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

Effects of Different Yeasts on Texture and Flavor of Sweet Potato Bread

In order to investigate the effects of different yeasts on the quality and flavor of sweet potato bread, the rheological properties, color, texture and flavor of sweet potato bread were compared and analyzed. The results showed that different yeasts had significant effects on the color, texture and flavor of sweet potato bread. The results of dynamic rheology showed that the G' and G" of yeast No.4 fermented dough were significantly higher than other groups(P<0.05). The hardness, chewiness, elasticity, cohesion and resilience of commercial yeast fermented bread were significantly lower than those of old yeast fermented bread(P<0.05). The L* value and W value of No.4 old dough yeast fermented bread were significantly higher than others(P<0.05). The results of electronic nose test showed that the main flavor substance of sweet potato bread fermented by 7 different yeasts was inorganic sulfide. A total of 61 volatile compounds were detected by GC-IMS, which were mainly alcohols, ketones and acids, followed by aldehydes, ethers, esters and pyridines. Principal component analysis showed that there were significant differences in volatile flavor compounds of 7 kinds of yeast fermented breads, two principal component contribution rate of 85%, indicating GC-IMS technology could distinguish bread fermented by different yeasts. To sum up, this paper made a detailed comparative analysis of the nature and flavor differences of bread fermented by different yeasts, and would provide a scientific basis for yeast selection in bread production

Nutrient Limitation on Ecosystem Productivity and Processes of Mature and Old-Growth Subtropical Forests in China

<div><p>Nitrogen (N) is considered the dominant limiting nutrient in temperate regions, while phosphorus (P) limitation frequently occurs in tropical regions, but in subtropical regions nutrient limitation is poorly understood. In this study, we investigated N and P contents and N:P ratios of foliage, forest floors, fine roots and mineral soils, and their relationships with community biomass, litterfall C, N and P productions, forest floor turnover rate, and microbial processes in eight mature and old-growth subtropical forests (stand age >80 yr) at Dinghushan Biosphere Reserve, China. Average N:P ratios (mass based) in foliage, litter (L) layer and mixture of fermentation and humus (F/H) layer, and fine roots were 28.3, 42.3, 32.0 and 32.7, respectively. These values are higher than the critical N:P ratios for P limitation proposed (16–20 for foliage, ca. 25 for forest floors). The markedly high N:P ratios were mainly attributed to the high N concentrations of these plant materials. Community biomass, litterfall C, N and P productions, forest floor turnover rate and microbial properties were more strongly related to measures of P than N and frequently negatively related to the N:P ratios, suggesting a significant role of P availability in determining ecosystem production and productivity and nutrient cycling at all the study sites except for one prescribed disturbed site where N availability may also be important. We propose that N enrichment is probably a significant driver of the potential P limitation in the study area. Low P parent material may also contribute to the potential P limitation. In general, our results provided strong evidence supporting a significant role for P availability, rather than N availability, in determining ecosystem primary productivity and ecosystem processes in subtropical forests of China.</p> </div

Characterization and Gel Properties of Low-Molecular-Weight Carrageenans Prepared by Photocatalytic Degradation

Low-molecular-weight carrageenan has attracted great interest because it shows advantages in solubility, absorption efficiency, and bioavailability compared to original carrageenan. However more environment-friendly and efficient methods to prepare low-molecular-weight carrageenan are still in great need. In the present study, a photocatalytic degradation method with only TiO2 has been developed and it could decrease the average molecular weight of &kappa;-carrageenan to 4 kDa within 6 h. The comparison of the chemical compositions of the degradation products with those of carrageenan by FT-IR, NMR, etc., indicates no obvious removement of sulfate group, which is essential for bioactivities. Then 20 carrageenan oligosaccharides in the degradation products were identified by HPLC-MSn, and 75% of them possessed AnGal or its decarbonylated derivative at their reducing end, indicating that photocatalysis is preferential to break the glycosidic bond of AnGal. Moreover, the analysis results rheology and Cryo-SEM demonstrated that the gel property decreased gradually. Therefore, the present study demonstrated that the photocatalytic method with TiO2 as the only catalyst has the potential to prepare low-molecular-weight carrageenan with high sulfation degree and low viscosity, and it also proposed the degradation rules after characterizing the degradation products. Thus, the present study provides an effective green method for the degradation of carrageenan

Correlations between nutrient measures in the plant and soil samples.

<p>For soil total fraction, inclusion and exclusion of the pine forest (PF) site showed distinct results and thus, correlations for all data and data excluding PF were both shown.</p

Relationships between community biomass and soil nutrient measures.

<p>PF indicates the pine forest. * <i>P</i><0.05; *** <i>P</i><0.001.</p

Preparation of Low-Molecular-Weight Fucoidan with Anticoagulant Activity by Photocatalytic Degradation Method

It is a challenge to degrade sulfated polysaccharides without stripping sulfate groups. In the present study, a photocatalytic method was applied to degrade fucoidan, a sulfated polysaccharide from brown algae. The degradation with varying addition amounts of H2O2 and TiO2 were monitored by high performance gel permeation chromatography (HPGPC) and thin layer chromatography (TLC), and fucoidan was efficiently degraded with 5% TiO2 and 0.95% H2O2. A comparison of the chemical compositions of 2 products obtained after 0.5 h and 3 h illumination, DF-0.5 (average Mw 90 kDa) and DF-3 (average Mw 3 kDa), respectively, with those of fucoidan indicates the photocatalytic degradation did not strip the sulfate groups, but reduced the galactose/fucose ratio. Moreover, 12 oligosaccharides in DF-3 were identified by HPLC-ESI-MSn and 10 of them were sulfated. In addition, DF-0.5 showed anticoagulant activity as strong as fucoidan while DF-3 could specifically prolong the activated partial thromboplastin time. All samples exerted inhibition effects on the intrinsic pathway FXII in a dose-dependent manner. Thus, photocatalytic degradation demonstrated the potential to prepare sulfated low-molecular-weight fucoidan with anticoagulant activity

Mean N and P concentrations of plant materials of eight study forests.

<p>Dashed lines depict N:P ratios of 16, 20 and 25 on a mass basis. Ratios of 16 and 20 are P limitation thresholds of plant growth proposed by Koerselman and Meuleman (1996) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052071#pone.0052071-Koerselman1" target="_blank">[34]</a> and Güsewell (2004) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052071#pone.0052071-Gsewell1" target="_blank">[31]</a>, respectively; ratio of 25 is the critcial N:P ratio that indicates P limitation on litter decomposition proposed by Güsewell and Verhoeven (2006) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052071#pone.0052071-Gsewell3" target="_blank">[61]</a>.</p

Relationships between forest floor turnover rate with F/H layer N:P ratio.

<p>Relationships between forest floor turnover rate with F/H layer N:P ratio.</p