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

Biophysically Based Mathematical Modeling of Interstitial Cells of Cajal Slow Wave Activity Generated from a Discrete Unitary Potential Basis

Spontaneously rhythmic pacemaker activity produced by interstitial cells of Cajal (ICC) is the result of the entrainment of unitary potential depolarizations generated at intracellular sites termed pacemaker units. In this study, we present a mathematical modeling framework that quantitatively represents the transmembrane ion flows and intracellular Ca2+ dynamics from a single ICC operating over the physiological membrane potential range. The mathematical model presented here extends our recently developed biophysically based pacemaker unit modeling framework by including mechanisms necessary for coordinating unitary potential events, such as a T-Type Ca2+ current, Vm-dependent K+ currents, and global Ca2+ diffusion. Model simulations produce spontaneously rhythmic slow wave depolarizations with an amplitude of 65 mV at a frequency of 17.4 cpm. Our model predicts that activity at the spatial scale of the pacemaker unit is fundamental for ICC slow wave generation, and Ca2+ influx from activation of the T-Type Ca2+ current is required for unitary potential entrainment. These results suggest that intracellular Ca2+ levels, particularly in the region local to the mitochondria and endoplasmic reticulum, significantly influence pacing frequency and synchronization of pacemaker unit discharge. Moreover, numerical investigations show that our ICC model is capable of qualitatively replicating a wide range of experimental observations

Downhole seismic logging for high‐resolution reflection surveying in unconsolidated overburden

Downhole seismic velocity logging techniques have been developed and applied in support of high‐resolution reflection seismic surveys. For shallow high‐resolution reflection surveying within unconsolidated overburden, velocity‐depth control can sometimes be difficult to achieve; as well, unambiguous correlation of reflections with overburden stratigraphy is often problematic. Data obtained from downhole seismic logging can provide accurate velocity‐depth functions and directly correlate seismic reflections to depth. The methodologies described in this paper are designed for slimhole applications in plastic‐cased boreholes (minimum ID of 50 mm) and with source and detector arrays that yield similar frequency ranges and vertical depth resolutions as the surface reflection surveys. Compressional- (P-) wave logging uses a multichannel hydrophone array with 0.5-m detector spacings in a fluid‐filled borehole and a high‐frequency, in‐hole shotgun source at the surface. Overlapping array positions downhole results in redundant first‐arrival data (picked using interactive computer techniques), which can be processed to provide accurate interval velocities. The data also can be displayed as a record suite, showing reflections and directly correlating reflection events with depths. Example applications include identification of gas zones, lithological boundaries within unconsolidated sediments, and the overburden‐bedrock interface. Shear- (S-) wave logging uses a slimhole, well‐locked, three‐component (3-C) geophone pod and a horizontally polarized, hammer‐and‐loaded‐plate source at ground surface. The pod is moved in successive 0.5- or 1-m intervals downhole with no redundancy of overlapping data as in the P-wave method. First‐arrival data can be obtained by picking the crossover onset of polarized energy or by closely examining particle‐motion plots using all three components of motion. In unconsolidated sediments, shear‐wave velocity contrasts can be associated with changes in material density or dynamic shear modulus, which in turn can be related to consolidation. Example applications include identification of a lithological boundary for earthquake hazard applications and mapping massive ice within permafrost materials.</p