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

Field assessment of thermal after-ripening time for dormancy release prediction in Lolium rigidum seeds

Dormancy release was studied in four populations of annual ryegrass (Lolium rigidum) seeds to determine whether loss of dormancy in the field can be predicted from temperature alone or whether seed water content (WC) must also be considered. Freshly matured seeds were after-ripened at the northern and southern extremes of the Western Australian cereal cropping region and at constant 37degreesC. Seed WC was allowed to fluctuate with prevailing humidity, but full hydration was avoided by excluding rainfall. Dormancy was measured regularly during after-ripening by germinating seeds with 12-hourly light or in darkness. Germination was lower in darkness than in light/dark and dormancy release was slower when germination was tested in darkness. Seeds were consistently drier, and dormancy release was slower, during after-ripening at 37degreesC than under field conditions. However, within each population, the rate of dormancy release in the field (north and south) in terms of thermal time was unaffected by after-ripening site. While low seed WC slowed dormancy release in seeds held at 37degreesC, dormancy release in seeds after-ripened under Western Australian field conditions was adequately described by thermal after-ripening time, without the need to account for changes in WC elicited by fluctuating environmental humidity

Tissue-specific soluble sugars in seeds as indicators of storage category

The accumulation of specific soluble carbohydrates has been implicated in the acquisition of desiccation tolerance and improved longevity in orthodox seeds, leading to the hypothesis that carbohydrate composition might be used as a diagnostic marker for seed storage category. We have studied the sugar composition of 46 tissues from seeds of 18 species, covering 13 genera and ten families, and representing three seed storage categories: orthodox, intermediate and recalcitrant. Soluble carbohydrate extracts from each tissue were analysed using High pH Anion Exchange Chromatography. Total sugar content and sucrose level of the embryo were highly variable across all species and no simple association with seed storage physiology was evident. Monosaccharide levels were found to be low in most seeds studied, including those of the recalcitrant category. Sucrosyl-oligosaccharides, raffinose and stachyose, were observed to be lower in recalcitrant seeds compared to orthodox seeds. In general, orthodox and recalcitrant seeds had tissues with sucrosyl-oligosaccharide:sucrose mass ratios of > 0.143 (i.e. 1:7) and < 0.083 (1:12) respectively. Moreover, large variations in the content of these sugars were noted between different tissues within the recalcitrant and intermediate seeds. The results from the present study in combination with data in the literature show that the ratio of sucrosyl-oligosaccharide:sucrose in seed tissues is generally a good indicator of seed storage category. (C) 1996 Annals of Botany Company

Purification and molecular structure of two digalactosyl D-chiro-inositols and two trigalactosyl D-chiro-inositols from buckwheat seeds

Two digalactosyl D-chiro-inositols and two trigalactosyl D-chiuo-inositols, members of the fagopyritol A series and fagopyritol B series, were isolated from buckwheat (Fagopyrum esculentum Moench) seeds. Structures of the first three were determined by H-1 and C-13 NMR. Fagopyritol B2 is alpha -D-galactopyranosyl-(1->6)-alpha -D-galactopyranosyl-(1->2)-1D-chiro-inositol , and fagopyritol A2 is alpha -D-galactopyranosyl-(1->6)-alpha -D-galactopyranosyl-(1->3)-1D-chiro-inositol. Fagopyritol A3, a trigalactosyl D-chiro-inositol, is alpha -D-galactopyranosyl-(1->6)-alpha -D-galacto-pyranosyl-(1->6)-alpha -D-galactopyranosyl-(1->3)-1D-chiro-inositol. From analysis of hydrolysis products, the second trigalactosyl D-chiro-inositol, fagopyritol B3, is alpha -D-galactopyranosyl-(1->6)-alpha -D-galactopyranosyl-(1->6)-alpha -D-galactopyranosyl-(1->2)-1D-chiro-inositol. (C) 2001 Elsevier Science Ltd. All rights reserved

Dormancy release in Australian fire ephemeral seeds during burial increases germination response to smoke water or heat

Fire ephemerals are short-lived plants that primarily germinate after fire. Fresh and laboratory-stored seeds are difficult to germinate ex situ, even in response to fire-related cues such as heat and smoke. Seeds of eight Australian fire ephemeral species were buried in unburnt and recently burnt sites of natural bushland during autumn. Seeds were exhumed after 6 and 12 months and incubated in water and smoke water, either with or without a heat treatment at 70 degrees C for 1 h. Generally, germination did not increase after 6 months of burial, but after 12 months of burial germination was enhanced in seven of the eight species. Actinotus leucocephalus produced higher germination following 12 months of burial without any further treatment, and smoke water and heat further improved germination. The four Gyrostemonaceae species, Codonocarpus cotinifolius, Gyrostemon racemiger, Gyrostemon ramulosus and Tersonia cyathiflora, only germinated in the presence of smoke water, and their germination was enhanced by burial. Burial improved germination in response to a heat treatment in Grevillea scapigera and Alyogyne huegelii seeds, but did not enhance Alyogyne hakeifolia germination. During concurrent dry laboratory storage of seeds at 15 degrees C, only Actinotus leucocephalus produced increased germination in response to smoke water and heat over time. In summary, soil burial can alter the dormancy status of a number of Australian fire ephemeral seeds, rendering them more responsive to germination cues such as smoke water and heat. The requirement for a period of burial before seeds become responsive to smoke and/or heat would ensure that seeds persist in the soil until a subsequent fire, when there is an increase in nutrients available for growth and reduced competition from other plants