Evaluating the use of lake sedimentary DNA in palaeolimnology:A comparison with long‐term microscopy‐based monitoring of the phytoplankton community

Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research

Evaluating the use of lake sedimentary DNA in palaeolimnology: a comparison with long-term microscopy-based monitoring of the phytoplankton community

Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research

Mars analysis correction data assimilation: a multi-annual reanalysis of atmospheric observations for the red planet

Ever-increasing numbers of atmospheric observations from orbiting spacecraft, and increasingly sophisticated numerical atmospheric models, have recently permitted data assimilation techniques to be applied to planets beyond the Earth. Mars is the first extra-terrestrial planet for which reanalyses of the atmospheric state are now available. The Thermal Emission Spectrometer (TES) on board NASA’s Mars Global Surveyor (MGS) has produced an extensive atmospheric data set during its scientific mapping phase between 1999 and 2004. Nadir thermal profiles for the atmosphere below about 40 km altitude, and total dust and water ice opacities, have been retrieved from TES spectra, covering almost three complete Martian seasonal cycles (each seasonal cycle on Mars corresponds to 668.6 mean solar days, and the Martian mean solar day is about 24 hours and 40 minutes). Note that dust on Mars plays a key role in the weather and climate, mainly through its strong absorption of short wave radiation with a short radiative relaxation timescale of 1-2 days. Assimilating dust opacities correctly is, therefore, particularly important for atmospheric data assimilation on the Red Planet. TES retrieved observations have been analysed by assimilation into a Mars general circulation model (MGCM), making use of a sequential procedure known as the Analysis Correction scheme, a form of successive corrections method which has proved simple and robust under Martian conditions, even during the less-than-ideal MGS aerobraking period. The MGCM used at the University of Oxford and at The Open University consists of a spectral dynamical solver and a tracer transport scheme developed in the UK. Its package of state-of-the-art physical parameterization routines is shared with the LMD-MarsGCM, developed by the Laboratoire de Météorologie Dynamique in Paris (France). One limitation of TES is that relatively few limb profiles are available, compared to nadir soundings. Our MGS/TES reanalysis, therefore, does not include observations of temperature above about 40 km altitude, nor 3D information on dust opacity (the vertical distribution of dust opacity is prescribed assuming a well mixed dust layer with a rapid transition to a clear upper atmosphere at a height which depends on latitude and season. In September 2006 NASA’s Mars Reconnaissance Orbiter (MRO) started its mapping phase. The Mars Climate Sounder (MCS) on board MRO is a radiometer with eight mid- and far-infrared channels and one visible channel, which takes measurements in limb and off-nadir geometries. Retrieved vertical profiles of temperature, dust and water ice opacities from MCS observations can now be assimilated using the same scheme we used for TES, with the advantage of the extension in altitude (thermal profiles can extend to above 80 km altitude, although errors become larger at greater altitudes), the increased vertical resolution (~ 5km compared to > 10km for TES nadir retrievals), and the direct information on the vertical distribution of dust and water ice. Overall, the application of our data assimilation scheme to retrieved observations from TES and MCS spans almost six complete Martian seasonal cycles. This represents a multi-annual climatology for Mars, which has the advantage of being a complete, dynamically-balanced, four-dimensional best-fit to observations for all the atmospheric variables, including those for which no direct measurements are available (e.g. wind and surface pressure) and with regions of no observations filled-in in a physically-consistent way. The reanalysis represents, therefore, a unique opportunity to study the inter-annual variability of the Martian weather and climate with respect to all its components, such as the dust cycle, the water cycle, the CO2 cycle, the atmospheric tides and other prominent waves, such as high latitude baroclinic waves. In this contribution we present the first results of a complete assimilation of both datasets, using a consistent model and data assimilation scheme, and highlight the challenges of combining TES and MCS data assimilation to produce a multi-annual climatology. Particular attention will be devoted to the inter-annual variability of the atmospheric thermal field in response to dust storm activity. We will also provide an insight into the dynamics, looking in particular at the high latitude winds, waves and polar vortices. Our data assimilation products are freely available to the community for both science- and engineering-oriented purposes. The British Atmospheric Data Centre (BADC, http://badc.nerc.ac.uk) hosts our datasets, which, for the time being, are limited to the MGS/TES reanalysis. People may contact the corresponding author in order to register their interest and be updated about the status of the project. New versions of the MGS/TES reanalysis as well as the MRO/MCS reanalysis will be made available through the BADC in future. Interested people can download the current TES reanalysis dataset by registering at the BADC and searching for the MACDA (“Mars Analysis Correction Data Assimilation”) project. The direct link to the project is provided by the following URL: http://badc.nerc.ac.uk/view/badc.nerc.ac.uk__ATOM__DE_095e8da2-cf02-11e0-8b7a-00e08147026

Establishing effective conservation management strategies for a poorly known endangered species: A case study using Australia’s night parrot (Pezoporus occidentalis)

An evidence-based approach to the conservation management of a species requires knowledge of that species’ status, distribution, ecology, and threats. Coupled with budgets for specific conservation strategies, this knowledge allows prioritisation of funding toward activities that maximise benefit for the species. However, many threatened species are poorly known, and determining which conservation strategies will achieve this is difficult. Such cases require approaches that allow decision-making under uncertainty. Here we used structured expert elicitation to estimate the likely benefit of potential management strategies for the Critically Endangered and, until recently, poorly known Night Parrot (Pezoporus occidentalis). Experts considered cat management the single most effective management strategy for the Night Parrot. However, a combination of protecting and actively managing existing intact Night Parrot habitat through management of grazing, controlling feral cats, and managing fire specifically to maintain Night Parrot habitat was thought to result in the greatest conservation gains. The most cost-effective strategies were thought to be fire management to maintain Night Parrot habitat, and intensive cat management using control methods that exploit local knowledge of cat movements and ecology. Protecting and restoring potentially suitable, but degraded, Night Parrot habitat was considered the least effective and least cost-effective strategy. These expert judgements provide an informed starting point for land managers implementing on-ground programs targeting the Night Parrot, and those developing policy aimed at the species’ longer-term conservation. As a set of hypotheses, they should be implemented, assessed, and improved within an adaptive management framework that also considers the likely co-benefits of these strategies for other species and ecosystems. The broader methodology is applicable to conservation planning for the management and conservation of other poorly known threatened species

A Lorenz/Boer energy budget for the atmosphere of Mars from a “reanalysis” of spacecraft observations

We calculate a Lorenz energy budget for the Martian atmosphere from reanalysis derived from Mars Global Surveyor data for Mars years 24–27. We present global, annual mean energy and conversion rates per unit area and per unit mass and compare these to Earth data. The directions of the energy conversion terms for Mars are similar to Earth, with the exception of the barotropic conversion between zonal and eddy kinetic energy reservoirs. Further, seasonal and hemispheric decomposition reveals a strong conversion between zonal energy reservoirs over the year, but these balance each other out in global and annual mean. On separating the diurnal timescale, the contribution to the conversion terms and eddy kinetic energy for diurnal and shorter timescales in many cases (especially during planet-encircling dust storms) exceeds the contribution of longer timescales. This suggests that thermal tides have a significant effect on the generation of eddy kinetic energy

The solsticial pause on Mars: 2 modelling and investigation of causes

The martian solsticial pause, presented in a companion paper (Lewis et al. [this issue]. Icarus), was investigated further through a series of model runs using the UK version of the LMD/UK Mars Global Climate Model. It was found that the pause could not be adequately reproduced if radiatively active water ice clouds were omitted from the model. When clouds were used, along with a realistic time-dependent dust opacity distribution, a substantial minimum in near-surface transient eddy activity formed around solstice in both hemispheres. The net effect of the clouds in the model is, by altering the thermal structure of the atmosphere, to decrease the vertical shear of the westerly jet near the surface around solstice, and thus reduce baroclinic growth rates. A similar effect was seen under conditions of large dust loading, implying that northern midlatitude eddy activity will tend to become suppressed after a period of intense flushing storm formation around the northern cap edge. Suppression of baroclinic eddy generation by the barotropic component of the flow and via diabatic eddy dissipation were also investigated as possible mechanisms leading to the formation of the solsticial pause but were found not to make major contributions. Zonal variations in topography were found to be important, as their presence results in weakened transient eddies around winter solstice in both hemispheres, through modification of the near-surface flow. The zonal topographic asymmetry appears to be the primary reason for the weakness of eddy activity in the southern hemisphere relative to the northern hemisphere, and the ultimate cause of the solsticial pause in both hemispheres. The meridional topographic gradient was found to exert a much weaker influence on near-surface transient eddies

Chedoke Arm and Hand Activity Inventory-9 (CAHAI-9): Perceived clinical utility within 14 days of stroke

Purpose: The Chedoke Arm and Hand Activity Inventory-9 (CAHAI-9) is an activity-based assessment developed to include relevant functional tasks and to be sensitive to clinically important changes in upper limb function. The aim of this study was to explore both therapists' and clients' views on the clinical utility of CAHAI-9 within 14 days of stroke. Method: Twenty-one occupational therapists actively working in stroke settings were recruited by convenience sampling from 8 hospitals and participated in semistructured focus groups. Five clients within 14 days of stroke were recruited by consecutive sampling from 1 metropolitan hospital and participated in structured individual interviews. The transcripts were analyzed thematically. Results: Six themes emerged from the focus groups and interviews: collecting information, decisions regarding client suitability, administration and scoring, organizational demands, raising awareness, and clients' perceptions of CAHAI-9 utility. All therapists agreed CAHAI-9 was suited for the stroke population and assisted identification of client abilities or difficulties within functional contexts. Opinions varied as to whether CAHAI-9 should be routinely administered with clients who had mild and severe upper limb deficits, but therapists agreed it was appropriate for clients with moderate deficits. Therapists made suggestions regarding refinement of the scoring and training to increase utility. All clients with stroke felt that the assessment provided reassurance regarding their recovery. Conclusion: The findings indicate that CAHAI-9 shows promise as an upper limb ability assessment for clients within 14 days of stroke

Comparison of CATs, CURB-65 and PMEWS as Triage Tools in Pandemic Influenza Admissions to UK Hospitals: Case Control Analysis Using Retrospective Data

Triage tools have an important role in pandemics to identify those most likely to benefit from higher levels of care. We compared Community Assessment Tools (CATs), the CURB-65 score, and the Pandemic Medical Early Warning Score (PMEWS); to predict higher levels of care (high dependency - Level 2 or intensive care - Level 3) and/or death in patients at or shortly after admission to hospital with A/H1N1 2009 pandemic influenza. This was a case-control analysis using retrospectively collected data from the FLU-CIN cohort (1040 adults, 480 children) with PCR-confirmed A/H1N1 2009 influenza. Area under receiver operator curves (AUROC), sensitivity, specificity, positive predictive values and negative predictive values were calculated. CATs best predicted Level 2/3 admissions in both adults [AUROC (95% CI): CATs 0.77 (0.73, 0.80); CURB-65 0.68 (0.64, 0.72); PMEWS 0.68 (0.64, 0.73), p<0.001] and children [AUROC: CATs 0.74 (0.68, 0.80); CURB-65 0.52 (0.46, 0.59); PMEWS 0.69 (0.62, 0.75), p<0.001]. CURB-65 and CATs were similar in predicting death in adults with both performing better than PMEWS; and CATs best predicted death in children. CATs were the best predictor of Level 2/3 care and/or death for both adults and children. CATs are potentially useful triage tools for predicting need for higher levels of care and/or mortality in patients of all ages

Guidance on noncorticosteroid systemic immunomodulatory therapy in noninfectious uveitis: fundamentals of care for uveitis (focus) initiative

Topic: An international, expert-led consensus initiative to develop systematic, evidence-based recommendations for the treatment of noninfectious uveitis in the era of biologics. Clinical Relevance: The availability of biologic agents for the treatment of human eye disease has altered practice patterns for the management of noninfectious uveitis. Current guidelines are insufficient to assure optimal use of noncorticosteroid systemic immunomodulatory agents. Methods: An international expert steering committee comprising 9 uveitis specialists (including both ophthalmologists and rheumatologists) identified clinical questions and, together with 6 bibliographic fellows trained in uveitis, conducted a Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol systematic reviewof the literature (English language studies from January 1996 through June 2016; Medline [OVID], the Central Cochrane library, EMBASE,CINAHL,SCOPUS,BIOSIS, andWeb of Science). Publications included randomized controlled trials, prospective and retrospective studies with sufficient follow-up, case series with 15 cases or more, peer-reviewed articles, and hand-searched conference abstracts from key conferences. The proposed statements were circulated among 130 international uveitis experts for review.Atotal of 44 globally representativegroupmembersmet in late 2016 to refine these guidelines using a modified Delphi technique and assigned Oxford levels of evidence. Results: In total, 10 questions were addressed resulting in 21 evidence-based guidance statements covering the following topics: when to start noncorticosteroid immunomodulatory therapy, including both biologic and nonbiologic agents; what data to collect before treatment; when to modify or withdraw treatment; how to select agents based on individual efficacy and safety profiles; and evidence in specific uveitic conditions. Shared decision-making, communication among providers and safety monitoring also were addressed as part of the recommendations. Pharmacoeconomic considerations were not addressed. Conclusions: Consensus guidelines were developed based on published literature, expert opinion, and practical experience to bridge the gap between clinical needs and medical evidence to support the treatment of patients with noninfectious uveitis with noncorticosteroid immunomodulatory agents

Diel surface temperature range scales with lake size

Ecological and biogeochemical processes in lakes are strongly dependent upon water temperature. Long-term surface warming of many lakes is unequivocal, but little is known about the comparative magnitude of temperature variation at diel timescales, due to a lack of appropriately resolved data. Here we quantify the pattern and magnitude of diel temperature variability of surface waters using high-frequency data from 100 lakes. We show that the near-surface diel temperature range can be substantial in summer relative to long-term change and, for lakes smaller than 3 km2, increases sharply and predictably with decreasing lake area. Most small lakes included in this study experience average summer diel ranges in their near-surface temperatures of between 4 and 7°C. Large diel temperature fluctuations in the majority of lakes undoubtedly influence their structure, function and role in biogeochemical cycles, but the full implications remain largely unexplored