Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Klystron Measurement and Protection System for XFEL on the uTCA Architecture

The European XFEL free-electron laser is under construction at the DESY. The driving engineof the superconducting accelerator will be 27 RF station. Each of an underground RF stationconsist from multi beam horizontal klystron which can provide up to 10MW of power at1.3GHz. The XFEL should work continuously over 20 years with only 1 day per month formaintenance. In order to meet so demanding requirement lifetime of the MBK should be aslong as possible. In the real operation the lifetime of tube can be thoroughly reduced by serviceconditions. To minimize the influence of service conditions to the klystrons lifetime thespecial fast protection system named as Klystron Lifetime Management System (KLM) hasbeen developed, the main task of this system is to detect all events which can destroy thetube as quickly as possible, and then stop input power to the tube and send signal to stopHV pulse. The tube recovery procedure should depend on the kind of events has happened.KLM is based on the standard LLRF uTCA system for XFEL with additional DC channels.This article gives an overview of implementation of measurement and protection systeminstalled at klystron test stand

The Self Excited Loop Cavity Field Controller and the Cavity Simulator Implemented in MTCA.4 System

The superconducting cavity vertical test stand at DESY is going to be updated with the MTCA.4 based system. The digital self exited loop (SEL) LLRF controller has been developed to fulfill the requirements for the controller to drive the cavity with high QL up to 1e10 and high cavity detuning up to 10kHz. In order to test the SEL controller, additionally the real-time cavity simulator has been developed. The electrical and mechanical model of a cavity represented by a differential equation, is implemented inside the FPGA. The model takes the forward power as an input and produces a probe signal based on given detuning and half-bandwidth parameters of a cavity. Microphonic disturbance is also added to simulate the high Ql operation.Both, the cavity simulator and the SEL controller has been implemented in the SIS8300KU, DRTM-DW8VM1 pair boards

A Model-Based Fast Protection System for High-Power RF Tube Amplifiers Used at the European XFEL Accelerator

The driving engine of the superconducting accelerator of the European X-ray free electron laser (XFEL) is a set of 27 radio frequency (RF) stations. Each of the underground RF stations consists of a multibeam horizontal klystron that can provide up to 10 MW of power at 1.3 GHz. Klystrons are sensitive devices with a limited lifetime and a high mean time between failures. In real operation, the lifetime of the tube can be significantly reduced because of failures. The special fast protection klystron lifetime management (KLM) system has been developed to minimize the influence of service conditions on the lifetime of klystrons. The main task of this system is to detect all events which can destroy the tube as quickly as possible, and switch off the driving RF signal or the high voltage. Detection of events is based on a comparison of the value of the real signal obtained at the system output with the value estimated on the basis of a high-power RF amplifier model and input signals. The KLM system has been realized in field-programmable gate array (FPGA) and implemented in XFEL. Implementation is based on the standard low-level RF micro telecommunications computing architecture (MTCA.4 or xTCA). The main part of the paper focuses on an estimation of the klystron model and the implementation of KLM in FPGA. The results of the performance of the KLM system will also be presented

A Model Based Fast Protection System for High Power RF Tube Amplifiers Used at the European XFEL Accelerator

The driving engine of the superconducting accelerator of the European X-ray free electron laser (XFEL) is a set of 27 radio frequency (RF) stations. Each of the underground RF stations consists of a multibeam horizontal klystron that can provide up to 10 MW of power at 1.3 GHz. Klystrons are sensitive devices with a limited lifetime and a high mean time between failures. In real operation, the lifetime of the tube can be significantly reduced because of failures. The special fast protection klystron lifetime management (KLM) system has been developed to minimize the influence of service conditions on the lifetime of klystrons. The main task of this system is to detect all events which can destroy the tube as quickly as possible, and switch off the driving RF signal or the high voltage. Detection of events is based on a comparison of the value of the real signal obtained at the system output with the value estimated on the basis of a high-power RF amplifier model and input signals. The KLM system has been realized in field-programmable gate array (FPGA) and implemented in XFEL. Implementation is based on the standard low-level RF micro telecommunications computing architecture (MTCA.4 or xTCA). The main part of the paper focuses on an estimation of the klystron model and the implementation of KLM in FPGA. The results of the performance of the KLM system will also be presented

Model Based Fast Protection System for High Power RF Tube Amplifiers Used at European XFEL Accelerator

The driving engine of the superconducting accelerator of the European X-ray Free-Electron Laser (XFEL) are 27 Radio Frequency (RF) stations. Each of an underground RF station consists from multi-beam horizontal klystron which can provide up to 10MW of power at 1.3GHz. Klystrons are sensitive devices with limited lifetime and high mean time between failures. In the real operation the lifetime of the tube can be thoroughly reduced by failures. To minimize the influence of service conditions to the klystrons lifetime the special fast protection system named as Klystron Lifetime Management System (KLM) has been developed. The main task of this system is to detect all events which can destroy the tube as quickly as possible and switch off driving signal. Detection of events is based on comparison of model of high power RF amplifier with real signals. All algorithms are implemented in Field Programmable Gate Array (FPGA). For the XFEL implementation of KLM is based on the standard Low Level RF (LLRF) Mi-cro TCA technology (MTCA.4 or xTCA).This article focus on the klystron model estimation for protection system and implementation of KLM in FPGA on MTCA.4 architecture

Controller Latency Improvements at REGAE

REGAE is a facility for ultrafast electron diffraction (UED) experiments based on a normal conducting S-band gun and buncher cavity. Their RF regulation is performed by a single cavity controller, implemented by an FPGA firmware and operating at 125 MHz. With a variant of the Struck SIS8300-KU controller board that is equipped with 250 MSps ADCs we were able to increase the frequency of the complete digital processing chain to 250 MHz. This includes the ADCs, field detection, feedback controller and DAC. Doubling the frequency reduced the overall controller latency by almost a factor of two. In the poster we show which firmware components had to be optimized or rewritten to achieve the 250 MHz clock rate

Co-Simulation of HDL Using Python and MATLAB Over Tcl TCP/IP Socket in Xilinx Vivado and Modelsim Tools

This paper presents the solution, which helps in the simulation and verification of the implementation of the Digital Signal Processing (DSP) algorithms written in hardware description language (HDL). Many vendor tools such as Xilinx ISE/Vivado or Mentor Graphics ModelSim are using Tcl as an application programming interface. The main idea of the co-simulation is to use the Tcl TCP/IP socket, which is Tcl build in feature, as the interface to the simulation tool. Over this interface the simulation is driven by the external tool. The stimulus vectors as well as the model and verification are implemented in Python or MATLAB and the data with simulator is exchanged over dedicated protocol. The tool, which was called cosimtcp, was developed in Deutsches Elektronen-Synchrotron (DESY). The tool is a set of scripts that provide a set of functions. This tool has been successfully used to verify many DSP algorithms implemented in the FPGA chips of the Low Level Radio Frequency (LLRF) and synchronization systems of the European X-Ray Free Electron Laser (E-XFEL) accelerator. Cosimtcp is an open source available tool