Library Cultures of Data Curation: Adventures in Astronomy

University libraries are partnering with disciplinary data producers to provide long-term digital curation of research datasets. Managing dataset producer expectations and guiding future development of library services requires understanding the decisions libraries make about curatorial activities, why they make these decisions, and the effects on future data reuse. We present a study, comprising interviews (n=43) and ethnographic observation, of two university libraries who partnered with the Sloan Digital Sky Survey (SDSS) collaboration to curate a significant astronomy dataset. The two libraries made different choices of the materials to curate and associated services, which resulted in different reuse possibilities. Each of the libraries offered partial solutions to the SDSS leaders’ objectives. The libraries’ approaches to curation diverged due to contextual factors, notably the extant infrastructure at their disposal (including technical infrastructure, staff expertise, values and internal culture, and organizational structure). The Data Transfer Process case offers lessons in understanding how libraries choose curation paths and how these choices influence possibilities for data reuse. Outcomes may not match data producers’ initial expectations but may create opportunities for reusing data in unexpected and beneficial ways

The distribution of soil micro-nutrients and the effects on herbage micro-nutrient uptake and yield in three different pasture systems

Pasture micro-nutrient concentrations are often deficient for herbage productivity and the health of livestock. The aim of this study was to investigate soil and herbage micro-nutrient content and the effects on yield on the three pasture systems of the North Wyke Farm Platform (NWFP): high-sugar grass + legume mix minus nitrogen (N) fertilizer (blue/HSG + L); permanent pasture plus N fertilizer (green/P + N); high-sugar grass plus N fertilizer (red/HSG + N). The locations with high soil total micro-nutrient concentrations had a greater slope and higher soil organic matter (SOM) content. Herbage micro-nutrient concentrations were often greater at the locations with high soil total micro-nutrient concentrations. The concentration and uptake of nearly all mi-cro-nutrients was greatest in the herbage of the green/P + N system, which had the highest SOM content, whereas they were often lowest in the red/HSG + N system, which had the lowest SOM and the highest yield, indicating biomass dilution of micro-nutrients in the herbage. At the loca-tions with high soil micro-nutrient concentrations, yield was higher than at locations with low micro-nutrient concentrations, and was equal across the three pasture systems, regardless of fertilizer N treatment. Variation in micro-nutrient uptake/yield in the blue grass–legume system was predominantly explained by the soil molybdenum (Mo) concentration, possibly relating to the requirement for Mo in biological nitrogen fixation. There was, therefore, a trade-off in ploughing and re-seeding for higher yield, with the maintenance of SOM being important for herbage micro-nutrient content

The effect of soil type on yield and micronutrient content of pasture species

The use of multispecies swards on livestock farms is growing due to the wide range of benefits they bring, such as improved biomass yield and animal performance. Preferential uptake of micronutrients by some plant species means the inclusion of legumes and forbs in grass-dominated pasture swards could improve micronutrient provision to livestock via careful species selection. However, although soil properties affect plant micronutrient concentrations, it is unknown whether choosing ‘best-performing’ species, in terms of their micronutrient content, needs to be soil-specific or whether the recommendations can be more generic. To address this question, we carried out an experiment with 15 common grass, forb and legume species grown on four soils for five weeks in a controlled environment. The soils were chosen to have contrasting properties such as texture, organic matter content and micronutrient concentrations. The effect of soil pH was tested on two soils (pH 5.4 and 7.4) chosen to minimise other confounding variables. Yield was significantly affected by soil properties and there was a significant interaction with botanical group but not species within a botanical group (grass, forb or legume). There were differences between botanical groups and between species in both their micronutrient concentrations and total uptake. Micronutrient herbage concentrations often, but not always, reflected soil micronutrient concentrations. There were soil-botanical group interactions for micronutrient concentration and uptake by plants, but the interaction between plant species (within a botanical group) and soil was significant only for forbs, and predominantly occurred when considering micronutrient uptake rather than concentration. Generally, plants had higher yields and micronutrient contents at pH 5.4 than 7.4. Forbs tended to have higher concentrations of micronutrients than other botanical groups and the effect of soil on micronutrient uptake was only significant for forbs

Phosphorus Use Efficiency and Fertilizers: future opportunities for improvements

The continued supply of phosphate fertilizers that underpin global food production is an imminent crisis. The rock phosphate deposits on which the world depends are not only finite, but some are contaminated, and many are located in geopolitically unstable areas, meaning that fundamental changes will have to take place in order to maintain food production for a growing global population. No single solution exists, but a combination of approaches to phosphorus management is required not only to extend the lifespan of the remaining non-renewable rock phosphate reserves, but to result in a more efficient, sustainable phosphorus cycle. Solutions include improving the efficiency of fertilizer applications to agricultural land, alongside a better understanding of phosphorus cycling in soil-plant systems, and the interactions between soil physics, chemistry and biology, coupled with plant traits. Opportunities exist for the development of plants that can access different forms of soil phosphorus (e.g., organic phosphorus) and that use internal phosphorus more efficiently. The development of different sources of phosphorus fertilizers are inevitably required given the finite nature of the rock phosphate supplies. Clear opportunities exist, and it is now important that a concerted effort to make advances in phosphorus use efficiency is prioritized

Assessment of bioavailable organic phosphorus in tropical forest soils by organic acid extraction and phosphatase hydrolysis

Soil organic phosphorus contributes to the nutrition of tropical trees, but is not accounted for in standard soil phosphorus tests. Plants and microbes can release organic anions to solubilize organic phosphorus from soil surfaces, and synthesize phosphatases to release inorganic phosphate from the solubilized compounds. We developed a procedure to estimate bioavailable organic phosphorus in tropical forest soils by simulating the secretion processes of organic acids and phosphatases. Five lowland tropical forest soils with contrasting properties (pH 4.4–6.1, total P 86–429 mg P kg− 1) were extracted with 2 mM citric acid (i.e., 10 μmol g− 1, approximating rhizosphere concentrations) adjusted to soil pH in a 4:1 solution to soil ratio for 1 h. Three phosphatase enzymes were then added to the soil extract to determine the forms of hydrolysable organic phosphorus. Total phosphorus extracted by the procedure ranged between 3.22 and 8.06 mg P kg− 1 (mean 5.55 ± 0.42 mg P kg− 1), of which on average three quarters was unreactive phosphorus (i.e., organic phosphorus plus inorganic polyphosphate). Of the enzyme-hydrolysable unreactive phosphorus, 28% was simple phosphomonoesters hydrolyzed by phosphomonoesterase from bovine intestinal mucosa, a further 18% was phosphodiesters hydrolyzed by a combination of nuclease from Penicillium citrinum and phosphomonoesterase, and the remaining 51% was hydrolyzed by a broad-spectrum phytase from wheat. We conclude that soil organic phosphorus can be solubilized and hydrolyzed by a combination of organic acids and phosphatase enzymes in lowland tropical forest soils, indicating that this pathway could make a significant contribution to biological phosphorus acquisition in tropical forests. Furthermore, we have developed a method that can be used to assess the bioavailability of this soil organic phosphorus

The uptake of selenium by perennial ryegrass in soils of different organic matter contents receiving sheep excreta

Background and Aims The intake of selenium, an essential element for animals and humans, in ruminants is largely determined by selenium concentration in ingested forages, which take up selenium mainly from soil. Ruminant excreta is a common source of organic fertilizer, which provides both nutrients and organic matter. This study aims to unentangle the unclear effect of applying different types of ruminant excreta in soils of different organic matter contents on selenium uptake by forage. Methods Perennial ryegrass (Lolium perenne) was grown in soils of different organic matter contents. Urine and/or feces collected from sheep fed with organic or inorganic mineral supplements, including selenium, were applied to the soils. The selenium in the collected samples were analyzed using ICP-MS. The associated biogeochemical reactions were scrutinized by wet chemistry. Results The application of urine and/or feces resulted in either the same or lower selenium concentrations in perennial ryegrass. The excreta type did not affect total selenium accumulation in grass grown in low organic matter soil, whereas in high organic matter soil, feces resulted in significantly lower total selenium accumulation than urine, which was attributed to a possible interaction of selenium sorption in soil and microbial reduction of Se. Conclusion This one-time excreta application did not increase, but further decrease in some treatments, selenium concentration and accumulation in the perennial ryegrass. Consequently, to increase ruminant selenium intake, supplementing selenium directly to animals is more recommended than applying animal manure to soil, which might drive selenium reduction and decrease selenium uptake by grass

Late night salivary cortisol and cortisone should be the initial screening test for Cushing’s syndrome

Endogenous Cushing’s syndrome (CS) poses considerable diagnostic challenges. Although late night salivary cortisol (LNSC) is recommended as a first line screening investigation, it remains the least widely used test in many countries. The combined measurement of LNSC and late-night salivary cortisone (LNS cortisone) has shown to further improve diagnostic accuracy1. We present a retrospective study in a tertiary referral centre comparing LNSC, LNS cortisone, overnight dexamethasone suppression test, low dose dexamethasone suppression test and 24-hour urinary free cortisol results of patients investigated for CS. Patients were categorised into those who had CS (21 patients) and those who did not (33 patients).LNSC had a sensitivity of 95% and a specificity of 91%. LNS cortisone had a specificity of 100% and a sensitivity of 86%. With an optimal cut-off for LNS cortisone of >14.5 nmol/l the sensitivity was 95.2%, and the specificity was 100% with an area under the curve of 0.997, for diagnosing CS. Saliva collection is non-invasive and can be carried out at home.We therefore advocate simultaneous measurement of LNSC and LNS cortisone as the first-line screening test to evaluate patients with suspected CS

The Mineral Composition of Wild Type and Cultivated Varieties of Pasture Species

Mineral deficiencies in livestock are often prevented by using prophylactic supplementation, which is imprecise and inefficient. Instead, the trend for increased species diversity in swards is an opportunity to improve mineral concentrations in the basal diet. Currently there are limited data on the mineral concentrations of different species and botanical groups, particularly for I and Se, which are among the most deficient minerals in livestock diets. We grew 21 pasture species, including some cultivar/wild type comparisons, of grasses, legumes and forbs, as single species stands in a pot study in a standard growth medium. Herbage concentrations of Co, Cu, I, Mn, Se, Zn, S, Mo and Fe showed no consistent differences between the wild and cultivated types. There were significant differences between botanical groups for many minerals tested. Forbs were highest in I and Se, grasses in Mn, and legumes in Cu, Co, Zn and Fe. Comparing species concentrations to recommended livestock intakes, the forbs Achillea millefolium, Cichorium intybus and Plantago lanceolate, and the legumes Medicago lupulina, Trifolium hybridum, and Lotus corniculatus, appear good sources of Co, Cu, I, Se and Zn. Further work is required to ensure these results are consistent in multispecies mixtures, in different soil types, and in field trials

Cooperative secretions facilitate host range expansion in bacteria

The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses