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

Can Your Food Prevent Cancer?

28-29COMMON everyday fruits, vegetables, grains and spices contain many constituents that have been shown to prevent cancer. A balanced diet, therefore, containing these foods can keep the onset of cancer at bay

PEROXIDASE ACTIVITY IN TOMATO CULTIVARS SUSCEPTIBLE TO FUSARIUM OXSYPORUM

Not AvailableThe total phenol content, peroxidase and polyphenol oxidase enzyme activities and the total protein profile in tomato cultivars (Lycopersicon esculantum Mill.), tolerant and susceptible to Fusarium wilt disease was studied. The tolerant cultivars of tomato viz., FEB-2, FEB-4, FloraDade and NF-31 had significantly higher phenol content as well as peroxidase and polyphenol oxidase activities than the susceptible ones (Sel-7, Sel-18 and Punjab Chhuhara). The maximum peroxidase activity was recorded in the resistant cultivar, Flora Dade (02.073unit/ml) and minimum in the susceptible cultivar,Sel-18 (0.241unit/ml). Major differences in soluble protein banding pattern were observed in the susceptible and resistant cultivars. The hierarchical cluster analysis was performed using NTSYS-pc(V.1.8) software. The dendrogram using the average linkage between the groups, showed proximity of resistant cultivars viz., FEB-4,FEB-2, Flora Dade and NF-31 to the wild species with respect to similarity of banding patterns. The three susceptible cultivars viz., Sel-7, Punjab Chhuhara and Sel-18 were grouped separately.Not Availabl

CHANGES IN ANTIOXIDANT AND PHYTOCHEMICAL PROPERTIES OF TOMATO

Not AvailableDuration of storage increased TSS and pH of tomato juice, while ascorbic acid content decreased gradually during storage. Carotenoids content increased approximately 3.5 times during storage in tomato because of advancement of ripening stage. During ripening chlorophyll gradually degrades and the carotenoid synthesis is enhanced. Increased levels of lycopene in tomato during storage might also be due to ripening of tomato fruits. The spoilage in fruits gradually increased in all cultivars with the advancement of storage period. Spoilage of fruits started on 6th day of storage in all cultivars except Avinash-2. The average shelf life of tomato fruits ranged from 6-12 days among cultivars based on 40% spoilage. The lowest shelf life of 6 days was noted in H-86 and highest of 12 days in Avinash-2. It was concluded that the tomato harvested at breaker stage may be utilized for almost one week along with increased contents of carotenoids and lycopene compensated for the decreased levels of acidity and ascorbic acid contents.Not Availabl

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Not AvailableTerminal heat stress severely affects the growth of wheat crop causing drastic reduction in the yield and nutritional quality of the grains. Various technologies have been developed in the past to alleviate the effect of terminal heat stress (HS) in wheat, but with limited success. Silicon (Si), being quasi-essential element, has many beneficial advantages to the plants. Here, we observed exogenous application of 2.5 mM Si to be very effective in modulating the thermo-tolerance and quality of the grains. The application of Si2.5 has been observed to trigger the expression of signalling molecules (MAPK, CDPK), and stress-associated genes (SAGs) like HSFs (HD97, HSFA6e), HSPs (HSP17, HSP23, HSP70 and HSP90) and genes of antioxidant enzyme (GPX and SOD) under HS. Thermo-tolerant wheat cv. HD3086 showed more abundance of SAGs transcripts, as compared to thermo-susceptible cv. BT-Schomburgk. We observed increase in the accumulation of photosynthetic enzyme (RuBisCo activase) in leaves and storage protein (gliadin) in wheat grains under Si2.5 treatment. Heat stress downregulates the expression of genes linked with starch biosynthesis pathway; the percent decrease observed was minimum under Si2.5 treatment. Improved grain quality in both cvs. in response to Si2.5 under HS was observed. Si2.5 inhibits the activity of starch-degrading enzyme in endospermic tissue of grains. Si2.5 application was very effective, cheap and non-hazardous for mitigating the effect of terminal HS in wheat, stabilizing yield without compromising the quality of the grains.Not Availabl

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Not AvailableTerminal heat stress has detrimental effect on the growth and yield of wheat. Very limited information is available on heat stress-associated active proteins (SAAPs) in wheat. Here, we have identified 159 protein groups with 4271 SAAPs in control (22 +/- 3 degrees C) and HS-treated (38 degrees C, 2h) wheat cvs. HD2985 and HD2329 using iTRAQ. We identified 3600 proteins to be upregulated and 5825 proteins to be downregulated in both the wheat cvs. under HS. We observed 60.3% of the common SAAPs showing upregulation in HD2985 (thermotolerant) and downregulation in HD2329 (thermosusceptible) under HS. GO analysis showed proton transport (molecular), photosynthesis (biological), and ATP binding (cellular) to be most altered under HS. Most of the SAAPs identified were observed to be chloroplast localized and involved in photosynthesis. Carboxylase enzyme was observed most abundant active enzymes in wheat under HS. An increase in the degradative isoenzymes (/-amylases) was observed, as compared to biosynthesis enzymes (ADP-glucophosphorylase, soluble starch synthase, etc.) under HS. Transcript profiling showed very high relative fold expression of HSP17, CDPK, Cu/Zn SOD, whereas downregulation of AGPase, SSS under HS. The identified SAAPs can be used for targeted protein-based precision wheat-breeding program for the development of climate-smart' wheat.Indian Council of Agriculture Research (ICAR) under National Innovation on Climate Resilient Agriculture (NICRA) project [12/115 TG 3079]CABin project [(21-56) TG3064

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Not AvailableWheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22 – 3C) and heat stress (42C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.Not Availabl

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Not AvailableTerminal heat stress has detrimental effect on the growth and yield of wheat. Very limited information is available on heat stress-associated active proteins (SAAPs) in wheat. Here, we have identified 159 protein groups with 4271 SAAPs in control (22 ± 3 °C) and HS-treated (38 °C, 2 h) wheat cvs. HD2985 and HD2329 using iTRAQ. We identified 3600 proteins to be upregulated and 5825 proteins to be downregulated in both the wheat cvs. under HS. We observed 60.3% of the common SAAPs showing upregulation in HD2985 (thermotolerant) and downregulation in HD2329 (thermosusceptible) under HS. GO analysis showed proton transport (molecular), photosynthesis (biological), and ATP binding (cellular) to be most altered under HS. Most of the SAAPs identified were observed to be chloroplast localized and involved in photosynthesis. Carboxylase enzyme was observed most abundant active enzymes in wheat under HS. An increase in the degradative isoenzymes (α/β-amylases) was observed, as compared to biosynthesis enzymes (ADP-glucophosphorylase, soluble starch synthase, etc.) under HS. Transcript profiling showed very high relative fold expression of HSP17, CDPK, Cu/Zn SOD, whereas downregulation of AGPase, SSS under HS. The identified SAAPs can be used for targeted protein-based precision wheat-breeding program for the development of 'climate-smart' wheat.Not Availabl

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Not AvailableWheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22°±3° C) and heat stress (42° C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively.Not Availabl