The Computer Science Ontology: A Large-Scale Taxonomy of Research Areas

Ontologies of research areas are important tools for characterising, exploring, and analysing the research landscape. Some fields of research are comprehensively described by large-scale taxonomies, e.g., MeSH in Biology and PhySH in Physics. Conversely, current Computer Science taxonomies are coarse-grained and tend to evolve slowly. For instance, the ACM classification scheme contains only about 2K research topics and the last version dates back to 2012. In this paper, we introduce the Computer Science Ontology (CSO), a large-scale, automatically generated ontology of research areas, which includes about 26K topics and 226K semantic relationships. It was created by applying the Klink-2 algorithm on a very large dataset of 16M scientific articles. CSO presents two main advantages over the alternatives: i) it includes a very large number of topics that do not appear in other classifications, and ii) it can be updated automatically by running Klink-2 on recent corpora of publications. CSO powers several tools adopted by the editorial team at Springer Nature and has been used to enable a variety of solutions, such as classifying research publications, detecting research communities, and predicting research trends. To facilitate the uptake of CSO we have developed the CSO Portal, a web application that enables users to download, explore, and provide granular feedback on CSO at different levels. Users can use the portal to rate topics and relationships, suggest missing relationships, and visualise sections of the ontology. The portal will support the publication of and access to regular new releases of CSO, with the aim of providing a comprehensive resource to the various communities engaged with scholarly data

Denitrification and nitrous oxide emissions from riparian forests soils exposed to prolonged nitrogen runoff

Compared to upland forests, riparian forest soils have greater potential to remove nitrate (NO3) from agricultural run-off through denitrification. It is unclear, however, whether prolonged exposure of riparian soils to nitrogen (N) loading will affect the rate of denitrification and its end products. This research assesses the rate of denitrification and nitrous oxide (N2O) emissions from riparian forest soils exposed to prolonged nutrient run-off from plant nurseries and compares these to similar forest soils not exposed to nutrient run-off. Nursery run-off also contains high levels of phosphate (PO4). Since there are conflicting reports on the impact of PO4 on the activity of denitrifying microbes, the impact of PO4 on such activity was also investigated. Bulk and intact soil cores were collected from N-exposed and non-exposed forests to determine denitrification and N2O emission rates, whereas denitrification potential was determined using soil slurries. Compared to the non-amended treatment, denitrification rate increased 2.7- and 3.4-fold when soil cores collected from both N-exposed and non-exposed sites were amended with 30 and 60 μg NO3-N g-1 soil, respectively. Net N2O emissions were 1.5 and 1.7 times higher from the N-exposed sites compared to the non-exposed sites at 30 and 60 μg NO3-N g-1 soil amendment rates, respectively. Similarly, denitrification potential increased 17 times in response to addition of 15 μg NO3-N g-1 in soil slurries. The addition of PO4 (5 μg PO4–P g-1) to soil slurries and intact cores did not affect denitrification rates. These observations suggest that prolonged N loading did not affect the denitrification potential of the riparian forest soils; however, it did result in higher N2O emissions compared to emission rates from non-exposed forests

Reducing non-attendance rates for assessment at an eating disorders service: a quality improvement initiative

Rates of non-attendance at initial appointments within community eating disorder (ED) services are frequently high, although this has received relatively little research attention and no reports of interventions designed to address this. The current report describes outcomes following a change of procedure introducing a ‘partial booking’ system. Attendance rates at first appointments (N = 1260) were audited following introduction of a system designed to reduce non-attendance in January 2013 within a UK ED service. Rates were compared following implementation of the new system, using a historical control group for comparison, and showed a decline from 20.4 to 15.1%, a medium-sized effect. Use of a system asking patients to book an appointment reduced non-attendance at initial appointments and may be of use to similar services experiencing high non-attendance rates. Opt-in initiatives can reduce burden resulting from long waiting times and can be easily adapted to individual services

Options for early breast cancer follow-up in primary and secondary care : a systematic review

Background Both incidence of breast cancer and survival have increased in recent years and there is a need to review follow up strategies. This study aims to assess the evidence for benefits of follow-up in different settings for women who have had treatment for early breast cancer. Method A systematic review to identify key criteria for follow up and then address research questions. Key criteria were: 1) Risk of second breast cancer over time - incidence compared to general population. 2) Incidence and method of detection of local recurrence and second ipsi and contra-lateral breast cancer. 3) Level 1–4 evidence of the benefits of hospital or alternative setting follow-up for survival and well-being. Data sources to identify criteria were MEDLINE, EMBASE, AMED, CINAHL, PSYCHINFO, ZETOC, Health Management Information Consortium, Science Direct. For the systematic review to address research questions searches were performed using MEDLINE (2011). Studies included were population studies using cancer registry data for incidence of new cancers, cohort studies with long term follow up for recurrence and detection of new primaries and RCTs not restricted to special populations for trials of alternative follow up and lifestyle interventions. Results Women who have had breast cancer have an increased risk of a second primary breast cancer for at least 20 years compared to the general population. Mammographically detected local recurrences or those detected by women themselves gave better survival than those detected by clinical examination. Follow up in alternative settings to the specialist clinic is acceptable to women but trials are underpowered for survival. Conclusions Long term support, surveillance mammography and fast access to medical treatment at point of need may be better than hospital based surveillance limited to five years but further large, randomised controlled trials are needed

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods

Global variation in the cost of increasing ecosystem carbon

Slowing the reduction, or increasing the accumulation, of organic carbon stored in biomass and soils has been suggested as a potentially rapid and cost-effective method to reduce the rate of atmospheric carbon increase(1). The costs of mitigating climate change by increasing ecosystem carbon relative to the baseline or business-as-usual scenario has been quantified in numerous studies, but results have been contradictory, as both methodological issues and substance differences cause variability(2). Here we show, based on 77 standardized face-to-face interviews of local experts with the best possible knowledge of local land-use economics and sociopolitical context in ten landscapes around the globe, that the estimated cost of increasing ecosystem carbon varied vastly and was perceived to be 16-27 times cheaper in two Indonesian landscapes dominated by peatlands compared with the average of the eight other landscapes. Hence, if reducing emissions from deforestation and forest degradation (REDD+) and other land-use mitigation efforts are to be distributed evenly across forested countries, for example, for the sake of international equity, their overall effectiveness would be dramatically lower than for a cost-minimizing distribution.Peer reviewe

A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants

Activated forms of jasmonic acid (JA) are central signals coordinating plant responses to stresses, yet tools to analyse their spatial and temporal distribution are lacking. Here we describe a JA perception biosensor termed Jas9-VENUS that allows the quantification of dynamic changes in JA distribution in response to stress with high spatiotemporal sensitivity. We show that Jas9-VENUS abundance is dependent on bioactive JA isoforms, the COI1 co-receptor, a functional Jas motif and proteasome activity. We demonstrate the utility of Jas9-VENUS to analyse responses to JA in planta at a cellular scale, both quantitatively and dynamically. This included using Jas9-VENUS to determine the cotyledon-to-root JA signal velocities on wounding, revealing two distinct phases of JA activity in the root. Our results demonstrate the value of developing quantitative sensors such as Jas9-VENUS to provide high-resolution spatiotemporal data about hormone distribution in response to plant abiotic and biotic stresses

Lessons from the removal of lead from gasoline for controlling other environmental pollutants: A case study from New Zealand

<p>Abstract</p> <p>Background</p> <p>It took over two decades to achieve the removal of leaded gasoline in this country. This was despite international evidence and original research conducted in New Zealand on the harm to child cognitive function and behaviour from lead exposure.</p> <p>Objective</p> <p>To identify lessons from the New Zealand experience of removing leaded gasoline that are potentially relevant to the control of other environmental pollutants.</p> <p>Discussion</p> <p>From the available documentation, we suggest a number of reasons for the slow policy response to the leaded gasoline hazard. These include: (1) industry power in the form of successful lobbying by the lead additive supplier, Associated Octel; (2) the absence of the precautionary principle as part of risk management policy; and (3) weak policymaking machinery that included: (a) the poor use of health research evidence (from both NZ and internationally), as well as limited use of expertise in academic and non-governmental organisations; (b) lack of personnel competent in addressing technically complex issues; and (c) diffusion of responsibility among government agencies.</p> <p>Conclusion</p> <p>There is a need for a stronger precautionary approach by policymakers when considering environmental pollutants. Politicians, officials and health workers need to strengthen policymaking processes and effectively counter the industry tactics used to delay regulatory responses.</p

Height and timing of growth spurt during puberty in young people living with vertically acquired HIV in Europe and Thailand.

OBJECTIVE: The aim of this study was to describe growth during puberty in young people with vertically acquired HIV. DESIGN: Pooled data from 12 paediatric HIV cohorts in Europe and Thailand. METHODS: One thousand and ninety-four children initiating a nonnucleoside reverse transcriptase inhibitor or boosted protease inhibitor based regimen aged 1-10 years were included. Super Imposition by Translation And Rotation (SITAR) models described growth from age 8 years using three parameters (average height, timing and shape of the growth spurt), dependent on age and height-for-age z-score (HAZ) (WHO references) at antiretroviral therapy (ART) initiation. Multivariate regression explored characteristics associated with these three parameters. RESULTS: At ART initiation, median age and HAZ was 6.4 [interquartile range (IQR): 2.8, 9.0] years and -1.2 (IQR: -2.3 to -0.2), respectively. Median follow-up was 9.1 (IQR: 6.9, 11.4) years. In girls, older age and lower HAZ at ART initiation were independently associated with a growth spurt which occurred 0.41 (95% confidence interval 0.20-0.62) years later in children starting ART age 6 to 10 years compared with 1 to 2 years and 1.50 (1.21-1.78) years later in those starting with HAZ less than -3 compared with HAZ at least -1. Later growth spurts in girls resulted in continued height growth into later adolescence. In boys starting ART with HAZ less than -1, growth spurts were later in children starting ART in the oldest age group, but for HAZ at least -1, there was no association with age. Girls and boys who initiated ART with HAZ at least -1 maintained a similar height to the WHO reference mean. CONCLUSION: Stunting at ART initiation was associated with later growth spurts in girls. Children with HAZ at least -1 at ART initiation grew in height at the level expected in HIV negative children of a comparable age