Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases (ICD) as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the ICD, which is currently under active development by the WHO contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding how these stakeholders collaborate will enable us to improve editing environments that support such collaborations. We uncover how large ontology-engineering projects, such as the ICD in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users subsequently change) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology-engineering projects and tools in the biomedical domain.Comment: Published in the Journal of Biomedical Informatic

Decellularized homograft for aortic valve replacement two years after lung transplantation

Cardiac valvular surgery in patients after lung transplantation is a challenging procedure, reports are scarce. We report a 29-year-old patient who underwent concomitant mitral valve reconstruction and implantation of a decellularized aortic homograft two years after bilateral lung transplantation.Cardiac valvular surgery in patients after lung transplantation is a challenging procedure, reports are scarce. We report a 29-year-old patient who underwent concomitant mitral valve reconstruction and implantation of a decellularized aortic homograft two years after bilateral lung transplantation

Preliminary study of kaonic deuterium X-rays by the SIDDHARTA experiment at DAFNE

The study of the KbarN system at very low energies plays a key role for the understanding of the strong interaction between hadrons in the strangeness sector. At the DAFNE electron-positron collider of Laboratori Nazionali di Frascati we studied kaonic atoms with Z=1 and Z=2, taking advantage of the low-energy charged kaons from Phi-mesons decaying nearly at rest. The SIDDHARTA experiment used X-ray spectroscopy of the kaonic atoms to determine the transition yields and the strong interaction induced shift and width of the lowest experimentally accessible level (1s for H and D and 2p for He). Shift and width are connected to the real and imaginary part of the scattering length. To disentangle the isospin dependent scattering lengths of the antikaon-nucleon interaction, measurements of Kp and of Kd are needed. We report here on an exploratory deuterium measurement, from which a limit for the yield of the K-series transitions was derived: Y(K_tot)<0.0143 and Y(K_alpha)<0.0039 (CL 90%). Also, the upcoming SIDDHARTA-2 kaonic deuterium experiment is introduced.Comment: Accepted by Nuclear Physics

X-ray transition yields of low-Z kaonic atoms produced in Kapton

The X-ray transition yields of kaonic atoms produced in Kapton polyimide (C22H10N2O5) were measured for the first time in the SIDDHARTA experiment. X-ray yields of the kaonic atoms with low atomic numbers (Z = 6, 7, and 8) and transitions with high principal quantum numbers (n = 5-8) were determined. The relative yield ratios of the successive transitions and those of carbon-to-nitrogen (C:N) and carbon-to-oxygen (C:O) were also determined. These X-ray yields provide important information for understanding the capture ratios and cascade mechanisms of kaonic atoms produced in a compound material, such as Kapton.Comment: Accepted in Nucl. Phys. A (2013

First measurement of kaonic helium-3 X-rays

The first observation of the kaonic 3He 3d - 2p transition was made using slow K- mesons stopped in a gaseous 3He target. The kaonic atom X-rays were detected with large-area silicon drift detectors using the timing information of the K+K- pairs of phi-meson decays produced by the DAFNE e+e- collider. The strong interaction shift of the kaonic 3He 2p state was determined to be -2+-2 (stat)+-4 (syst) eV.Comment: Accepted for publication in Phys. Lett.

A New Measurement of Kaonic Hydrogen X rays

The $\bar{K}N$ system at threshold is a sensitive testing ground for low energy QCD, especially for the explicit chiral symmetry breaking. Therefore, we have measured the $K$-series x rays of kaonic hydrogen atoms at the DA$\Phi$NE electron-positron collider of Laboratori Nazionali di Frascati, and have determined the most precise values of the strong-interaction energy-level shift and width of the $1s$ atomic state. As x-ray detectors, we used large-area silicon drift detectors having excellent energy and timing resolution, which were developed especially for the SIDDHARTA experiment. The shift and width were determined to be $\epsilon_{1s} = -283 \pm 36 \pm 6 {(syst)}$ eV and $\Gamma_{1s} = 541 \pm 89 {(stat)} \pm 22 {(syst)}$ eV, respectively. The new values will provide vital constraints on the theoretical description of the low-energy $\bar{K}N$ interaction.Comment: 5 figures, submitted to Physics Letters

The importance of individual variation for the interpretation of behavioural studies: ethanol effects vary with basal activity level in zebrafish larvae

Standardization and reduction of variation is key to behavioural screening of animal models in toxicological and pharmacological studies. However, individual variation in behavioural and physiological phenotypes remains in each laboratory population and can undermine the understanding of toxicological and pharmaceutical effects and their underlying mechanisms. Here, we used zebrafish (ABTL-strain) larvae to explore individual consistency in activity level and emergence time, across subsequent days of early development (6-8 dpf). We also explored the correlation between these two behavioural parameters. We found inter-individual consistency over time in activity level and emergence time, but we did not find a consistent correlation between these parameters. Subsequently, we investigated the impact of variation in activity level on the effect of a 1% ethanol treatment, suitable for our proof-of-concept case study about whether impact from pharmacological treatments might be affected by inter-individual variation in basal locomotion. The inter-individual consistency over time in activity level did not persist in this test. This was due to the velocity change from before to after exposure, which turned out to be a dynamic individual trait related to basal activity level: low-activity individuals raised their swimming velocity, while high-activity individuals slowed down, yielding diametrically opposite response patterns to ethanol exposure. We therefore argue that inter-individual consistency in basal activity level, already from 6 dpf, is an important factor to take into account and provides a practical measure to improve the power of statistical analyses and the scope for data interpretation from behavioural screening studies.Animal science

Kaonic hydrogen X-ray measurement in SIDDHARTA

Kaonic hydrogen atoms provide a unique laboratory to probe the kaon-nucleon strong interaction at the energy threshold, allowing an investigation of the interplay between spontaneous and explicit chiral symmetry breaking in low-energy QCD. The SIDDHARTA Collaboration has measured the $K$-series X rays of kaonic hydrogen atoms at the DA$\Phi$NE electron-positron collider of Laboratori Nazionali di Frascati, and has determined the most precise values of the strong-interaction induced shift and width of the $1s$ atomic energy level. This result provides vital constraints on the theoretical description of the low-energy $\bar{K}N$ interaction.Comment: 11 pages, 7 figures, Nuclear Physics A (in press) Special Issue on Strangeness Nuclear Physic