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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Creation, trapping and manipulation of a cold argon gas

This thesis describes the construction and characterisation of a unique cold argon atom source for sympathetic cooling of molecules. Argon atoms were laser cooled from their lowest lying metastable state using the 4s[3/2]2 → 4p[5/2]3 transition at 811.5 nm. A magneto-optical trap (MOT) was used to cool the metastable argon (Ar*) atoms to 73.2 ± 0.4 μK and trap them at a density of 3.93 × 10^9 cm-3. Cooling was facilitated using an external-cavity diode laser which was frequency-stabilised to the cooling transition using a magnetic dichroism technique. This was the first application of this technique to a plasma operated at our pressures where the applied magnetic field affected the gas behaviour. The Ar* atoms in the MOT were used to demonstrate chirped optical Stark acceleration for the first time. Atoms were accelerated up to velocities of 191 ± 1 ms-1 while maintaining narrow energy spreads in the accelerated ensemble (30-100 mK). The acceleration occurred over tens of nanoseconds and on micrometre length scales. Control over the number of particles accelerated was achieved by tailoring the depth of the optical lattice potential. Monte Carlo numerical simulations of acceleration were used to fit experimental results and study the dynamics of particles over the acceleration duration. Trapping of Ar* atoms in a quasi-electrostatic trap (QUEST) has also been demonstrated. The QUEST was formed at the focus of a 100 W laser beam with a wavelength of 10.6 μm. A trap lifetime of 18.3 ± 0.3 ms was measured

The Impact of Forest Certification on Firm Financial Performance in Canada and the U.S.

abnormal returns, buy-and-hold abnor- mal returns, cumulative abnormal returns, environmental performance, event study, financial performance, forest certification,