A refinement strategy for identification of scientific software from bioinformatics publications

In the field of bioinformatics, a large number of classical software becomes a necessary research tool. To measure the influence of scientific software as one kind of important intellectual products, a few strategies have been proposed to identify the software names from full texts of papers to collect the usage data of packages in bioinformatics research. However, the performance of these strategies is limited because of the highly imbalance of data in the full texts. This study proposes EnsembleSVMs-CRF, a two-step refinement strategy based on ensemble learning that gradually increases the sentences that contain software mentions to improve the performance of named entity recognition. The experiment on the bioinformatics corpus shows that the performance of EnsembleSVMs-CRF, in terms of the local F1 (78.81%) and the global F1-A (73.49%), is superior to the rule-based bootstrapping method and direct CRF. Application of this strategy to the articles published between 2013 and 2017 in 27 bioinformatics journals extracted 8,239 unique packages. The most popular 50 packages thus identified demonstrate that most of them are professional software which generally requires inter-discipline knowledge, rather than programming skill. Meanwhile, we found that researchers in bioinformatics tend to use free scientific software, and the application of general software is increasing compared with professional software.

     

Effect of current density on the densification of 3%mol yttria-stabilized zirconia/carbon nanotube by flash sintering

Journal of Materials Science: Materials in Electronics - Flash sintering (FS) is a promising method with a great potential for the ceramic fabrication with rapid densification process. However, the...     

Effects of cation doping on thermoelectric properties of Bi2S3 materials

Bi₂S₃ polycrystals doped with Al, Mn, Ag, and In were fabricated by vacuum melting and plasma activated sintering process, and the phase, microstructure, electrical, and thermal properties were investigated. The electrical conductivity is enhanced via Al and Ag doping. Compared with the Ag dopant, a higher electrical conductivity is achieved in the Al-doped sample, resulting in a peak power factor value of 1.96 μW/cmK² at 423 K. Meanwhile, the thermal conductivity of Bi_1.99Al_0.01S₃ sample is very low in the Bi₂S₃ system due to the high-density defects, and is only 0.39 Wm^?1 K^?1 at 740 K. By combining a power factor and a low thermal conductivity, a peak ZT value of 0.29 at 740 K is achieved in the Bi_1.99Al_0.01S₃ sample, being about two times larger than that of pristine Bi₂S₃.

     

Effect of pasteurization on membrane proteins and oxidative stability of oil bodies in various crops

Oil bodies (OBs) are natural pre-emulsion systems and an ideal green food additive. However, their proclivity to oxidation limits the applications of OBs. In this study, the effect of pasteurization (85 and 125 °C; 1 min) on membrane proteins and the oxidative stability of various OBs (soybean, sunflower, peanut, sesame, and walnut) were investigated. The membrane proteins are extracted from the OBs. The ultrahigh-temperature pasteurization (125 °C, 1 min) eliminated lipoxygenase of soybean and peanut OBs. Furthermore, oleosin exhibited a higher denaturation temperature (approximately 100 °C) than extrinsic proteins (approximately 50 °C). Pasteurization induced the conversion of the α-helix structure to a disordered structure by rearranging the hydrogen bonds. The pasteurized soybean and peanut OBs exhibited a high oxidative stability owing to their stable membrane structures and decreased lipoxygenase activity, while sunflower, sesame, and walnut OBs did not exhibit good oxidative stability because of their vulnerable membranes, a large number of unsaturated fatty acids, and severe aggregation of droplets. Simulated milk based on pasteurized soybean and peanut OBs (125 °C, 1 min) maintained outstanding storage stability. These results confirmed that pasteurized soybean and peanut OBs have the potential as a skim milk additive for the benefit of the consumer.     

Administration of xylo-oligosaccharides improves depressive-like behaviour in mice caused by chronic unpredictable mild stress by altering microbiota composition

Xylo-oligosaccharides (XOS) is a functional oligosaccharide with prebiotic properties, and could be fermented by gut microbiota. In this study, the modulatory effects of XOS on emotions and behaviours at different dose were investigated based on the mouse model of chronic unpredictable mild stress-induced depression. The result showed that 0.23 and 0.50 g kg⁻¹ doses of XOS significantly increased sucrose preference index and decreased the immobility time in tail suspension and forced swimming tests. Meanwhile, the dose of 0.23 g kg⁻¹ day⁻¹ XOS significantly increased the concentration of neurotransmitters, such as 5-hydroxytryptamine and γ- aminobutyric acid. Furthermore, the analysis of the faecal microbiota with XOS intervention showed a higher relative abundance of Akkermansia, Bifidobacterium and Lactobacillus, fewer Desulfovibrio and the SCFA concentrations increased with XOS prevention treatment. These results suggested that the dietary supplementation XOS could improve chronic stress-induced depressive-like behaviour by modulating neurotransmitters and reverting gut microbiota changes in mice. These findings present XOS as a potential prebiotic targeting to the gut microbiota for mood disorders.     

Ultralow-threshold wideband-tunable single-mode ultraviolet lasing from lanthanide-doped upconversion nanomaterials

Ultraviolet (UV) lasers with dynamic wavelength-tunability and high monochromaticity are crucial in a multitude of practical applications yet still remarkable challenges. Here, we show wide wavelength-tuning of single-mode UV lasing based on lanthanide-doped upconversion nanoparticles (UCNPs). The rationally designed Yb³⁺/Er³⁺/Tm³⁺/Gd³⁺/Ce³⁺ co-doped multilayer UCNPs, which exhibits a broad gain spectrum with the full width of half maximum of around 57 nm in the UV regime, are developed. More importantly, by taking advantages of a diffraction grating as the tuning component, stable single-mode emission can be achieved in the UCNPs-based external-cavity-extended Fabry–Pérot laser at room temperature. Specifically, the lasing threshold is around 137 µJ cm^–2, which is two orders of magnitude lower than that in the previously reported articles. Precise wavelength-tuning from 310 to 363 nm can be realized by adjusting the Littrow angle. This achievement highlights a portable alternative to continuously wideband-tunable UV lasers and opens up new opportunities for constructing compact solid-state UV photon sources.