brat: a Web-based Tool for NLP-Assisted Text Annotation

We introduce the brat rapid annotation tool (BRAT), an intuitive web-based tool for text annotation supported by Natural Language Processing (NLP) technology. BRAT has been developed for rich structured annotation for a variety of NLP tasks and aims to support manual curation efforts and increase annotator productivity using NLP techniques. We discuss several case studies of real-world annotation projects using pre-release versions of BRAT and present an evaluation of annotation assisted by semantic class disambiguation on a multicategory entity mention annotation task, showing a 15 % decrease in total annotation time. BRAT is available under an opensource license from

Analysis of time-profiles with in-beam PET monitoring in charged particle therapy

Background: Treatment verification with PET imaging in charged particle therapy is conventionally done by comparing measurements of spatial distributions with Monte Carlo (MC) predictions. However, decay curves can provide additional independent information about the treatment and the irradiated tissue. Most studies performed so far focus on long time intervals. Here we investigate the reliability of MC predictions of space and time (decay rate) profiles shortly after irradiation, and we show how the decay rates can give an indication about the elements of which the phantom is made up. Methods and Materials: Various phantoms were irradiated in clinical and near-clinical conditions at the Cyclotron Centre of the Bronowice proton therapy centre. PET data were acquired with a planar 16x16 cm$^2$ PET system. MC simulations of particle interactions and photon propagation in the phantoms were performed using the FLUKA code. The analysis included a comparison between experimental data and MC simulations of space and time profiles, as well as a fitting procedure to obtain the various isotope contributions in the phantoms. Results and conclusions: There was a good agreement between data and MC predictions in 1-dimensional space and decay rate distributions. The fractions of $^{11}$C, $^{15}$O and $^{10}$C that were obtained by fitting the decay rates with multiple simple exponentials generally agreed well with the MC expectations. We found a small excess of $^{10}$C in data compared to what was predicted in MC, which was clear especially in the PE phantom.Comment: 9 pages, 5 figures, 1 table. Proceedings of the 20th International Workshop on Radiation Imaging Detectors (iWorid2018), 24-28 June 2018, Sundsvall, Swede

Monitoring Proton Therapy Through In-Beam PET: An Experimental Phantom Study

In this paper, we investigate the use of a positron emission tomography (PET) system to monitor the proton therapy. The monitoring procedure is based on the comparison between the β+ activity generated in the irradiated volume during the treatment, with the β+ activity distribution obtained with Monte Carlo (MC) simulation. The dedicated PET system is a dual head detection system; each head is composed of nine scintillating LYSO crystal matrices read out independently with a custom modularized acquisition system. Our experimental data were acquired at the Cyclotron Centre Bronowice, Institute Nuclear Physics in Kraków, Poland, and were simulated with the FLUKA MC code. Homogeneous and heterogeneous plastic phantoms were irradiated with monoenergetic 130 MeV protons. The capabilities of our PET system to distinguish different irradiated materials were investigated, and the proton pencil-beams were used as probes. Our focus was to analyze the activity width and the total activity event number in several cases. Irradiations were performed using either single pencil-beams one at a time, or two pencil-beams during the same data taking. The comparison of 1-D activity profile for experimental data and MC simulation were always in good agreement showing that, the treatment quality assessment in proton therapy can be based on β+ activity measurements

Adaptive model-driven user interface development systems

Adaptive user interfaces (UIs) were introduced to address some of the usability problems that plague many software applications. Model-driven engineering formed the basis for most of the systems targeting the development of such UIs. An overview of these systems is presented and a set of criteria is established to evaluate the strengths and shortcomings of the state-of-the-art, which is categorized under architectures, techniques, and tools. A summary of the evaluation is presented in tables that visually illustrate the fulfillment of each criterion by each system. The evaluation identified several gaps in the existing art and highlighted the areas of promising improvement

Toward High Performance Computing Education

High Performance Computing (HPC) is the ability to process data and perform complex calculations at extremely high speeds. Current HPC platforms can achieve calculations on the order of quadrillions of calculations per second with quintillions on the horizon. The past three decades witnessed a vast increase in the use of HPC across different scientific, engineering and business communities, for example, sequencing the genome, predicting climate changes, designing modern aerodynamics, or establishing customer preferences. Although HPC has been well incorporated into science curricula such as bioinformatics, the same cannot be said for most computing programs. This working group will explore how HPC can make inroads into computer science education, from the undergraduate to postgraduate levels. The group will address research questions designed to investigate topics such as identifying and handling barriers that inhibit the adoption of HPC in educational environments, how to incorporate HPC into various curricula, and how HPC can be leveraged to enhance applied critical thinking and problem solving skills. Four deliverables include: (1) a catalog of core HPC educational concepts, (2) HPC curricula for contemporary computing needs, such as in artificial intelligence, cyberanalytics, data science and engineering, or internet of things, (3) possible infrastructures for implementing HPC coursework, and (4) HPC-related feedback to the CC2020 project

Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study

Electrophysiological studies of the human heart face the fundamental challenge that experimental data can be acquired only from patients with underlying heart disease. Regarding human atria, there exist sizable gaps in the understanding of the functional role of cellular Ca2+ dynamics, which differ crucially from that of ventricular cells, in the modulation of excitation-contraction coupling. Accordingly, the objective of this study was to develop a mathematical model of the human atrial myocyte that, in addition to the sarcolemmal (SL) ion currents, accounts for the heterogeneity of intracellular Ca2+ dynamics emerging from a structurally detailed sarcoplasmic reticulum (SR). Based on the simulation results, our model convincingly reproduces the principal characteristics of Ca2+ dynamics: 1) the biphasic increment during the upstroke of the Ca2+ transient resulting from the delay between the peripheral and central SR Ca2+ release, and 2) the relative contribution of SL Ca2+ current and SR Ca2+ release to the Ca2+ transient. In line with experimental findings, the model also replicates the strong impact of intracellular Ca2+ dynamics on the shape of the action potential. The simulation results suggest that the peripheral SR Ca2+ release sites define the interface between Ca2+ and AP, whereas the central release sites are important for the fire-diffuse-fire propagation of Ca2+ diffusion. Furthermore, our analysis predicts that the modulation of the action potential duration due to increasing heart rate is largely mediated by changes in the intracellular Na+ concentration. Finally, the results indicate that the SR Ca2+ release is a strong modulator of AP duration and, consequently, myocyte refractoriness/excitability. We conclude that the developed model is robust and reproduces many fundamental aspects of the tight coupling between SL ion currents and intracellular Ca2+ signaling. Thus, the model provides a useful framework for future studies of excitation-contraction coupling in human atrial myocytes

Peripheral nerve findings in hereditary coproporphyria. Light and ultrastructural studies in two sural nerve biopsies.

In spite of several cases reported in the literature, the exact pathogenetic mechanism of neuropathic changes in porphyric neuropathy remains uncertain. Various authors have ascribed the neuropathologic findings to either a dying-back axonal degeneration or segmental demyelination. In recent years, the hypothesis of an axonal and myelinic disorder has received support by the demonstration of a combined and simultaneous involvement of both these structures. Such different opinions are also a consequence of the reduced number of detailed bioptic observations in the different forms of acute porphyria not only during acute phases but also between attacks. In this paper we report the results of light- and electron-microscopic examination of two sural nerve biopsies from subjects with hereditary coproporphyria. The first was performed 6 months after an acute attack, the second specimen was obtained from a patient without acute attacks, who had clinical and electrophysiologic signs of a chronic progressive neuropathy. In both cases a dying-back axonal degeneration is considered the primary change. The pathogenetic mechanism of peripheral nerve lesions in porphyric neuropathy will be discussed finally

Hereditary coproporphyria: unusual nervous system involvement in two cases.

Two cases of hereditary coproporphyria showed unusual nervous system involvement, one epilepsy with onset in childhood, and the other chronic central and peripheral nervous system damage. The literature is briefly discussed