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

FPGA Firmware Framework for MTCA.4 AMC Modules

Many of the modules in specific hardware architectures use the same or similar communication interfaces and IO connectors. MicroTCA (MTCA.4) is one example of such a case. All boards: communicate with the central processing unit (CPU) over PCI Express (PCIe), send data to each other using Multi-Gigabit Transceivers (MGT), use the same backplane resources and have the same Zone3 IO or FPGA mezzanine card (FMC) connectors. All those interfaces are connected and implemented in Field Programmable Gate Array (FPGA) chips. It makes possible to separate the interface logic from the application logic. This structure allows to reuse already done firmware for one application and to create new application on the same module. Also, already developed code can be reused in new boards as a library. Proper structure allows the code to be reused and makes it easy to create new firmware. This paper will present structures of firmware framework and scripting ideas to speed up firmware development for MTCA.4 architecture. European XFEL control systems firmware, which uses the described framework, will be presented as example

Automated interactive video playback for studies of animal communication

Video playback is a widely-used technique for the controlled manipulation and presentation of visual signals in animal communication. In particular, parameter-based computer animation offers the opportunity to independently manipulate any number of behavioral, morphological, or spectral characteristics in the context of realistic, moving images of animals on screen. A major limitation of conventional playback, however, is that the visual stimulus lacks the ability to interact with the live animal. Borrowing from video-game technology, we have created an automated, interactive system for video playback that controls animations in response to real-time signals from a video tracking system. We demonstrated this method by conducting mate-choice trials on female swordtail fish, Xiphophorus birchmanni. Females were given a simultaneous choice between a courting male conspecific and a courting male heterospecific (X. malinche) on opposite sides of an aquarium. The virtual male stimulus was programmed to track the horizontal position of the female, as courting males do in the wild. Mate-choice trials on wild-caught X. birchmanni females were used to validate the prototype's ability to effectively generate a realistic visual stimulus. © 2011 Journal of Visualized Experiments

Evaluation of an ATCA Based LLRF System at FLASH.

Abstract: Future RF Control systems will require simultaneous data acquisition of up to 100 fast ADC channels at sampling rates of around 100 MHz and real time signal processing within a few hundred nanoseconds. At the same time the standardization of Low-Level RF systems are common objectives for all laboratories for cost reduction, performance optimization and machine reliability. Also desirable are modularity and scalability of the design as well as compatibility with accelerator instrumentation needs including the control system. All these requirements can be fulfilled with the new telecommunication standard ATCA when adopted to the domain of instrumentation. We describe the architecture and design of an ATCA based LLRF system for the European XFEL. Initial results of the demonstration of such a system at the FLASH user facility will be presented. Presented are the results of operating essential components of a prototyp