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

Crude extracts of Sesamum Indicum roots used as anthraquinone source effect on pulping with sodium hydroxide of Sudanese bagasse

Abstract The objectives The work was carried out for extraction of natural anthrasesamones from roots of Sesamum Indicum using different organic solvents and utilization of extracts as catalyst in pulping with sodium hydroxide for a by-product of sugar industry (Sudanese bagasse). Results Sesamum Indicum roots when extracted with ethanol, it gave the highest extracts yield % (0.964), followed by ethyl acetate, chloroform, dichloromethane and petroleum ether extracts. The chemical pulping of Bagasse was done by using of sodium hydroxide, sodium hydroxide with anthraquinone, and sodium hydroxide with extract instead of anthraquinone keeping constant conditions at temperature 160 °C and applied sodium oxide 10.9% and time was 120 min, gave promising screened yield between 49.84 and 53.68%, bleachable kappa number between 15.57 and 8.26 for sodium hydroxide only and cooking with sodium hydroxide with anthraquinone. Cooking with sodium hydroxide of bagasse with anthrasesamones gave good pulping yields and kappa number

Application of soda-AQ pulping to agricultural waste (okra stalks) from Sudan

Abstract Abelmoschus esculentus okra as whole stalks was examined for its suitability for pulp and paper production. It’s, fiber dimensions, morphological and chemical characteristics were reported. The pulping trials with soda- Anthraquinone (AQ,) at different chemical charges. Application of 21% as NaOH with 0.1% AQ gave good results in degree of delignification, mechanical properties. Utilization of okra pulps and blender is recommended due to good pulp properties. Evaluation of general characteristics of okra stalks in terms of fiber dimensions morphological indices, chemical components, Soda-AQ cooking and to study their suitability for paper production. Okra Fiber dimension evaluation done after maceration with a mixture of 30% hydrogen peroxide and acetic acid (1:1) for core and bark parts separately and was carried out under microscope staining with aqueous safranin. The Soda-AQ cooks at different active alkali levels were calculated as NaOH on oven dry raw material. The fibers from okra stalks studied (core and bark) were in the range of hardwood fibers, with short fiber length, especially the core with more or less moderate walls, narrow lumen and fiber width. The fiber width of bark was medium –narrow with medium wall thickness. The ash content was rather high whereas the silica content was comparatively high The hot water extractives from okra stalks was (4.1%), cold water (0.4) ethanol/ cyclohexane (1.1), ethanol extractives (1.2%) and 1% NaOH (27.6%) were rather high. The cellulose (Kurschner-Hoffer) was (48.5%) The lignin content was (15.3%) which was relatively moderate. The use of 0.1% AQ enhanced the delignification in the three trials applied. The screened yield increase with increase of chemical dose applied while the rejects decrease. When 21% NaOH was applied, the screened yield was 32.2% with negligible amount of rejects, however with lower alkali charge 18% the screened yield was decreased to 28% with very low rejects 1.5%. on the other hand rejects were increased to 7% when 15% NaOH was applied with very low screened yield 19%.The pulps produced from okra soda-AQ are suitable for production of printing and writing papers and it is advisable to use them in blending due to good papermaking properties

Physiochemical, Insecticidal, and Antidiabetic Activities of Senna occidentalis Linn Root

The present study aimed to investigate the physiochemical activities of Senna occidentalis (Linn) roots and phytochemicals as insecticidal (ethyl acetate and methanol) and antidiabetic (ethanolic extract) activities. Physicochemical properties were carried out by using Association of Official Analytical Chemist methods; thin layer chromatography was carried out according to the Stahl method. Larvicidal activity and LD50 were studied against the third instar of Culex quinquefasciatus mosquito larvae to detect and extract toxicity. The ethanolic extracts of the roots were orally tested at the dose 200 mg/kg for the hypoglycemic effect on induced hyperglycemia in normal rats, assessed in the ethanol extract, and were compared with diabetic control and standards glibenclamide 10 mg/kg. Physiochemical parameters showed high rate in the nitrogen-free extract (69.6%), curd fiber (14.5%), crude proteins (8.15%), ether extract (3.75%), and both ash and moisture (2%), and high concentrations values were found in potassium (43 mg/l) followed by phosphorous (28.5 mg/l), calcium (15 mg/l), sodium (3.65 mg/l), and magnesium (0.145 mg/l). In this part, phytochemical compounds showed high amount of alkaloids, triterpene, flavonoids, tannins, sugars, and few amount of anthraquinone glycosides. Thin-layer chromatography (TLC) studies different colored phytochemical constituted with different Rf values. All the spots are colored under UV light, but some are localized colorless after spaying. The ethyl acetate (EtAc) extract showed eight spots, and the methanol (MeOH) extract showed thirteen spots. The larvicidal activity showed that the ethyl acetate extract was safe against mosquito larvae with an LD50 value 1412.54 (p<0.05), and the methanol extract had moderate larvicidal activity against mosquito larvae with an LD50 value 257.54 (p<0.05), while the ethanolic extract of Senna occidentalis (L.) causes a favorable hypoglycemic activity when compared to control significant reduction by [53.15%, 32.87%, and 20.94%], respectively, as well as standard glibenclamide. Based on the various data of the physicochemical parameters, TLC spots, and phytochemical compounds of Senna occidentalis root, they could be used as references standards for manufacturing units of Senna occidentalis root larvicidal and antidiabetic drugs