Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

Fixation locations when grasping partly occluded objects

When grasping an object, subjects tend to look at the contact positions of the digits (A. M. Brouwer, V. H. Franz, D. Kerzel, & K. R. Gegenfurtner, 2005; R. S. Johansson, G. Westling, A. Bäckström, & J. R. Flanagan, 2001). However, these contact positions are not always visible due to occlusion. Subjects might look at occluded parts to determine the location of the contact positions based on extrapolated information. On the other hand, subjects might avoid looking at occluded parts since no object information can be gathered there. To find out where subjects fixate when grasping occluded objects, we let them grasp flat shapes with the index finger and thumb at predefined contact positions. Either the contact position of the thumb or the finger or both was occluded. In a control condition, a part of the object that does not involve the contact positions was occluded. The results showed that subjects did look at occluded object parts, suggesting that they used extrapolated object information for grasping. Additionally, they preferred to look in the direction of the index finger. When the contact position of the index finger was occluded, this tendency was inhibited. Thus, an occluder does not prevent fixations on occluded object parts, but it does affect fixation locations especially in conditions where the preferred fixation location is occluded. © ARVO

Magnetic states at the surface of alpha Fe2O3 thin films doped with Ti, Zn, or Sn

The spin states at the surface of epitaxial thin films of hematite, both undoped and doped with 1% Ti, Sn or Zn, respectively, were probed with x-ray magnetic linear dichroism (XMLD) spectroscopy. Morin transitions were observed for the undoped (T_M~200 K) and Sn-doped (T_M~300 K) cases, while Zn and Ti-doped samples were always in the high and low temperature phases, respectively. In contrast to what has been reported for bulk hematite doped with the tetravalent ions Sn4+ and Ti4+, for which T_M dramatically decreases, these dopants substantially increase T_M in thin films, far exceeding the bulk values. The normalized Fe LII-edge dichroism for T<T_M does not strongly depend on doping or temperature, except for an apparent increase of the peak amplitudes for T<100 K. We observed magnetic field-induced inversions of the dichroism peaks. By applying a magnetic field of 6.5 T on the Ti-doped sample, a transition into the T>T_M state was achieved. The temperature dependence of the critical field for the Sn-doped sample was characterized in detail. It was demonstrated the sample-to-sample variations of the Fe LIII-edge spectra were, for the most part, determined solely by the spin orientation state. Calculations of the polarization-depedent spectra based on a spin-multiplet model were in reasonable agreement with the experiment and showed a mixed excitation character of the peak structures.Comment: 8 pages, 8 figure

The spin temperature of high-redshift damped Lyman-α\alpha systems

We report results from a programme aimed at investigating the temperature of neutral gas in high-redshift damped Lyman-$\alpha$ absorbers (DLAs). This involved (1) HI 21cm absorption studies of a large DLA sample, (2) VLBI studies to measure the low-frequency quasar core fractions, and (3) optical/ultraviolet spectroscopy to determine DLA metallicities and velocity widths. Including literature data, our sample consists of 37 DLAs with estimates of the spin temperature $T_s$ and the covering factor. We find a strong $4\sigma$) difference between the $T_s$ distributions in high-z (z>2.4) and low-z (z<2.4) DLA samples. The high-z sample contains more systems with high $T_s$ values, $\gtrsim 1000$ K. The $T_s$ distributions in DLAs and the Galaxy are also clearly (~$6\sigma$) different, with more high-$T_s$ sightlines in DLAs than in the Milky Way. The high $T_s$ values in the high-z DLAs of our sample arise due to low fractions of the cold neutral medium. For 29 DLAs with metallicity [Z/H] estimates, we confirm the presence of an anti-correlation between $T_s$ and [Z/H], at $3.5\sigma$ significance via a non-parametric Kendall-tau test. This result was obtained with the assumption that the DLA covering factor is equal to the core fraction. Monte Carlo simulations show that the significance of the result is only marginally decreased if the covering factor and the core fraction are uncorrelated, or if there is a random error in the inferred covering factor. We also find evidence for redshift evolution in DLA $T_s$ values even for the z>1 sub-sample. Since z>1 DLAs have angular diameter distances comparable to or larger than those of the background quasars, they have similar efficiency in covering the quasars. Low covering factors in high-z DLAs thus cannot account for the observed redshift evolution in spin temperatures. (Abstract abridged.)Comment: 37 pages, 22 figures. Accepted for publication in Monthly Notices of the Royal Astronomical Societ