Temporal and Vertical Oxygen Gradients Modulate Nitrous Oxide Production in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia

Nitrous oxide (N2O) is a strong greenhouse gas and an ozone depleting agent. In marine environments, N2O is produced biologically via ammonium oxidation, nitrite, and nitrate reduction. The relative importance of these principle production pathways is strongly influenced by oxygen availability. We conducted 15N tracer experiments of N2O production in parallel with measurements of N2O concentration and natural abundance isotopes/isotopomers in Saanich Inlet, a seasonally anoxic fjord, to investigate how temporal and vertical oxygen gradients regulate N2O production pathways and rates. In April, June, and August 2018, the depth of the oxic‐anoxic interface (dissolved oxygen = 2.5 μmol L−1 isoline) progressively deepened from 110 to 160 m. Within the oxygenated and suboxic water column, N2O supersaturation coincided with peak ammonium oxidation activity. Conditions in the anoxic deep water were potentially favorable to N2O production from nitrate and nitrite reduction, but N2O undersaturation was observed indicating that N2O consumption exceeded rates of production. In October, tidal mixing introduced oxygenated water from outside the inlet, displacing the suboxic and anoxic deep water. This oxygenation event stimulated N2O production from ammonium oxidation and increased water column N2O supersaturation while inhibiting nitrate and nitrite reduction to N2O. Results from 15N tracer incubation experiments and natural abundance isotopomer measurements both implicated ammonium oxidation as the dominant N2O production pathway in Saanich Inlet, fueled by high ammonium fluxes (0.6–3.5 nmol m−2 s−1) from the anoxic depths. Partial denitrification contributed little to water column N2O production because of low availability of nitrate and nitrite

Investigating the effect of El Niño on nitrous oxide distribution in the Eastern Tropical South Pacific

The open ocean is a major source of nitrous oxide (N2O), an atmospheric trace gas attributable to global warming and ozone depletion. Intense sea-to-air N2O fluxes occur in major oceanic upwelling regions such as the eastern tropical South Pacific (ETSP). The ETSP is influenced by the El Niño–Southern Oscillation that leads to inter-annual variations in physical, chemical, and biological properties in the water column. In October 2015, a strong El Niño event was developing in the ETSP; we conduct field observations to investigate (1) the N2O production pathways and associated biogeochemical properties and (2) the effects of El Niño on water column N2O distributions and fluxes using data from previous non-El Niño years. Analysis of N2O natural abundance isotopomers suggested that nitrification and partial denitrification (nitrate and nitrite reduction to N2O) were occurring in the near-surface waters; indicating that both pathways contributed to N2O effluxes. Higher-than-normal sea surface temperatures were associated with a deepening of the oxycline and the oxygen minimum layer. Within the shelf region, surface N2O supersaturation was nearly an order of magnitude lower than that of non-El Niño years. Therefore, a significant reduction of N2O efflux (75 %–95 %) in the ETSP occurred during the 2015 El Niño. At both offshore and coastal stations, the N2O concentration profiles during El Niño showed moderate N2O concentration gradients, and the peak N2O concentrations occurred at deeper depths during El Niño years; this was likely the result of suppressed upwelling retaining N2O in subsurface waters. At multiple stations, water-column inventories of N2O within the top 1000 m were up to 160 % higher than those measured in non-El Niño years, indicating that subsurface N2O during El Niño could be a reservoir for intense N2O effluxes when normal upwelling is resumed after El Niño

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

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

Temporal and Vertical Oxygen Gradients Modulate Nitrous Oxide Production in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia

Nitrous oxide (N2O) is a strong greenhouse gas and an ozone depleting agent. In marine environments, N2O is produced biologically via ammonium oxidation, nitrite, and nitrate reduction. The relative importance of these principle production pathways is strongly influenced by oxygen availability. We conducted 15N tracer experiments of N2O production in parallel with measurements of N2O concentration and natural abundance isotopes/isotopomers in Saanich Inlet, a seasonally anoxic fjord, to investigate how temporal and vertical oxygen gradients regulate N2O production pathways and rates. In April, June, and August 2018, the depth of the oxic‐anoxic interface (dissolved oxygen = 2.5 μmol L−1 isoline) progressively deepened from 110 to 160 m. Within the oxygenated and suboxic water column, N2O supersaturation coincided with peak ammonium oxidation activity. Conditions in the anoxic deep water were potentially favorable to N2O production from nitrate and nitrite reduction, but N2O undersaturation was observed indicating that N2O consumption exceeded rates of production. In October, tidal mixing introduced oxygenated water from outside the inlet, displacing the suboxic and anoxic deep water. This oxygenation event stimulated N2O production from ammonium oxidation and increased water column N2O supersaturation while inhibiting nitrate and nitrite reduction to N2O. Results from 15N tracer incubation experiments and natural abundance isotopomer measurements both implicated ammonium oxidation as the dominant N2O production pathway in Saanich Inlet, fueled by high ammonium fluxes (0.6–3.5 nmol m−2 s−1) from the anoxic depths. Partial denitrification contributed little to water column N2O production because of low availability of nitrate and nitrite

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 science. © The Author(s) 2019. Published by Oxford University Press