Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information

BACKGROUND: The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest. RESULTS: This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a set of easily implemented rules. Applying these techniques to 12,300 abstracts, a precision of 0.61 and a recall of 0.97 were obtained, (f = 0.74) and when allowing for two-hop and three-hop relations discovered by graphical analysis, the precision was 0.74 (f = 0.83). CONCLUSION: This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches

Moving Difference (MDIFF) Non-adiabatic Rapid Sweep (NARS) EPR of Copper(II)

Non-adiabatic rapid sweep (NARS) EPR spectroscopy has been introduced for application to nitroxide-labeled biological samples (Kittell et al., 2011). Displays are pure absorption, and are built up by acquiring data in spectral segments that are concatenated. In this paper we extend the method to frozen solutions of copper-imidazole, a square planar copper complex with four in-plane nitrogen ligands. Pure absorption spectra are created from concatenation of 170 5-gauss segments spanning 850 G at 1.9 GHz. These spectra, however, are not directly useful since nitrogen superhyperfine couplings are barely visible. Application of the moving difference (MDIFF) algorithm to the digitized NARS pure absorption spectrum is used to produce spectra that are analogous to the first harmonic EPR. The signal intensity is about four times higher than when using conventional 100 kHz field modulation, depending on line shape. MDIFF not only filters the spectrum, but also the noise, resulting in further improvement of the SNR for the same signal acquisition time. The MDIFF amplitude can be optimized retrospectively, different spectral regions can be examined at different amplitudes, and an amplitude can be used that is substantially greater than the upper limit of the field modulation amplitude of a conventional EPR spectrometer, which improves the signal-to-noise ratio of broad lines

Reply to the Letter to the Editor

Reply to the letter to the edito

Workload, Risks, and Goal Framing as Antecedents of Shortcut Behaviors

The final publication is available at Springer via: http://dx.doi.org/10.1007/s10869-016-9450-0Purpose: Shortcut behaviors are methods of completing a task that require less time than typical or standard procedures. These behaviors carry the benefit of increasing efficiency, yet can also carry risks (e.g., of an accident). The purpose of this research is to understand the reasons individuals engage in shortcut behaviors, even when doing so is known to be risky. Design/Methodology/Approach: We present two laboratory studies (N = 121 and N = 144) in which participants performed an air traffic control simulation. Participants could improve efficiency by taking shortcuts; that is, by sending aircraft off the prescribed flight paths. This design allowed for direct and unobtrusive observation of shortcut behaviors. Findings: Individuals who were told that efficiency was an obligation tended to believe that shortcut behaviors had utility for managing high workloads, even when the risks associated with shortcuts were high. Downstream, utility perceptions were positively related to actual shortcut behavior. Implications: Although communicating risks may be used to help individuals balance the “pros” and “cons” of shortcut behaviors, goal framing is also important. Subtle cues indicating that efficiency is an obligation can lead to elevated perceptions of the utility of shortcut behaviors, even when knowing that engaging in shortcut behaviors is very risky. Originality/Value: Past research has provided limited insights into the reasons individuals sometimes engage in shortcut behaviors even when doing so is known to be risky. The current research speaks to this issue by identifying workload and obligation framing as antecedents of the decision to take shortcuts.Social Sciences and Humanities Research Council of Canada Grant [SSHRC #435-2014-1263

Experimental Investigation of Premixed Turbulent Combustion in High Reynolds Number Regimes using PLIF

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140710/1/6.2014-0314.pd

NIHAO project II: Halo shape, phase-space density and velocity distribution of dark matter in galaxy formation simulations

We use the NIHAO (Numerical Investigation of Hundred Astrophysical Objects) cosmological simulations to study the effects of galaxy formation on key properties of dark matter (DM) haloes. NIHAO consists of $\simeq 90$ high-resolution SPH simulations that include (metal-line) cooling, star formation, and feedback from massive stars and SuperNovae, and cover a wide stellar and halo mass range: $10^6 < M_* / M_{\odot} < 10^{11}$ ( $10^{9.5} < M_{\rm halo} / M_{\odot} < 10^{12.5}$). When compared to DM-only simulations, the NIHAO haloes have similar shapes at the virial radius, R_{\rm vir}, but are substantially rounder inside $\simeq 0.1R_{\rm vir}$. In NIHAO simulations $c/a$ increases with halo mass and integrated star formation efficiency, reaching $\sim 0.8$ at the Milky Way mass (compared to 0.5 in DM-only), providing a plausible solution to the long-standing conflict between observations and DM-only simulations. The radial profile of the phase-space $Q$ parameter ($\rho/\sigma^3$) is best fit with a single power law in DM-only simulations, but shows a flattening within $\simeq 0.1R_{\rm vir}$ for NIHAO for total masses $M>10^{11} M_{\odot}$. Finally, the global velocity distribution of DM is similar in both DM-only and NIHAO simulations, but in the solar neighborhood, NIHAO galaxies deviate substantially from Maxwellian. The distribution is more symmetric, roughly Gaussian, with a peak that shifts to higher velocities for Milky Way mass haloes. We provide the distribution parameters which can be used for predictions for direct DM detection experiments. Our results underline the ability of the galaxy formation processes to modify the properties of dark matter haloes.Comment: 19 pages, 17 figures, analysis strongly improved, main conclusions unchanged, accepted for publication in MNRA