Generic Airspace Research Phase 5 Report

Human-in-the-loop testing was completed to assess the subjective preferences, usage, and operational benefits of Integrated and Separated Controller Information Tools (CITs) in support of Generic Airspace Research. Participants controlled traffic in in a busy, high altitude sector with the aid of the CITs. When the participants were asked which CIT that they preferred to use, they overwhelmingly chose the integrated version of the CIT. The primary reason for this seemed to be that it allowed participants to remain focused on the traffic situation, whereas the Standalone CIT required them to focus their attention for short periods away from the radar presentation. In contrast to their preference, there were little or no differences in the CIT usage and the operational differences. There were similar numbers of losses of separation and participants accessed each CIT equally. Although the information accessed was the similar for the two conditions, participants actively turned off the data on the Integrated CIT, presumably to reduce the clutter on the radar scope. Further work is needed to isolate which information can and should be available to controllers in the Integrated vs. Standalone format

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Conformational heterogeneity of the allosteric drug and metabolite (ADaM) site in AMP-activated protein kinase (AMPK).

AMP-activated protein kinase (AMPK) is a master regulator of energy homeostasis and a promising drug target for managing metabolic diseases such as type 2 diabetes. Many pharmacological AMPK activators, and possibly unidentified physiological metabolites, bind to the allosteric drug and metabolite (ADaM) site at the interface between the kinase domain (KD) in the α-subunit and the carbohydrate-binding module (CBM) in the β-subunit. Here, using double electron-electron resonance (DEER) spectroscopy, we demonstrate that the CBM-KD interaction is partially dissociated and the interface highly disordered in the absence of pharmacological ADaM site activators as inferred from a low depth of modulation and broad DEER distance distributions. ADaM site ligands such as 991, and to a lesser degree phosphorylation, stabilize the KD-CBM association and strikingly reduce conformational heterogeneity in the ADaM site. Our findings that the ADaM site, formed by the KD-CBM interaction, can be modulated by diverse ligands and by phosphorylation suggest that it may function as a hub for integrating regulatory signals

Long-Range Distance Measurements in Proteins at Physiological Temperatures Using Saturation Recovery EPR Spectroscopy

Site-directed spin labeling in combination with EPR is a powerful method for providing distances on the nm scale in biological systems. The most popular strategy, double electron–electron resonance (DEER), is carried out at cryogenic temperatures (50–80 K) to increase the short spin–spin relaxation time (T₂) upon which the technique relies. A challenge is to measure long-range distances (20–60 Å) in proteins near physiological temperatures. Toward this goal we are investigating an alternative approach based on the distance-dependent enhancement of spin–lattice relaxation rate (T₁^–1) of a nitroxide spin label by a paramagnetic metal. With a commonly used nitroxide side chain (R1) and Cu²⁺, it has been found that interspin distances ≤25 Å can be determined in this way (Jun et al. <i>Biochemistry</i> <b>2006</b>, <i>45</i>, 11666). Here, the upper limit of the accessible distance is extended to ≈40 Å using spin labels with long T₁, a high-affinity 5-residue Cu²⁺ binding loop inserted into the protein sequence, and pulsed saturation recovery to measure relaxation enhancement. Time-domain Cu²⁺ electron paramagnetic resonance, quantum mechanical calculations, and molecular dynamics simulations provide information on the structure and geometry of the Cu²⁺ loop and indicate that the metal ion is well-localized in the protein. An important aspect of these studies is that both Cu²⁺/nitroxide DEER at cryogenic temperatures and T₁ relaxation measurements at room temperature can be carried out on the same sample, allowing both validation of the relaxation method and assessment of the effect of freezing on protein structure