9 research outputs found
A Comparison of Nuggets and Clusters for Evaluating Timeline Summaries
There is growing interest in systems that generate timeline summaries by filtering high-volume streams of documents to retain only those that are relevant to a particular event or topic. Continued advances in algorithms and techniques for this task depend on standardized and reproducible evaluation methodologies for comparing systems. However, timeline summary evaluation is still in its infancy, with competing methodologies currently being explored in international evaluation forums such as TREC. One area of active exploration is how to explicitly represent the units of information that should appear in a 'good' summary. Currently, there are two main approaches, one based on identifying nuggets in an external 'ground truth', and the other based on clustering system outputs. In this paper, by building test collections that have both nugget and cluster annotations, we are able to compare these two approaches. Specifically, we address questions related to evaluation effort, differences in the final evaluation products, and correlations between scores and rankings generated by both approaches. We summarize advantages and disadvantages of nuggets and clusters to offer recommendations for future system evaluation
MOESM2 of Kinetic modelling: an integrated approach to analyze enzyme activity assays
Additional file 2. PDC_model
Data_Sheet_1_Metabolic Responses to Low Temperature of Three Peach Fruit Cultivars Differently Sensitive to Cold Storage.PDF
<p>Refrigerated storage is widely applied in order to maintain peach quality but it can also induce chilling injuries (CIs) such as flesh browning and bleeding, and mealiness. Peach fruit from three cultivars (‘Red Haven’, RH, ‘Regina di Londa’, RL, and ‘Flaminia’, FL) were stored for 4 weeks under low temperatures (0.5 and 5.5°C). GC-MS was employed to study changes in both metabolome and volatilome induced by cold storage in the mesocarp. CIs were assessed both at the end of each week of storage and after subsequent shelf-life (SL) at 20°C. Flesh browning and mealiness appeared to be more related to 5.5°C storage, while flesh bleeding revealed high incidence following 0.5°C storage. Compared to RL and FL, RH showed a marked lower incidence of CIs. Multivariate statistical analyses indicate that RH peaches indeed differ from RL and FL in particular when considering data from samples collected at the end of the cold storage. Common and divergent responses have been identified in terms of metabolic responses to the applied low temperatures. In all three cultivars raffinose, glucose-6P, fucose, xylose, sorbitol, GABA, epicatechin, catechin, and putrescine markedly increased during cold storage, while citramalic, glucuronic, mucic and shikimic acids decreased. Among volatile organic compounds (VOCs), aldehydes and alcohols generally accumulated more under low temperature conditions while esters and lactones evolved during subsequent SL. The main cultivar differences developed after cold storage during SL although some common responses (e.g., an increased production of ethyl acetate) were observed. The lower levels of flesh browning and bleeding displayed by RH peaches were related to compounds with antioxidant activity, or acting as osmotic protectants and membrane stabilizer. Indeed, RH showed higher levels of amino acids and urea, together with a marked increase in putrescine, sorbitol, maltitol, myoinositol and sucrose detected during storage and SL.</p
Effects of vitamin D on blood pressure, arterial stiffness, and cardiac function in older people after 1 year: BEST‐D (Biochemical Efficacy and Safety Trial of Vitamin D)
<strong>Background:</strong> The relevance of vitamin D for prevention of cardiovascular disease is uncertain. The BEST-D trial previously reported effects of vitamin D on plasma markers of vitamin D status, and the present report describes the effects on blood pressure, heart rate, arterial stiffness and cardiac function.
<strong>Methods and Results:</strong> Randomized, double-blind, placebo-controlled trial of 305 older people living in UK, allocated vitamin D 4000 IU (100 μg), vitamin D 2000 IU (50 μg), or placebo daily. Primary outcomes were plasma concentrations of 25-hydroxy-vitamin D (25[OH]D) and secondary outcomes were blood pressure, heart rate and arterial stiffness in all participants at 6 and 12 months, plasma N-terminal prohormone of brain natriuretic peptide (NT-proBNP) levels in all participants at 12 months, and echocardiographic measures of cardiac function in a randomly selected subset (n=177) at 12 months. Mean (SE) plasma 25(OH)D concentrations were 50 (SE 2) nmol/L at baseline and increased to 137 (2.4), 102 (2.4) and 55 (2.4) nmol/L after 12 months in those allocated 4000 IU/day, 2000 IU/day of vitamin D or placebo, respectively. Allocation to vitamin D had no significant effect on mean levels of blood pressure, heart rate or arterial stiffness at either 6 or 12 months, nor on any echocardiographic measures of cardiac function, or plasma NT-proBNP concentration at 12 months.
<strong>Conclusions:</strong> The absence of any significant effect of vitamin D on blood pressure, arterial stiffness or cardiac function suggests that any beneficial effects of vitamin D on cardiovascular disease are unlikely to be mediated through these mechanisms
Additional file 1: Table S1. of Gene expression and metabolism preceding soft scald, a chilling injury of ‘Honeycrisp’ apple fruit
Quality and maturity of fruit from ‘Honeycrisp’ orchards used for the metabolomic (all orchards) and transcriptomic (orchards A_H1, A_H2, A_H3, M, and P) analyses. (DOCX 34 kb
Additional file 8: Figure S5. of Gene expression and metabolism preceding soft scald, a chilling injury of âHoneycrispâ apple fruit
Expression levels (RPKM) of Malus domestica housekeeping genes from Bowen et al. (2015) in RNA-seq analyses. (DOCX 174Â kb
Additional file 2: Figure S1. of Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
Principal Components Analysis (PCA) bi-plots of metabolite (top) and gene expression level data (bottom) from ‘Granny Smith’ apple peel from fruit stored in air at 1 °C for up to 183 days (6 months). Apples were treated immediately following harvest with 2000 μL L−1 DPA or 1 mL L−1 1-MCP. Gene expression and metabolite datasets were analyzed separately. Shapes represent scores for each observation where symbol size increases with storage duration and symbol color represents scald severity. Gray points represent loadings for individual metabolites or transcripts. (DOCX 2373 kb
Additional file 4: Figure S2. of Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
Comparative expression of scald VIPs and the “refined” methanol and CTOL subnetworks within different MapMan cell wall metabolism bins. Darker blue squares indicate elevated expression compared with the other lists within that category. (DOCX 29 kb
Additional file 3: Table S3. of Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis
Gene cluster assignment for correlation networks. To summarize gene expression data, genes expression patterns from all time points (0–183 d) and treatments (control, diphenylamine, and 1-methylcyclopropene) were clustered using k-means clustering. Average gene expression values from each cluster were correlated along with relative metabolite levels to generate 2 month and 6 month networks. The number of Variables Important in the Projection (VIP) for the “scald severity” response variable from the PLS-DA model is included for each gene cluster. (DOCX 18 kb