Defining ecological buffer mechanisms should consider diverse approaches

In their response letter, Gascoigne et al. propose a relevant approach to characterizing ecological buffer mechanisms, akin to the study of buffer mechanisms in chemistry [1]. Their chemistry-inspired viewpoint enables them to pinpoint opportunities for further advances in the population buffering framework. We welcome the authors' response and concur with their belief that ecology stands to gain significantly from increased crosstalk with chemistry and other more mechanistic, first-principles-driven fields of natural sciences.acceptedVersio

Local buffer mechanisms for population persistence

Assessing and predicting the persistence of populations is essential for the conservation and control of species. Here, we argue that local mechanisms require a better conceptual synthesis to facilitate a more holistic consideration along with regional mechanisms known from metapopulation theory. We summarise the evidence for local buffer mechanisms along with their capacities and emphasise the need to include multiple buffer mechanisms in studies of population persistence. We propose an accessible framework for local buffer mechanisms that distinguishes between damping (reducing fluctuations in population size) and repelling (reducing population declines) mechanisms. We highlight opportunities for empirical and modelling studies to investigate the interactions and capacities of buffer mechanisms to facilitate better ecological understanding in times of ecological upheaval.acceptedVersio

Lateglacial and Holocene climate and environmental change in the northeastern Mediterranean region: Diatom evidence from Lake Dojran (Republic of Macedonia/Greece)

The juncture between the west-east and north-south contrasting Holocene climatic domains across the Mediterranean is complex and poorly understood. Diatom analysis of Lake Dojran (Republic of Macedonia/Greece) provides a new insight into lake levels and trophic status during the Lateglacial and Holocene periods in the northeastern Mediterranean. Following a very shallow or even desiccated state at the core base at ca. 12,500 cal yr BP, indicated by sedimentological and hydro-acoustic data, diatoms indicate lake infilling, from a shallow state with abundant benthos to a plankton-dominated relatively high lake level and eutrophic state thereafter. Diatom-inferred shallowing between ca. 12,400 - 12,000 cal yr BP and a very low lake level and eutrophic, oligosaline state between ca. 12,000 - 11,500 cal yr BP provide strong evidence for Younger Dryas aridity. The earliest Holocene (ca. 11,500 - 10,700 cal yr BP) was characterised by a high lake level, followed by a lake-level reduction and increased trophic level between ca. 10,700-8,500 cal yr BP. The lake was relatively deep and exhibited peak Holocene trophic level between ca. 8,500-3,000 cal yr BP, becoming shallow thereafter. The diatom data provide more robust evidence and strengthen previous lake-level interpretation based on sedimentological and geochemical data during the earliest, mid and late Holocene, and also clarify previous uncertainty in interpretation of Lateglacial and early-Holocene lake-level change. Our results are also important in disentangling regional climate effects from local catchment dynamics during the Holocene, and to this end we exploit extant regional palynological evidence for vegetation change in the highlands and lowlands. The importance of seasonality in driving Holocene climate change is assessed by reference to the summer and winter latitudinal temperature gradient (LTG) model of Davis and Brewer (2009). We suggest that increased precipitation drove the high lake level during the earliest Holocene. The early- Holocene low lake level and relatively high trophic state may result climatically from high seasonality of precipitation and locally from limited, nutrient-rich catchment runoff. We argue that the mid- Holocene relatively deep and eutrophic state was driven mainly by local vegetation succession and associated changes in catchment processes, rather than showing a close relationship to climate change. The late-Holocene shallow state may have been influenced by a temperature-induced increase in evaporative concentration, but was coupled with clear evidence for intensified human impact. This study improves understanding of Lateglacial and Holocene climate change in the northeastern Mediterranean, suggests the important role of the LTG on moisture availability during the Holocene, and clarifies the influence of catchment processes on palaeohydrology

Quality of chronic disease care in general practice: the development and validation of a provider interview tool

BACKGROUND: This article describes the development and psychometric evaluation of an interview instrument to assess provider-reported quality of general practice care for patients with diabetes, cardiovascular disease and asthma – the Australian General Practice Clinical Care Interview (GPCCI). METHODS: We administered the GPCCI to 28 general practitioners (family physicians) in 10 general practices. We conducted an item analysis and assessed the internal consistency of the instrument. We next assessed the quality of care recorded in the medical records of 462 of the general practitioners' patients with Type 2 diabetes, ischaemic heart disease/hypertension and/or moderate to severe asthma. This was then compared with results of the GPCCI for each general practice. RESULTS: Good internal consistency was found for the overall GPCCI (Cronbach's alpha = 0.75). As far as the separate sub-scales were concerned, diabetes had good internal consistency (0.76) but the internal consistency of the heart disease and asthma subscales was not strong (0.49 and 0.16 respectively). There was high inter-rater reliability of the adjusted scores of data extracted from patients' medical notes for each of the three conditions. Correlations of the overall GPCCI and patients' medical notes audit, combined across the three conditions and aggregated to practice level, showed that a strong relationship (r = 0.84, p = 0.003) existed between the two indices of clinical care. CONCLUSION: This study suggests that the GPCCI has good internal consistency and concurrent validity with patients' medical records in Australian general practice and warrants further evaluation of its properties, validity and utility

Disentangling the pollen signal from fen systems : modern and Holocene studies from southern and eastern England

Thick deposits of peat derived from fen environments accumulated in the coastal lowland areas adjacent to the North Sea during the middle and late Holocene. These sediments are frequently used in pollen-based reconstructions of in situ and more distant vegetation. However, discriminating between wetland and dry land originating pollen signals, and between the potential fen communities present in the wetland, is complex. In this study, a suite of analytical approaches are used to explore the pollen signal of modern fen communities and compare them against Holocene pollen assemblages. At two sites in eastern England, Woodwalton Fen and Upton Broad, vegetation composition was recorded around a series of moss polster sampling points. The communities investigated included herbaceous fen communities under different cutting regimes, a grazed area, glades, and woodland with canopies dominated by Alnus glutinosa and Betula. Cluster analysis is used to provide an overview of, and compare the structure within, the datasets consisting of the vegetation, the vegetation converted to palynological equivalents, and the pollen data. It is demonstrated that any loss of taxonomic precision in pollen identifications does not pose particular problems when attempting to identify fen communities, including tall-herbaceous vegetation, in the pollen record. Indices of Association imply pollen presence can be interpreted as indicating the local presence for some taxa, though few of these are confined to a particular community. Herbaceous fen vegetation subject to different management regimes are, however, shown to produce distinctive pollen signatures. Middle and late Holocene pollen assemblages from eastern (Fenland) and southern (Romney Marsh) England, interpreted as derived from fen vegetation, are compared against the modern pollen dataset using ordination. Most of the fossil samples plot out within or adjacent to the groupings produced by the modern samples in the ordinations. While these investigations demonstrate that modern pollen work can help improve the interpretation of Holocene assemblages they also call attention to a number of limitations including the restricted range of communities from which modern samples are currently available and the potential for non-analogous modern vegetation. The paper concludes with ideas to aid the interpretation of pollen data collected from fen peats and suggestions for future work

Changing Bee and Hoverfly Pollinator Assemblages along an Urban-Rural Gradient

The potential for reduced pollination ecosystem service due to global declines of bees and other pollinators is cause for considerable concern. Habitat degradation, destruction and fragmentation due to agricultural intensification have historically been the main causes of this pollinator decline. However, despite increasing and accelerating levels of global urbanization, very little research has investigated the effects of urbanization on pollinator assemblages. We assessed changes in the diversity, abundance and species composition of bee and hoverfly pollinator assemblages in urban, suburban, and rural sites across a UK city.Bees and hoverflies were trapped and netted at 24 sites of similar habitat character (churchyards and cemeteries) that varied in position along a gradient of urbanization. Local habitat quality (altitude, shelter from wind, diversity and abundance of flowers), and the broader-scale degree of urbanization (e.g. percentage of built landscape and gardens within 100 m, 250 m, 500 m, 1 km, and 2.5 km of the site) were assessed for each study site. The diversity and abundance of pollinators were both significantly negatively associated with higher levels of urbanization. Assemblage composition changed along the urbanization gradient with some species positively associated with urban and suburban land-use, but more species negatively so. Pollinator assemblages were positively affected by good site habitat quality, in particular the availability of flowering plants.Our results show that urban areas can support diverse pollinator assemblages, but that this capacity is strongly affected by local habitat quality. Nonetheless, in both urban and suburban areas of the city the assemblages had fewer individuals and lower diversity than similar rural habitats. The unique development histories of different urban areas, and the difficulty of assessing mobile pollinator assemblages in just part of their range, mean that complementary studies in different cities and urban habitats are required to discover if these findings are more widely applicable

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

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