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

Combining alders, frankiae, and mycorrhizae for the revegetation and remediation of contaminated ecosystems

Alder shrubs and trees that are capable of forming symbioses with mycorrhizal fungi and the nitrogen-fixing actinomycete Frankia sp. are particularly hardy species found worldwide in harsh and nutrient-deficient ecosystems. The mycorrhizal symbiosis may assist alders in nutrient and water uptake, while the actinorhizal symbiosis provides assimilable nitrogen. It is through these highly efficient symbioses, in which microsymbionts benefit from plant photosynthates, that actinorhizal plants such as alders colonize poor substrates, enrich soil, and initiate plant succession. These natural capabilities, combined with careful screening of microsymbionts and host plants, may prove useful for the rehabilitation of disturbed ecosystems. Although alders have been used extensively at industrial scales in forestry, nurse planting, and contaminated land revegetation, relatively little research has focussed on their actinorhizal and mycorrhizal plant-microbe interactions in contaminated environments. To study such a topic is, however, critical to the successful development of phytotechnologies, and to understand the impact of anthropogenic stress on these organisms. In this review, we discuss two alder-based phytotechnologies that hold promise: the stimulation of organic contaminant biodegradation (rhizodegradation) by soil microflora in the presence of alders, and the phytostabilization of inorganic contaminants. We also summarize the plant-microbe interactions that characterize alders, and discuss important issues related to the study of actinorhizal and (or) mycorrhizal alders for the rehabilitation of disturbed soils.Les aulnes arbustifs et arborescents, formant des symbioses avec des champignons mycorhiziens et les actinomyc\ue8tes fixateurs Frankia sp., sont des esp\ue8ces particuli\ue8rement robustes qu'on retrouve partout au monde, dans des \ue9co-syst\ue8mes inhospitaliers et pauvres en nutriments. La symbiose mycorhizienne peut assister les aulnes dans l'absorption de l'eau et des nutriments, alors que la symbiose actinorhizienne fournit l'azote assimilable. c'est par l'interm\ue9diaire de ces symbioses tr\ue8s efficaces, o\uf9 les microsymbiontes obtiennent les photosynth\ue9tats de la plante, que les plantes actinorhiziennes, telles que les aulnes, colonisent des substrats pauvres, enrichissent le sol et initient la succession v\ue9g\ue9tale. Ces capacit\ue9s naturelles combin\ue9es avec une s\ue9lection soign\ue9e des microsymbiontes et des plantes h\uf4tes, peuvent s'av\ue9rer utiles pour la r\ue9habilitation d'\ue9cosyst\ue8mes perturb\ue9s. Bien qu'on ait largement utilis\ue9 les aulnes \ue0 l'\ue9chelle industrielle en foresterie, comme plantes compagnes et pour la r\ue9habilitation des sols contamin\ue9s, relativement peu de recherches ont port\ue9 sur leurs interactions actinorhiziennes et mycorhiziennes plante-microbe, dans des environnements contamin\ue9s. Cependant, l'\ue9tude de ce sujet est n\ue9cessaire pour d\ue9velopper des phytotechnologies efficaces et pour comprendre l'impact des stress anthropog\ue8nes sur ces organismes. Dans cette revue, les auteurs discutent dux phytotechnologies prometteuses bas\ue9es sur l'aulne; la stimulation de la biod\ue9gradation (rhizod\ue9gradation) par la microflore du sol en pr\ue9sence d'aulnes, et la phytostabilisation, des contaminants organiques. Les auteurs r\ue9sument \ue9galement les interactions plante-microbe qui caract\ue9risent les aulnes et discutent de questions pertinentes reli\ue9es \ue0 l'\ue9tude des aulnes actinorhiziens et (ou) mycorhiziens, pour la r\ue9habilitation des sols perturb\ue9s.NRC publication: Ye

Field Performance of alder-Frankia Symbionts for the Reclamation of Oil Sands Sites

The Canadian province of Alberta is the world's largest producer of petroleum products from oil sands exploitation. Oil sands process-affected materials (OSPM), such as tailings sand, produced as a result of bitumen extraction, has low fertility, low organic matter content, it is alkaline, compactable, and contains residual hydrocarbons, making it a very inhospitable growth environment. The petroleum industry is currently involved in efforts to revegetate and remediate the tailings sand. One approach used is revegetation of the reclamation sites with Frankia-inoculated alders. Alders are primary succession trees that have the ability to grow in nutrient poor and waterlogged environments, in part because they form a symbiotic relationship with the nitrogen-fixing Actinobacteria, Frankia. In 2005, field trials were established at Syncrude Canada Ltd. The effect of Frankia-inoculated alders on soil quality was evaluated by monitoring the chemical and microbiological characteristics of the soil. The impact on the indigenous microbial community was also studied using hydrocarbon mineralization assays, and molecular approaches, such as denaturing gradient gel electrophoresis (DGGE). Plant parameters (biomass, nitrogen content) were measured to evaluate the impact of Frankia on alder health and growth. After two growth seasons, Frankia-inoculated and non-inoculated alders yielded comparable amounts of plant biomass and there was an increase in hydrocarbon (hexadecane, naphthalene and phenanthrene) mineralization where the reclamation site had been planted with alder-Frankia. The alder rhizosphere samples all had comparable hydrocarbon mineralization rates. DGGE profiles confirmed a change in the microbial communities of the bulk soil between unplanted and alder-Frankia treatments. Soil tests showed that alder-Frankia decreased soil pH (from 7.5 to 6.6, in 2006, and from 8.2 to 7.2 in 2007) and plant-available sodium content (70% reduction), and had a positive impact on soil organic matter content (increase in up to 6 times in alder-Frankia plots). The field results have confirmed that the alder-Frankia combination results in improved remediation capabilities and enhances soil quality. These improvements in soil quality of the reclamation site provide evidence of the potential of alder-Frankia symbionts to be part of a reclamation strategy for the reforestation of the site, and the re-establishment of a balanced ecosystem. Crown Copyright \ua9 2010.Peer reviewed: YesNRC publication: Ye

Phytoremediation of heavy metal and PAH-contaminated brownfield sites

NRC publication: Ye

Energy calibration and resolution of the CMS electromagnetic calorimeter in pp collisions at s\sqrt{s} = 7 TeV

The energy calibration and resolution of the electromagnetic calorimeter (ECAL) of the CMS detector have been determined using proton-proton collision data from LHC operation in 2010 and 2011 at a centre-of-mass energy of sqrt(s)=7 TeV with integrated luminosities of about 5 inverse femtobarns. Crucial aspects of detector operation, such as the environmental stability, alignment, and synchronization, are presented. The in-situ calibration procedures are discussed in detail and include the maintenance of the calibration in the challenging radiation environment inside the CMS detector. The energy resolution for electrons from Z-boson decays is better than 2% in the central region of the ECAL barrel (for pseudorapidity abs(eta)<0.8) and is 2-5% elsewhere. The derived energy resolution for photons from 125 GeV Higgs boson decays varies across the barrel from 1.1% to 2.6% and from 2.2% to 5% in the entraps. The calibration of the absolute energy is determined from Z to e+e- decays to a precision of 0.4% in the barrel and 0.8% in the endcaps

Search for heavy resonances in the W/Z-tagged dijet mass spectrum in pp collisions at 7 TeV

A search has been made for massive resonances decaying into a quark and a vector boson, qW or qZ, or a pair of vector bosons, WW, WZ, or ZZ, where each vector boson decays to hadronic final states. This search is based on a data sample corresponding to an integrated luminosity of 5.0 fb 121 of proton\u2013proton collisions collected in the CMS experiment at the LHC in 2011 at a center-of-mass energy of 7 TeV. For sufficiently heavy resonances the decay products of each vector boson are merged into a single jet, and the event effectively has a dijet topology. The background from QCD dijet events is reduced using recently developed techniques that resolve jet substructure. A 95% CL lower limit is set on the mass of excited quark resonances decaying into qW (qZ) at 2.38 TeV (2.15 TeV) and upper limits are set on the cross section for resonances decaying to qW, qZ, WW, WZ, or ZZ final states

Search for long-lived particles in events with photons and missing energy in proton\u2013proton collisions at sqrt(s)=7 TeV

Results are presented from a search for long-lived neutralinos decaying into a photon and an invisible particle, a signature associated with gauge-mediated supersymmetry breaking in supersymmetric models. The analysis is based on a 4.9 inverse femtobarn sample of proton-proton collisions at 1as = 7 TeV, collected with the CMS detector at the LHC. The missing transverse energy and the time of arrival of the photon at the electromagnetic calorimeter are used to search for an excess of events over the expected background. No significant excess is observed, and lower limits at the 95% confidence level are obtained on the mass of the lightest neutralino, m(neutralino) > 220 GeV (for c tau 6000 mm (for m(neutralino) < 150 GeV)