Food defense : protecting the food supply from intentional harm (2009)

New 11/09/2M

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

National Beef Tenderness Survey–2015: Palatability and Shear Force Assessments of Retail and Foodservice Beef

Beef retail steaks from establishments across 11 US cities and beef foodservice steaks from establishments in 6 US cities were evaluated using Warner-Bratzler shear (WBS) force and consumer sensory panels. The average post-fabrication aging time of steaks at retail establishments was 25.9 d with a range of 6 to 102 d, and those from foodservice establishments averaged 31.5 d with a range of 3 to 91 d. The retail steaks with the lowest WBS value ( < 0.05) was the boneless top loin, compared to the top round steaks, which had the higher ( < 0.05) average WBS value. For the foodservice sector, top loin and ribeye steaks had the lowest ( < 0.05) WBS values, whereas the top sirloin represented the highest ( < 0.05) WBS values. The top blade retail steaks received among the highest consumer ratings ( < 0.05), whereas the top round and bottom round steaks received among the lowest ( < 0.05) consumer ratings for overall liking, tenderness liking, tenderness level, flavor liking, and juiciness liking. For the foodservice sector, the ribeye and top loin steaks were rated higher ( < 0.05) than top sirloin steaks for all consumer rating categories. The WBS values and sensory ratings were comparable to previous surveys, indicating no substantial changes in tenderness. Additional emphasis in improving the tenderness of top and bottom round steaks is necessary to increase consumer acceptability of these cuts

Subunit architecture of multiprotein assemblies determined using restraints from gas-phase measurements

Protein interaction networks are becoming an increasingly important area of research within structural genomics. Here we present an ion mobility-mass spectrometry approach capable of distinguishing the overall subunit architecture of protein complexes. The approach relies on the simultaneous measurement in the gas phase of the mass and size of intact assemblies and subcomplexes. These data are then used as restraints to generate topological models of protein complexes. To test and develop our method, we have chosen two well-characterized homo-dodecameric protein complexes: ornithine carbamoyl transferase and glutamine synthetase. By forming subcomplexes related to the comparative strength of the subunit interfaces, acquiring ion mobility data, and subsequent modeling, we show that these ‘‘building blocks’’ retain their native interactions and do not undergo major rearrangement in either solution or gas phases. We apply this approach to study two subcomplexes of the human eukaryotic initiation factor 3, for which there is no high-resolution structure.Tara L. Pukala, Brandon T. Ruotolo, Min Zhou, Argyris Politis, Raluca Stefanescu, Julie A. Leary and Carol V. Robinso

Serum proteins reflecting inflammation, injury and repair as biomarkers of disease activity in ANCA-associated vasculitis

<p>Objective To identify circulating proteins that distinguish between active anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and remission in a manner complementary to markers of systemic inflammation.</p><p>Methods Twenty-eight serum proteins representing diverse aspects of the biology of AAV were measured before and 6months after treatment in a large clinical trial of AAV. Subjects (n=186) enrolled in the Rituximab in ANCA-Associated Vasculitis (RAVE) trial were studied. Erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels were available for comparison. The primary outcome was the ability of markers to distinguish severe AAV (Birmingham Vasculitis Activity Score for Wegener's granulomatosis (BVAS/WG)3 at screening) from remission (BVAS/WG=0 at month 6), using areas under receiver operating characteristic (ROC) curve (AUC).</p><p>Results All subjects had severe active vasculitis (median BVAS/WG=8) at screening. In the 137 subjects in remission at month 6, 24 of the 28 markers showed significant declines. ROC analysis indicated that levels of CXCL13 (BCA-1), matrix metalloproteinase-3 (MMP-3) and tissue inhibitor of metalloproteinases-1 (TIMP-1) best discriminated active AAV from remission (AUC>0.8) and from healthy controls (AUC>0.9). Correlations among these markers and with ESR or CRP were low.</p><p>Conclusions Many markers are elevated in severe active AAV and decline with treatment, but CXCL13, MMP-3 and TIMP-1 distinguish active AAV from remission better than the other markers studied, including ESR and CRP. These proteins are particularly promising candidates for future studies to address unmet needs in the assessment of patients with AAV.</p>

Early stage litter decomposition across biomes

peer reviewedThrough litter decomposition enormous amounts of carbon is emitted to the atmosphere. Numerous large-scale decomposition experiments have been conducted focusing on this fundamental soil process in order to understand the controls on the terrestrial carbon transfer to the atmosphere. However, previous studies were mostly based on site-specific litter and methodologies, adding major uncertainty to syntheses, comparisons and metaanalyses across different experiments and sites. In the TeaComposition initiative, the potential litter decomposition is investigated by using standardized substrates (Rooibos and Green tea) for comparison of litter mass loss at 336 sites (ranging from −9 to +26 °C MAT and from 60 to 3113mm MAP) across different ecosystems. In this study we tested the effect of climate (temperature and moisture), litter type and land-use on early stage decomposition (3 months) across nine biomes. We show that litter quality was the predominant controlling factor in early stage litter decomposition, which explained about 65% of the variability in litter decomposition at a global scale. The effect of climate, on the other hand, was not litter specific and explained b0.5% of the variation for Green tea and 5% for Rooibos tea, and was of significance only under unfavorable decomposition conditions (i.e. xeric versus mesic environments).When the data were aggregated at the biome scale, climate played a significant role on decomposition of both litter types (explaining 64% of the variation for Green tea and 72% for Rooibos tea).No significant effect of land-use on early stage litter decompositionwas notedwithin the temperate biome. Our results indicate that multiple drivers are affecting early stage littermass loss with litter quality being dominant. In order to be able to quantify the relative importance of the different drivers over time, long-term studies combined with experimental trials are needed