5 research outputs found
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
Structural Transformation of Wireframe DNA Origami <i>via</i> DNA Polymerase Assisted Gap-Filling
The
programmability of DNA enables constructing nanostructures
with almost any arbitrary shape, which can be decorated with many
functional materials. Moreover, dynamic structures can be realized
such as molecular motors and walkers. In this work, we have explored
the possibility to synthesize the complementary sequences to single-stranded
gap regions in the DNA origami scaffold cost effectively by a DNA
polymerase rather than by a DNA synthesizer. For this purpose, four
different wireframe DNA origami structures were designed to have single-stranded
gap regions. This reduced the number of staple strands needed to determine
the shape and size of the final structure after gap filling. For this,
several DNA polymerases and single-stranded binding (SSB) proteins
were tested, with T4 DNA polymerase being the best fit. The structures
could be folded in as little as 6 min, and the subsequent optimized
gap-filling reaction was completed in less than 3 min. The introduction
of flexible gap regions results in fully collapsed or partially bent
structures due to entropic spring effects. Finally, we demonstrated
structural transformations of such deformed wireframe DNA origami
structures with DNA polymerases including the expansion of collapsed
structures and the straightening of curved tubes. We anticipate that
this approach will become a powerful tool to build DNA wireframe structures
more material-efficiently, and to quickly prototype and test new wireframe
designs that can be expanded, rigidified, or mechanically switched.
Mechanical force generation and structural transitions will enable
applications in structural DNA nanotechnology, plasmonics, or single-molecule
biophysics
Structural Transformation of Wireframe DNA Origami <i>via</i> DNA Polymerase Assisted Gap-Filling
The
programmability of DNA enables constructing nanostructures
with almost any arbitrary shape, which can be decorated with many
functional materials. Moreover, dynamic structures can be realized
such as molecular motors and walkers. In this work, we have explored
the possibility to synthesize the complementary sequences to single-stranded
gap regions in the DNA origami scaffold cost effectively by a DNA
polymerase rather than by a DNA synthesizer. For this purpose, four
different wireframe DNA origami structures were designed to have single-stranded
gap regions. This reduced the number of staple strands needed to determine
the shape and size of the final structure after gap filling. For this,
several DNA polymerases and single-stranded binding (SSB) proteins
were tested, with T4 DNA polymerase being the best fit. The structures
could be folded in as little as 6 min, and the subsequent optimized
gap-filling reaction was completed in less than 3 min. The introduction
of flexible gap regions results in fully collapsed or partially bent
structures due to entropic spring effects. Finally, we demonstrated
structural transformations of such deformed wireframe DNA origami
structures with DNA polymerases including the expansion of collapsed
structures and the straightening of curved tubes. We anticipate that
this approach will become a powerful tool to build DNA wireframe structures
more material-efficiently, and to quickly prototype and test new wireframe
designs that can be expanded, rigidified, or mechanically switched.
Mechanical force generation and structural transitions will enable
applications in structural DNA nanotechnology, plasmonics, or single-molecule
biophysics