Six questions on the construction of ontologies in biomedicine

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today

Distributed Minimum Cut Approximation

We study the problem of computing approximate minimum edge cuts by distributed algorithms. We use a standard synchronous message passing model where in each round, $O(\log n)$ bits can be transmitted over each edge (a.k.a. the CONGEST model). We present a distributed algorithm that, for any weighted graph and any $\epsilon \in (0, 1)$, with high probability finds a cut of size at most $O(\epsilon^{-1}\lambda)$ in $O(D) + \tilde{O}(n^{1/2 + \epsilon})$ rounds, where $\lambda$ is the size of the minimum cut. This algorithm is based on a simple approach for analyzing random edge sampling, which we call the random layering technique. In addition, we also present another distributed algorithm, which is based on a centralized algorithm due to Matula [SODA '93], that with high probability computes a cut of size at most $(2+\epsilon)\lambda$ in $\tilde{O}((D+\sqrt{n})/\epsilon^5)$ rounds for any $\epsilon>0$. The time complexities of both of these algorithms almost match the $\tilde{\Omega}(D + \sqrt{n})$ lower bound of Das Sarma et al. [STOC '11], thus leading to an answer to an open question raised by Elkin [SIGACT-News '04] and Das Sarma et al. [STOC '11]. Furthermore, we also strengthen the lower bound of Das Sarma et al. by extending it to unweighted graphs. We show that the same lower bound also holds for unweighted multigraphs (or equivalently for weighted graphs in which $O(w\log n)$ bits can be transmitted in each round over an edge of weight $w$), even if the diameter is $D=O(\log n)$. For unweighted simple graphs, we show that even for networks of diameter $\tilde{O}(\frac{1}{\lambda}\cdot \sqrt{\frac{n}{\alpha\lambda}})$, finding an $\alpha$-approximate minimum cut in networks of edge connectivity $\lambda$ or computing an $\alpha$-approximation of the edge connectivity requires $\tilde{\Omega}(D + \sqrt{\frac{n}{\alpha\lambda}})$ rounds

Transverse Optical Mode Patterns for an RF Excited Ar-He-Xe Laser

Transverse optical modes for an RF excited Ar-He-Xe laser are studied both experimentally and theoretically. A diffraction model for a waveguide with a nonsaturable gain and refractive index gradients placed between two plane mirrors is formulated. The effects of gain and diffraction index gradients and of diffraction in free space are evaluated for typical experimental conditions. A direct comparison between theoretical mode patterns and experimentally measured ones at distances of 17 and 114 cm from the output mirror demonstrated a satisfactory agreement for various laser wavelengths and gas mixture composition

Measurement of the energy resolution and calibration of hybrid pixel detectors with GaAs:Cr sensor and Timepix readout chip

This paper describes an iterative method of per-pixel energy calibration of hybrid pixel detectors with GaAs:Cr sensor and Timepix readout chip. A convolution of precisely measured spectra of characteristic X-rays of different metals with the resolution and the efficiency of the pixel detector is used for the calibration. The energy resolution of the detector is also measured during the calibration. The use of per-pixel calibration allows to achieve a good energy resolution of the Timepix detector with GaAs:Cr sensor: 8% and 13% at 60 keV and 20 keV, respectively

The symbiotic star CH Cygni – II. The ejecta from the 1998-2000 active phase

We present Hubble Space Telescope (HST) imaging, a Very Large Array (VLA) radio map (4.74 GHz), optical high-resolution (echelle) spectroscopy and UBV photoelectric photometry of the symbiotic star CH Cyg obtained during its 1998–2000 active phase. The HST imaging, taken during eclipse, shows the central stars are embedded in a nebula extending to 620 ± 150 au for a distance of 270 ± 66 pc. The inner nebula is strongly influenced by the onset of activity and associated outflow in 1998. The surface brightness contours of the contemporaneous radio VLA observation agree well with HST images. Photometric observations of the broad 1999 U-minimum suggest that it is due to the eclipse of the active hot component by the giant on the long-period (14.5 yr) outer orbit. We also find that the onset of the 1998 and the 1992 active periods occur at the same orbital phase of the inner binary. Spectroscopic observations reveal two types of outflow from the active star: a high-velocity (>1200 km s−1) hot star wind sporadically alternating with a more massive outflow indicated by P-Cygni-like profiles. We present evidence connecting the extended nebulosity with the high-velocity shocked outflow, and hence the activity in the central binary

Distributed Testing of Excluded Subgraphs

We study property testing in the context of distributed computing, under the classical CONGEST model. It is known that testing whether a graph is triangle-free can be done in a constant number of rounds, where the constant depends on how far the input graph is from being triangle-free. We show that, for every connected 4-node graph H, testing whether a graph is H-free can be done in a constant number of rounds too. The constant also depends on how far the input graph is from being H-free, and the dependence is identical to the one in the case of testing triangles. Hence, in particular, testing whether a graph is K_4-free, and testing whether a graph is C_4-free can be done in a constant number of rounds (where K_k denotes the k-node clique, and C_k denotes the k-node cycle). On the other hand, we show that testing K_k-freeness and C_k-freeness for k>4 appear to be much harder. Specifically, we investigate two natural types of generic algorithms for testing H-freeness, called DFS tester and BFS tester. The latter captures the previously known algorithm to test the presence of triangles, while the former captures our generic algorithm to test the presence of a 4-node graph pattern H. We prove that both DFS and BFS testers fail to test K_k-freeness and C_k-freeness in a constant number of rounds for k>4

The role of emotional intelligence and self-care in the stress perception during COVID-19 outbreak: An intercultural moderated mediation analysis

Background: The relationship between emotional intelligence (EI) and stress has been widely studied, as well as the beneficial role of self-care to maintain health and wellbeing. However, the joint contribution of EI and self- care in predicting stress has not been examined during COVID-19 lockdown. This study aimed to examine the mediating role of self-care in the relationship between EI and stress and the potential moderator role of gender. Methods: A sample of 1082 participants from four Hispanic countries completed measures related to socio- demographic, trait emotional intelligence (Trait Meta-Mood Scale), self-care activities (Self-care Activities Screening Scale) and stress (Perceived Stress Scale). Results: Mediation analyses revealed that self-care increased the explained variance of the prediction of stress by EI dimensions after controlling gender and age. However, gender only moderated the relationship between selfcare and stress in the mediation model corresponding to emotional attention. Conclusions: Data supported a general model for the interaction of EI and self-care as contributing factors of stress. Further research is needed to replicate it in more culturally distant samples and to fully explore the po- tential role of gender differences. Future intervention programs should include a balanced combination of EI and self-care to increase their benefits on people’s healt