13 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
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High-resolution frequency-domain second-harmonic optical coherence tomography.
We used continuum generated in an 8.5 cm long fiber by a femtosecond Yb fiber laser to improve threefold the axial resolution of frequency domain second-harmonic optical coherence tomography (SH-OCT) to 12 microm. The acquisition time was shortened by more than 2 orders of magnitude compared to the time-domain SH-OCT. The system was applied to image biological tissue of fish scales, pig leg tendon, and rabbit eye sclera. Highly organized collagen fibrils can be visualized in the recorded images. Polarization dependence on the SH has been used to obtain polarization resolved images
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High-resolution frequency-domain second-harmonic optical coherence tomography.
We used continuum generated in an 8.5 cm long fiber by a femtosecond Yb fiber laser to improve threefold the axial resolution of frequency domain second-harmonic optical coherence tomography (SH-OCT) to 12 microm. The acquisition time was shortened by more than 2 orders of magnitude compared to the time-domain SH-OCT. The system was applied to image biological tissue of fish scales, pig leg tendon, and rabbit eye sclera. Highly organized collagen fibrils can be visualized in the recorded images. Polarization dependence on the SH has been used to obtain polarization resolved images
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Rotational multiphoton endoscopy with a 1 microm fiber laser system.
We present multiphoton microendoscopy with a rotational probe and a 1 microm fiber-based femtosecond laser. The rotational probe is based on a double-clad photonic crystal fiber, a gradient index lens, a microprism, and a rotational microelectronicmechanical system (MEMS) motor. The MEMS motor has a diameter of 2.2 mm and can provide 360 degrees full-view rotation. The fiber laser provides ultrashort pulses with a central wavelength at 1.034 microm and a repetition rate of 50 MHz. Second-harmonic-generation images of rat-tail tendon and fish scale are demonstrated with the rotational probe-based multiphoton system
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Rotational multiphoton endoscopy with a 1 microm fiber laser system.
We present multiphoton microendoscopy with a rotational probe and a 1 microm fiber-based femtosecond laser. The rotational probe is based on a double-clad photonic crystal fiber, a gradient index lens, a microprism, and a rotational microelectronicmechanical system (MEMS) motor. The MEMS motor has a diameter of 2.2 mm and can provide 360 degrees full-view rotation. The fiber laser provides ultrashort pulses with a central wavelength at 1.034 microm and a repetition rate of 50 MHz. Second-harmonic-generation images of rat-tail tendon and fish scale are demonstrated with the rotational probe-based multiphoton system
Miniaturized probe based on a microelectromechanical system mirror for multiphoton microscopy.
A factor that limits the use of multiphoton microscopy (MPM) in clinical and preclinical studies is the lack of a compact and flexible probe. We report on a miniaturized MPM probe employing a microelectromechanical system (MEMS) scanning mirror and a double-clad photonic crystal fiber (DCPCF). The use of a MEMS mirror and a DCPCF provides many advantages, such as size reduction, rapid and precise scanning, efficient delivery of short pulses, and high collection efficiency of fluorescent signals. The completed probe was 1 cm in outer diameter and 14 cm in length. The developed probe was integrated into an MPM system and used to image fluorescent beads, paper, and biological specimens