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

Design, Fabrication, And Characterization Of Linear Multiplexed Electrospray Atomizers Micro-Machined From Metal And Polymers

Multiplexed electrospray is a promising aerosol generation technique to produce high throughput quasi-monodisperse droplets in the nanometer and micron size range. Here we report the design, fabrication, analysis, and performance of a linear electrospray (LINES) system. The fabrication of the nozzle array is based on a precision computer numerical control (CNC) micromachining platform with 1-micron resolution. This rapid prototyping approach offers the flexibility of creating devices from a wide range of materials including metals and polymers with packing densities on par with silicon microfabrication at 20 sources/cm for LINES devices and 460 sources/cm2 for the two-dimensional array. The LINES device uses a slot extractor design to simplify alignment and enhance operation robustness. We also used dummy nozzles (posts without fluidic channels) to offset edge effect on electric field and improved droplet size uniformity. We derived the approximate spray expansion model from charge conservation and Gauss\u27 law. We applied the line-of-charge approximation to establish scaling laws for prescribing operating conditions. The devices show excellent droplet size uniformity from source to source, with relative standard deviation (RSD) of primary droplets \u3c3%. Copyright © American Association for Aerosol Research

Phenotypic and Genotypic Analysis of Biologically Cloned Human Immunodeficiency Virus Type 1 Isolates from Patients Treated with Zidovudine and Lamivudine

Mutations at reverse transcriptase codons 44, 118, 207, and 208 were significantly correlated with reduced zidovudine susceptibility in biologically cloned human immunodeficiency virus type 1 (HIV-1) isolates. Sequences from the Stanford HIV RT and Protease Sequence Database showed that these mutations were more common in HIV-1 isolates from patients treated with zidovudine and lamivudine than in patients not treated with these drugs

Submicroscopic chromosomal imbalances contribute to early abortion

Abstract Background Chromosomal abnormalities are one of the genetic mechanisms associated with abortion. However, the roles of submicroscopic chromosomal imbalances in early abortion are still unclear. This study aims to find out whether submicroscopic chromosomal imbalances contribute to early abortion. Methods A total of 78 chorionic villus specimens from early spontaneous abortion patients with no obvious abnormality are collected after miccroassay analysis (the case group). At the same time, 60 chorionic villus specimens from induced abortion patients with no obvious abnormality are selected as the control group. The submicroscopic structures of chromosomes from two groups are analyzed using an array-based comparative genomic hybridization (aCGH). Results In the case group, 15 specimens show submicroscopic chromosomal abnormalities including 14 micro-deletion/micro-duplication in chromosomes 2, 4, 5, 6, 7, 8, 9, 12, 15, 16, 18, and 22, and 1 uniparental disomy (UPD) in chromosome 19. Moreover, no pathogenic copy number variations are found in the control group. The results between these two groups exhibit significantly statistical difference. Conclusion Submicroscopic chromosomal imbalances may be one of the main reasons for early abortion

Structural Electromagnetic Absorber Based on MoS2/PyC‐Al2O3 Ceramic Metamaterials

Limited by the types of suitable absorbents as well as the challenges in engineering the nanostructures (e.g., defects, dipoles, and hetero-interface) using state-of-the-art additive manufacturing (AM) techniques, the electromagnetic (EM) wave absorption performance of the current ceramic-based materials is still not satisfying. Moreover, because of the high residual porosity and the possible formation of cracks during sintering or pyrolysis, AM-formed ceramic components may in many cases exhibit low mechanical strength. In this work, semiconductive MoS2 and conductive PyC modified Al2O3 (MoS2/PyC-Al2O3) ceramic-based structural EM metamaterials are developed by innovatively harnessing AM, precursor infiltration and pyrolysis (PIP), and hydrothermal methods. Three different meta-structures are successfully created, and the ceramic-based nanocomposite benefit from its optimization of EM parameters. Ultra-broad effective absorption bandwidth (EAB) of 35 GHz is achieved by establishment of multi-loss mechanism via nanostructure engineering and fabrication of meta-structures via AM. Due to the strengthening by the PyC phase, the bending strength of the resulting ceramics can reach approximate to 327 MPa, which is the highest value measured on 3D-printed ceramics of this type that has been reported so far. For the first time, the positive effect deriving from the engineering of the microscopic nano/microstructure and of the macroscopic meta-structure of the absorber on the permittivity and EM absorption performance is proposed. Integration of outstanding mechanical strength and ultra-broad EAB is innovatively realized through a multi-scale design route. This work provides new insights for the design of advanced ceramic-based metamaterials with outstanding performance under extreme environment

Additional file 1: of Submicroscopic chromosomal imbalances contribute to early abortion

Figure S1. The CNV plots of one patient are shown in Figure S1 as a representative. (TIF 396 kb