November 2020

To satisfy future computing demands of the Worldwide LHC Computing Grid (WLCG), opportunistic usage of third-party resources is a promising approach. While the means to make such resources compatible with WLCG requirements are largely satisfied by virtual machines and containers technologies, strategies to acquire and disband many resources from many providers are still a focus of current research. Existing meta-schedulers that manage resources in the WLCG are hitting the limits of their design when tasked to manage heterogeneous resources from many diverse resource providers.

To provide opportunistic resources to the WLCG as part of a regular WLCG site, we propose a new meta-scheduling approach suitable for opportunistic, heterogeneous resource provisioning. Instead of anticipating future resource requirements, our approach observes resource usage and promotes well-used resources. Following this approach, we have developed an inherently robust meta-scheduler, COBalD, for managing diverse, heterogeneous resources given unpredictable resource requirements. This paper explains the key concepts of our approach, and discusses the benefits and limitations of our new approach to dynamic resource provisioning compared to previous approaches.
Network Capabilities for the HL-LHC Era
Authors: Babik Marian , McKee Shawn
Published: November 2020

High Energy Physics (HEP) experiments rely on the networks as one of the critical parts of their infrastructure both within the participating laboratories and sites as well as globally to interconnect the sites, data centres and experiments instrumentation. Network virtualisation and programmable networks are two key enablers that facilitate agile, fast and more economical network infrastructures as well as service development, deployment and provisioning. Adoption of these technologies by HEP sites and experiments will allow them to design more scalable and robust networks while decreasing the overall cost and improving the effectiveness of the resource utilization.

The primary challenge we currently face is ensuring that WLCG and its constituent collaborations will have the networking capabilities required to most effectively exploit LHC data for the lifetime of the LHC. In this paper we provide a high level summary of the HEPiX NFV Working Group report that explored some of the novel network capabilities that could potentially be deployment in time for HL-LHC.
Characterizing network paths in and out of the clouds
Authors: Sfiligoi Igor , Graham John , Wuerthwein Frank
Published: November 2020

Commercial Cloud computing is becoming mainstream, with funding agencies moving beyond prototyping and starting to fund production campaigns, too. An important aspect of any scientific computing production campaign is data movement, both incoming and outgoing. And while the performance and cost of VMs is relatively well understood, the network performance and cost is not. This paper provides a characterization of networking in various regions of Amazon Web Services, Microsoft Azure and Google Cloud Platform, both between Cloud resources and major DTNs in the Pacific Research Platform, including OSG data federation caches in the network backbone, and inside the clouds themselves. The paper contains both a qualitative analysis of the results as well as latency and peak throughput measurements. It also includes an analysis of the costs involved with Cloud-based networking.
Unplugged Computing for Children
Authors: Alandes Pradillo Maria , Badinova Eszter , Chelba Anda-Catalina , Hermo Serans Miguel , Kane Natalie , Kriva Simona , Short Hannah
Published: November 2020

The number of women in technical and computing roles in the High Energy Physics (HEP) community hovers at around 15%. At the same time there is a growing body of research to suggest that diversity, in all its forms, brings positive impact on productivity and well-being. These aspects are directly in line with many organisations’ values and missions, including CERN. Although proactive efforts to recruit more women in our organisations and institutes may help, the percentage of female applicants in candidate pools is similarly low and limits the potential for change. Factors influencing the career choice of girls have been identified to start as early as primary school and are closely tied to encouragement and exposure. It is the hope of various groups in the HEP community that, by intervening early, there may be a change in demographics over the years to come. During 2019, the Women in Technology Community at CERN developed two workshops for 6-9 year olds, which make the fundamental concepts of ICT and Computer Science accessible to young people with no prior experience and minimal assumed background knowledge. The immediate objectives were to demystify computer science, and to allow the children to meet a diverse set of role models from technical fields through our volunteer tutors. The workshops were run multiple times over 2019. This paper contains an overview of our motivation, describes the content of the workshops, results, lessons learnt and the future evolution of such activities.
Dataset of tau neutrino interactions recorded by the OPERA experiment
Authors: De Lellis Giovanni , Dmitrievsky Sergey , Galati Giuliana , Lavasa Artemis , Šimko Tibor , Tsanaktsidis Ioannis , Ustyuzhanin Andrey
Published: November 2020

We describe the dataset of very rare events recorded by the OPERA experiment. The events represent tracks of particles associated with tau neutrino interactions coming from the transformation of muon neutrinos due to a process known as neutrino oscillations. The events have been published on the CERN Open Data Portal. We describe the dataset semantics and the interactive event display visualisation tool accompanying the data release.
Open data provenance and reproducibility: a case study from publishing CMS open data
Authors: Šimko Tibor , de Bittencourt Heitor Pascoal , Carrera Edgar , Delgado Lopez Diyaselis , Lange Clemens , Lassila-Perini Kati , Lintuluoto Adelina , Lloret Iglesias Lara , McCauley Thomas , Okraska Jan , Prelipcean Daniel , Savaniakas Mantas
Published: November 2020

In this paper we present the latest CMS open data release published on the CERN Oopen Data portal. Samples of collision and simulated datasets were released together with detailed information about the data provenance. The associated data production chains cover the necessary computing environments, the configuration files and the computational procedures used in each data production step. We describe data curation techniques used to obtain and publish the data provenance information and we study the possibility of reproducing parts of the released data using the publicly available information. The present work demonstrates the usefulness of releasing selected samples of raw and primary data in order to fully ensure the completeness of information about the data production chain for the attention of general data scientists and other non-specialists interested in using particle physics data for education or research purposes.
Enabling validated exascale nuclear science
Authors: Davis Andrew , Dubas Aleksander , Otin Ruben
Published: November 2020

The field of fusion energy is about to enter the ITER era, for the first time we will have access to a device capable of producing 500 MW of fusion power, with plasmas lasting more than 300 seconds and with core temperatures in excess of 100-200 Million K. Engineering simulation for fusion, sits in an awkward position, a mixture of commercial and licensed tools are used, often with email driven transfer of data. In order to address the engineering simulation challenges of the future, the community must address simulation in a much more tightly coupled ecosystem, with a set of tools that can scale to take advantage of current petascale and upcoming exascale systems to address the design challenges of the ITER era.
Exploiting network restricted compute resources with HTCondor: a CMS experiment experience
Authors: Acosta-Silva Carles , Delgado Peris Antonio , Flix Molina José , Frey Jaime , Hernández José M. , Livny Miron , Pérez-Calero Yzquierdo Antonio , Tannenbaum Todd
Published: November 2020

In view of the increasing computing needs for the HL-LHC era, the LHC experiments are exploring new ways to access, integrate and use non-Grid compute resources. Accessing and making efficient use of Cloud and High Performance Computing (HPC) resources present a diversity of challenges for the CMS experiment. In particular, network limitations at the compute nodes in HPC centers prevent CMS pilot jobs to connect to its central HTCondor pool in order to receive payload jobs to be executed. To cope with this limitation, new features have been developed in both HTCondor and the CMS resource acquisition and workload management infrastructure. In this novel approach, a bridge node is set up outside the HPC center and the communications between HTCondor daemons are relayed through a shared file system. This conforms the basis of the CMS strategy to enable the exploitation of the Barcelona Supercomputing Center (BSC) resources, the main Spanish HPC site. CMS payloads are claimed by HTCondor condor_startd daemons running at the nearby PIC Tier-1 center and routed to BSC compute nodes through the bridge. This fully enables the connectivity of CMS HTCondor-based central infrastructure to BSC resources via the PIC HTCondor pool. Other challenges include building custom singularity images with CMS software releases, bringing conditions data to payload jobs, and custom data handling between BSC and PIC. This report describes the initial technical prototype, its deployment and tests, and future steps. A key aspect of the technique described in this contribution is that it could be universally employed in similar network-restrictive HPC environments elsewhere.
Meeting the challenge of JUNO simulation with Opticks: GPU optical photon acceleration via NVIDIA® OptiXTM
Authors: Blyth Simon
Published: November 2020

Opticks is an open source project that accelerates optical photon simulation by integrating NVIDIA GPU ray tracing, accessed via NVIDIA OptiX, with Geant4 toolkit based simulations. A single NVIDIA Turing architecture GPU has been measured to provide optical photon simulation speedup factors exceeding 1500 times single threaded Geant4 with a full JUNO analytic GPU geometry automatically translated from the Geant4 geometry. Optical physics processes of scattering, absorption, scintillator reemission and boundary processes are implemented within CUDA OptiX programs based on the Geant4 implementations. Wavelength-dependent material and surface properties as well as inverse cumulative distribution functions for reemission are interleaved into GPU textures providing fast interpolated property lookup or wavelength generation. Major recent developments enable Opticks to benefit from ray trace dedicated RT cores available in NVIDIA RTX series GPUs. Results of extensive validation tests are presented.
Die Novellierungen des Transplantationsgesetzes von 2019 und 2020
Authors: Rahmel Axel
Published: November 2020

In Deutschland herrscht seit Jahrzehnten ein Mangel an Spenderorganen. Bereits 2012 fanden daher 2 Novellierungen des Transplantationsgesetzes statt, jedoch ohne eine nachhaltige Verbesserung zu erwirken. Analysen der letzten Jahre wiesen auf strukturelle Defizite bei der Spendererkennung und -meldung hin und ließen die Politik tätig werden: Das Gesetz zur Verbesserung der Zusammenarbeit und der Strukturen bei der Organspende trat am 1. April 2019 in Kraft. Es stärkt insbesondere die Position der Transplantationsbeauftragten in den Entnahmekrankenhäusern. Die Kliniken erhalten zudem eine aufwandsgerechte Vergütung ihrer organspendebezogenen Aufgaben. Ein Gemeinschaftlicher Initiativplan unterstützt bei der praxisnahen Umsetzung der einzelnen Maßnahmen. Am 16. Januar 2020 folgte die Abstimmung über die Neuregelung des Gesetzes zur Organspendebereitschaft: Das Gesetz über die Stärkung der Entscheidungsbereitschaft bei der Organspende tritt im 1. Quartal 2022 in Kraft. Es
soll durch vermehrte Aufklärung und Information der Bevölkerung bewirken, dass die Auseinandersetzung mit dem Thema Organspende weiter zunimmt.
Gerinnungsmanagement in der gastroenterologischen Akut- und Intensivmedizin
Authors: Mücke Marcus M. , Miesbach Wolfgang , Peiffer Kai-Henrik , Mücke Victoria T. , Bojunga Jörg
Published: November 2020

Neben der eigentlichen definitiven Therapie einer akuten Blutung (z. B. durch endoskopische/operative Blutstillung oder Angiografie mit Coiling) kommt in der Akut- und Intensivmedizin der Optimierung der Blutgerinnung eine Schlüsselrolle zu. Dazu ist die Kenntnis der gängigen Gerinnungstests und ihrer Schwächen ebenso notwendig wie die korrekte Anwendung und Dosierung von Gerinnungsprodukten. Das Gerinnungsmanagement kann insbesondere bei Patienten mit Leberzirrhose, angeborenen und erworbenen Gerinnungsstörungen sowie bei Patienten unter Antikoagulation herausfordernd sein. Dieses Review beleuchtet die wichtigsten Elemente der Gerinnungsdiagnostik und -therapie in der gastroenterologischen Intensiv- und Notfallmedizin inklusive neuer Antidote und erweiterter Gerinnungsdiagnostik bei Patienten mit Leberzirrhose, wie z. B. die Thrombelastometrie.
Hämophagozytische Syndrome beim Erwachsenen
Authors: Schenk Thomas , Birndt Sebastian , Rosée Paul La
Published: November 2020

Die Hämophagozytische Lymphohistiozytose (HLH) ist ein Zytokinsturm-Syndrom, das bei Erwachsenen in der Regel durch Malignome, Infektionen oder autoinflammatorische/autoimmunologische Erkrankungen ausgelöst wird. In der Rheumatologie ist das Erkrankungsbild besser als Makrophagenaktivierungs-Syndrom bekannt (MAS-HLH). Die HLH entsteht auf dem Boden eines genetisch bedingten und/oder erworbenen dysfunktionalen Immunsystems. Im Unterschied zur hereditären primären HLH (pHLH) bei Kindern findet sich bei der adulten, zumeist sekundären HLH (sHLH) nur sehr selten eine monogenetische Ursache. In Einzelfällen kann sich aber eine „late onset“-genetische HLH auch erst im Erwachsenenalter manifestieren. Die Diagnose von HLH und MAS wird verzögert durch die unspezifische Symptomatik (Fieber, Zytopenie, Ferritinanstieg, Splenomegalie, Multiorganversagen), die sich mit der Grunderkrankung oder einem SIRS überlagern kann. Die namengebende Hämophagozytose lässt sich nur bei einem Teil der Patienten nachweisen. sHLH und MAS-HLH weisen unbehandelt eine hohe Mortalität auf. Diagnosekriterien für pHLH und MAS sowie das standardisierte HLH-2004-Therapieprotokoll wurden in der Pädiatrie kontinuierlich in klinischen Studien entwickelt. In angepasster Form werden Kriterien und Substanzen des pädiatrischen HLH-Protokolls auch bei Erwachsenen angewendet. Zunehmend kommen neue Therapien zum Einsatz, welche die Hyperzytokinämie und deren Auswirkungen bei HLH und MAS bremsen (z. B. Ruxolitinib oder Anakinra). Der folgende Artikel soll eine Übersicht zu Epidemiologie, Diagnostik und Therapie von HLH und MAS bei Erwachsenen geben.
Alterations in BDNF Protein Concentrations in the Hippocampus do not Explain the Pro-Neurogenic Effect of Citalopram on Adult Neurogenesis
Authors: Petermann Markus , Kronenberg Golo , Hellweg Rainer , Klempin Friederike , Mosienko Valentina , Bader Michael , Alenina Natalia
Published: November 2020

Introduction Brain-derived neurotrophic factor (BDNF) has been implicated in the pro-neurogenic effect of selective serotonin reuptake inhibitors. In this study, we used Tph2

−/−
mice lacking brain serotonin to dissect the interplay between BDNF and the serotonin system in mediating the effects of antidepressant pharmacotherapy on adult neurogenesis in the hippocampus.

Methods Besides citalopram (CIT), we tested tianeptine (TIA), an antidepressant whose mechanism of action is not well understood. Specifically, we examined cell survival and endogenous concentrations of BDNF following daily injection of the drugs.

Results Twenty-one days of CIT, but not of TIA, led to a significant increase in the survival of newly generated cells in the dentate gyrus of wild-type mice, without a significant effect on BDNF protein levels by either treatment. In Tph2

−/−
mice, adult neurogenesis was consistently increased. Furthermore, Tph2

−/−
mice showed increased BDNF protein levels, which were not affected by TIA but were significantly reduced by CIT.

Discussion We conclude that the effects of CIT on adult neurogenesis are not explained by changes in BDNF protein concentrations in the hippocampus.
Mechanisms of ligand binding
Authors: Di Cera Enrico
Published: November 2020

Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
Turbulent wake suppression of circular cylinder flow by two small counter-rotating rods
Authors: Yu Zhipeng , Ping Huan , Liu Xu , Zhu Hongbo , Wang Rui , Bao Yan , Zhou Dai , Han Zhaolong , Xu Hui
Published: November 2020

In this paper, we employ the high-fidelity spectral/hp method to investigate the control of wake turbulence behind a circular cylinder by direct numerical simulations. The preliminary results at Re = 500 show that, for rod rotation rate α > 3, the cylinder wake is stabilized and the flow achieves a steady state. To further explore the efficiency of this control at the early turbulent regime, we further increase the Reynolds number to 3900. Compared to the bare cylinder, the drag coefficient is measured to reduce by 25.1% for α = 2. This drag reduction is expected to result from the pressure recovery effects of rotating rods. The statistical analysis, in terms of contours of Reynolds stresses and turbulence kinetic energy, and the turbulent wake visualization are then performed in order to show the alteration of turbulent flow. Furthermore, by applying Bernoulli equation to a streamline encircling the control rod, we show that the mechanism of pressure recovery is still viscous in the turbulent regime of Re = 3900. However, it is expected that the inertial effect sets out to play a significant role farther away from the main cylinder.
Modeling interaction between a Taylor bubble and small bubble in a rectangular column
Authors: Rohilla Lokesh , Das Arup Kumar
Published: November 2020

The slip of a small bubble (SB) from the annular film of the slug/Taylor bubble (TB) is often encountered in the chemical reactors and has intrigued many researchers. A combined experimental and numerical study has been performed to investigate the interaction of the SB and the slug bubble in a rectangular column with viscous fluids. The interaction behavior of the SB depends upon its diameter, deq, and thermo-physical properties of the fluid. The SB sprints away from the slug bubble at low Morton numbers, Mo=ρl−ρggμ4/ρl2σ3 (sprint-away regime). On the other hand, SB interacts with TB due to its lower terminal velocity at higher Mo (bubble slip regime). The SB behaves independently ahead of the TB nose but accelerates linearly into its annular film. A regime map has been proposed to differentiate between the bubble slip and the sprint-away regime. The entrapped film between TB and SB is continuously fed from the annular film and avoids the coalescence. An ad hoc pressure jump model has been proposed to explain the repulsion of SB in the annular film. Furthermore, a modified lubrication theory based model predicted the stability of the entrapped film due to interfacial velocities and curvature.
Index polarity inversion by helicity inversion in Stokes vortices
Authors: Pal Sushanta Kumar , Senthilkumaran P.
Published: November 2020

To describe the state of polarization (SOP) of light, the Stokes parameters are obtained using intensity measurements made at different component polarization states. Using these Stokes parameters, complex field distributions called Stokes fields can be synthesized, and the phase singularities present in these Stokes fields are called Stokes vortices. The SOP of a Stokes vortex can be either linear or circular at the singular point. Of the three types of Stokes vortices, only one of them has handedness associated with it. We show here that changing the handedness of this Stokes vortex results in index sign inversion for the other two types of Stokes vortices. To accomplish handedness inversion without Stokes index sign inversion, a new phase engineering method is introduced here. The current study may unfold applications in the optical chirality measurement and structured illumination microscopy.
Coarse graining molecular dynamics with graph neural networks
Authors: Husic Brooke E. , Charron Nicholas E. , Lemm Dominik , Wang Jiang , Pérez Adrià , Majewski Maciej , Krämer Andreas , Chen Yaoyi , Olsson Simon , de Fabritiis Gianni , Noé Frank , Clementi Cecilia
Published: November 2020

Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at an atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it are consistent with the conclusions we would draw from a model at a finer level of detail. It has been proved that a force matching scheme defines a thermodynamically consistent coarse-grained model for an atomistic system in the variational limit. Wang et al. [ACS Cent. Sci. 5, 755 (2019)] demonstrated that the existence of such a variational limit enables the use of a supervised machine learning framework to generate a coarse-grained force field, which can then be used for simulation in the coarse-grained space. Their framework, however, requires the manual input of molecular features to machine learn the force field. In the present contribution, we build upon the advance of Wang et al. and introduce a hybrid architecture for the machine learning of coarse-grained force fields that learn their own features via a subnetwork that leverages continuous filter convolutions on a graph neural network architecture. We demonstrate that this framework succeeds at reproducing the thermodynamics for small biomolecular systems. Since the learned molecular representations are inherently transferable, the architecture presented here sets the stage for the development of machine-learned, coarse-grained force fields that are transferable across molecular systems.
Consistent spin decontamination of broken-symmetry calculations of diradicals
Authors: David Grégoire , Trinquier Georges , Malrieu Jean-Paul
Published: November 2020

Broken-symmetry calculations of diradicals exploit the mean-field energies of determinants that are not eigenfunctions of the Ŝ2 operator, the mean value of which is close to 1 for the ms = 0 solution. This spin contamination must be corrected. Two different contributions affect ⟨Ŝ2⟩, namely, the mixing between neutral and ionic valence bond components, the so-called kinetic exchange, which decreases ⟨Ŝ2⟩, and the spin polarization of the supposedly closed shell orbitals, which increases ⟨Ŝ2⟩. The popular Yamaguchi formula is valid for the first effect but irrelevant for the second one. From a few constrained broken-symmetry calculations, one may treat separately the two contributions and apply their specific spin decontamination correction. This work proposes a consistent spin-decontaminated procedure for the evaluation of singlet–triplet gaps in diradicals.
Energetics of a bouncing drop: Coefficient of restitution, bubble entrapment, and escape
Authors: Sharma Praveen K. , Dixit Harish N.
Published: November 2020

Drops bouncing on an ultra-smooth solid surface can either make contact with the surface or be supported on a thin cushion of gas. If the surface is superhydrophobic, either complete or partial rebound usually occurs. Recent experiments have shed light on the lubrication effect of the underlying gas layer at the onset of impact. Using axisymmetric direct numerical simulations, we shed light on the energetics of a drop bouncing from a solid surface. A complete energy budget of the drop and the surrounding gas during one complete bouncing cycle reveals a complex interplay between various energies that occur during impact. Using a parametric study, we calculate the coefficient of restitution as a function of Reynolds and Weber numbers, and the results are in good agreement with the reported experiments. Our simulations reveal that the Weber number, not the Reynolds number, has a stronger effect on energy losses as the former affects the shape of the drop during impact. At higher Weber and Reynolds numbers, a tiny gas bubble gets trapped inside the drop during impact. We show that a large amount of dissipation occurs during the bubble entrapment and escape process. Finally, analysis of the flow field in the underlying gas layer reveals that maximum dissipation occurs in this layer, and a simple scaling law is derived for dissipation that occurs during impact.
Phylogenetic placement of the stone-nest orb-weaving spider Nemoscolus Simon, 1895 (Araneae : Araneidae) and the description of the first species from Australia
Authors: Kallal Robert J. , Hormiga Gustavo
Published: November 2020

The spider genus Nemoscolus Simon, 1895 (Araneidae) has been neglected taxonomically despite the unique retreat that several species construct in their horizontal orb-webs, composed of pebbles and other detritus. The distribution of Nemoscolus is poorly known and the genus includes species from Africa and Europe. Nemoscolus is placed in Simon’s Cycloseae species group along with Cyclosa Menge, 1866, Acusilas Simon, 1895, Arachnura Vinson, 1863, Witica O. Pickard-Cambridge, 1895, among others. Here we describe a new species from Queensland, Australia, N. sandersi, sp. nov., drastically expanding the distribution range of the genus. We use nucleotide sequence data to phylogenetically place Nemoscolus using model-based inference methods within Araneidae and to explore its affinities to Simon’s Cycloseae. The data support propinquity of Nemoscolus with Acusilas and Arachnura but not with Cyclosa. Our analyses suggest that Cycloseae is not a clade, with Cyclosa, Acusilas, Witica and Nemoscolus not sharing a recent common ancestor. This use of an integrated granular retreat represents at least the second independent evolution of such a structure within Araneidae. These results improve our understanding of both phylogeny and retreat evolution in araneid spiders.
Early growing season immobilisation affects post-tillering wheat nitrogen uptake from crop stubble and 15N fertiliser in a sandy soil
Authors: Muschietti Piana Pilar , McBeath Therese Marie , McNeill Ann Marie , Cipriotti Pablo Ariel , Gupta Vadakattu
Published: November 2020

In semiarid sandy soil environments there is a dual challenge of carbon and nitrogen (N) limitation that needs to be managed to ensure timely supply of N to crops. Management of N inputs to soil using combinations of legume stubble addition and fertiliser N in cereal systems is essential to meet crop demand and maintain N in soil organic matter. The aim of this study was to assess soil mineral and biological N pools that influence N supply and N uptake of wheat at early growth stages. The recovery of 15N-labelled fertiliser by wheat was evaluated using a factorial combination of either wheat, lupin or no stubble incorporated with or without 15N fertiliser in a sandy soil system. Soil and plant samples were collected at sowing, tillering, first node and booting to monitor changes in N pools and 15N uptake by the wheat. Crop stubble incorporation one week before sowing increased biological N pools in the surface soil (0–10 cm). Early N immobilisation (sowing–tillering) in all the treatments without 15N fertiliser may have limited N availability for wheat uptake in the subsequent period (tillering–first node), when fertiliser N appeared critical to maximise N supply for plant requirements. Up to 38% of the 15N fertiliser applied at sowing was incorporated into the soil microbial biomass pool, so that fertiliser N was critical to relieve short-term inherent N limitations for both plant and microbial growth, and to supply the longer-term biological pools (microbial biomass) to support subsequent mineralisation potential. Reducing the energy limitation to the microbial pool through inputs of carbon from stubble was also critical to ensure fertiliser N supplied sufficient N to satisfy plant demand later in the growing period. These results have implications for management decisions on semiarid sandy soil systems that aim to synchronise N from inputs of legume stubbles and fertiliser with crop N demand during early growth stages of wheat.
Corrigendum to: Prioritising fuels reduction for water supply protection
Authors: Gannon Benjamin M. , Wei Yu , MacDonald Lee H. , Kampf Stephanie K. , Jones Kelly W. , Cannon Jeffery B. , Wolk Brett H. , Cheng Antony S. , Addington Robert N. , Thompson Matthew P.
Published: November 2020

Concerns over wildfire impacts to water supplies have motivated efforts to mitigate risk by reducing forest fuels. Methods to assess fuel treatment effects and prioritise their placement are needed to guide risk mitigation efforts. We present a fuel treatment optimisation model to minimise risk to multiple water supplies based on constraints for treatment feasibility and cost. Risk is quantified as the expected sediment impact costs to water supplies by combining measures of fire likelihood and behaviour, erosion, sediment transport and water supply vulnerability. We demonstrate the model's utility for prioritising fuel treatments in two large watersheds in Colorado, USA, that are critical for municipal water supply. Our results indicate that wildfire risk to water supplies can be substantially reduced by treating a small portion of the watersheds that have dense, fire-prone forests on steep slopes that drain to water supply infrastructure. Our results also show that the cost of fuel treatments outweighs the expected cost savings from reduced sediment inputs owing to the low probability of fuel treatments encountering wildfire and the high cost of thinning forests. This highlights the need to expand use of more cost-effective treatments, like prescribed fire, and to identify fuel treatment projects that benefit multiple resources.
Bulk spin conductivity of three-dimensional topological insulators
Authors: Akzyanov R S
Published: November 2020

We study the spin conductivity of the bulk states of three-dimensional topological insulators within Kubo formalism. Spin Hall effect is the generation of the spin current that is perpendicular to the applied voltage. In the case of a three-dimensional topological insulator, applied voltage along x direction generates transverse spin currents along y and z directions with comparable values. We found that finite non-universal value of the spin conductivity exists in the gapped region due to the inversion of bands. Contribution to the spin conductivity from the vertex corrections enhances the spin conductivity from the filled states. These findings explain large spin conductivity that has been observed in topological insulators.
A two-stage optimal sensor placement method for multi-type structural response reconstruction
Authors: Liu Chengyin , Jiang Zhaoshuo , Gong Yi , Xiao Yongfeng
Published: November 2020

Optimal multi-type sensor placement has gained considerable attention in the structural health monitoring field during the past few years. Although a structural response reconstruction-oriented optimization method for a multi-type sensor has been developed, the challenge of information redundancy in the collected signal deserves further investigation. To tackle this challenge, this paper presents a two-stage optimization framework for response reconstruction with the capability to reduce the multi-type sensor information redundancy. In the first stage, the optimization of multi-type sensor placement for response reconstruction is performed to initially determine the optimal sensor deployment scheme. After the optimal sensor locations are selected, the second-stage optimization introduces a metric, called the distance coefficient, to evaluate the information independence level between sensor locations with the goal of reducing the sensor information redundancy. A numerical study on a bridge model is first performed to evaluate the feasibility of the proposed framework, after which a lab-scale physical bridge model is tested to validate its effectiveness. Both the numerical and experimental results demonstrate that the proposed two-stage optimization framework can reduce the sensor information redundancy and, at the same time, produce a satisfying result in the response reconstruction of key locations.