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

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 ‘Honeycrisp’ apple fruit

Expression levels (RPKM) of Malus domestica housekeeping genes from Bowen et al. (2015) in RNA-seq analyses. (DOCX 174 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

Phylogenetic tree of six rosids, four malvids, and three asterids constructed with 83 euKaryote Orthologous Genes (KOGs).

<p>Bootstrap values are listed on each branch. Nodes represent speciation events and branch length represents the degree of evolutional changes over time. The unit for the scale bar at the bottom is nucleotide substitutions per site. The high bootstrap values strongly support that the species in Rosaceae cluster together to the exclusion of any other, and that the European pear and Chinese pear separation event happened after apple speciation.</p

Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from [18].

<p>Comparison of <i>de novo</i> predicted repeated elements between the European pear, Chinese pear and apple genomes. na: not available from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092644#pone.0092644-Wu1" target="_blank">[18]</a>.</p

Basic statistics on the <i>Pyrus communis</i> ‘Bartlett’ genome sequence.

<p>Figures are given in bp.</p><p>*: the assumed genome size of pear is 600 Mb.</p