Ultra-fine grain landscape-scale quantification of dryland vegetation structure with drone-acquired structure-from-motion photogrammetry

This is the final version of the article. Available from Elsevier via the DOI in this record.Covering 40% of the terrestrial surface, dryland ecosystems characteristically have distinct vegetation structures that are strongly linked to their function. Existing survey approaches cannot provide sufficiently fine-resolution data at landscape-level extents to quantify this structure appropriately. Using a small, unpiloted aerial system (UAS) to acquire aerial photographs and processing theses using structure-from-motion (SfM) photogrammetry, three-dimensional models were produced describing the vegetation structure of semi-arid ecosystems at seven sites across a grass–to shrub transition zone. This approach yielded ultra-fine (< 1 cm2) spatial resolution canopy height models over landscape-levels (10 ha), which resolved individual grass tussocks just a few cm3 in volume. Canopy height cumulative distributions for each site illustrated ecologically-significant differences in ecosystem structure. Strong coefficients of determination (r2 from 0.64 to 0.95) supported prediction of above-ground biomass from canopy volume. Canopy volumes, above-ground biomass and carbon stocks were shown to be sensitive to spatial changes in the structure of vegetation communities. The grain of data produced and sensitivity of this approach is invaluable to capture even subtle differences in the structure (and therefore function) of these heterogeneous ecosystems subject to rapid environmental change. The results demonstrate how products from inexpensive UAS coupled with SfM photogrammetry can produce ultra-fine grain biophysical data products, which have the potential to revolutionise scientific understanding of ecology in ecosystems with either spatially or temporally discontinuous canopy cover.This research was supported by a NERC PhD studentship (NE/K500902/1) and Sevilleta LTER program research fellowship (NSF grant DEB-1232294) both awarded to AMC; neither funder had any further involvement in this experiment and the authors declare no conflict of interest. We thank Scott Collins, the Sevilleta LETR director and US Fish and Wildlife for their support during this research and for granting access to the field site. The 3D Robotics Y6 was supplied by the University of Exeter Environment and Sustainability Institute's (ESI) Environmental Monitoring DroneLab (EMDL). The authors wish to express their thanks to Leon DeBell and Agisoft's Alexey Pasumansky for the excellent technical support, to Susan Beck and Phil Cunliffe for facilitating access to archival material, and to Isla Myers-Smith and three anonymous reviewers whose comments allowed us to improve an earlier draft of this article. For access to the data presented herein please contact the first author

Effectiveness of commercial versus homemade sports drinks on fluid balance and exercise capacity during high-intensity intermittent exercise

Commercial sports drinks are used widely by athletes involved in high-intensity intermittent (HII) exercise. However, little has been reported on their relative effectiveness compared to simple homemade drink formulations. The purpose of this study was to investigate the effects of different sports drink formulations (commercial v homemade), water and no drink on fluid balance and exercise capacity during HII exercise. Twelve trained men (age: 27 ± 2.1 y) performed a 90-min HII running protocol designed to simulate activity experienced during a football match. The protocol was arranged in six 15-min stages where running speeds ranged between 55% and 120% of VO2max. The HII protocol included half-time and a run to fatigue post 90 min. Using a single-blind, randomized, cross-over design, participants ingested a preload of 5 mlkg-1 10 min before HII exercise and 3 mlkg-1 every 15 min of either Isostar® (ISO), a homemade sports drink (CHO), placebo (P) or no drink (ND). Blood lactate (Hla), blood glucose (Bgluc), heart rate (HR) and ratings of perceived exertion (RPE) were measured before, during (every 15 min) and after the 90-min HII protocol. Changes in plasma volume were measured at half-time and post 90 min. Sweat rate and fluid balance were calculated post each trial. Time to fatigue (TTF) was recorded at exhaustion. In the ND trial, TTF decreased by approximately 17%, 28% and 43% compared to P, CHO and ISO, respectively (p0.05). No differences were noted in HLa, RPE, PV or SR between the trials (p>0.05) but there were significant effects of time (p<0.05). Bgluc peaked at 30 minutes in ISO and CHO, but dropped by ~27% in ISO and by ~30% in CHO after half time. Absence of fluid ingestion surprisingly had no significant effect on altering plasma volume or decreasing sweat rate despite causing noticeable decreases in exercise capacity. The homemade drink improved exercise capacity in a similar manner to that of the commercial drink, but neither sports drink achieved superior hydration compared to water. Ingestion of exogenous carbohydrate through sports drink consumption caused an exercise-induced glycemic response when exercise was restarted after half-time. This decline in blood glucose after half-time appears to be marginally attenuated in P trial. A possible suggestion for team sports could be to drink water rather than sports drink prior to half-time period

Foetal developmental origins of adult onset non-insulin dependent diabetes mellitus

Abstract There is a global non-insulin dependent diabetes mellitus epidemic, and through understanding the foetal origins of the disease it may become possible to impact the development of the disease. During pregnancy a foetus is entirely dependent on nutrients supplied by the mother via the placenta, meaning alterations to the composition or quantity of maternal nutrition can lead to infants being born with low birth weights. Low birth weight is classified as a weight at birth of ≤ 2.5 kg by the World Health Organisation. In 1990 Dr. David Barker published the “foetal origins of adult disease” hypothesis in order to explain the observed epidemiological relationship between birth-weight and future disease development. It is now understood that alterations to gene expression occurring during foetal development, can then go on to increase the risk developing chronic non-communicable diseases, such as noninsulin dependent diabetes mellitus (NIDDM) in adulthood. However, the exact mechanisms through which this takes place remains unclear. The events during development which result in diminished foetal growth are multifactorial. A foetus’s maximal growth potential is determined genetically, however maternal nutrition both pre and post conception is capable of influencing growth trajectory. This review will examine the existing body of evidence regarding the role of adaptive changes occurring during foetal development in relation to the subsequent development of NIDDM in adulthood. As well as considering the potential mechanisms through which these events could be mediated

Natural Language Processing for Under-resourced Languages: Developing a Welsh Natural Language Toolkit

Language technology is becoming increasingly important across a variety of application domains which have become common place in large, well-resourced languages. However, there is a danger that small, under-resourced languages are being increasingly pushed to the technological margins. Under-resourced languages face significant challenges in delivering the underlying language resources necessary to support such applications. This paper describes the development of a natural language processing toolkit for an under-resourced language, Cymraeg (Welsh). Rather than creating the Welsh Natural Language Toolkit (WNLT) from scratch, the approach involved adapting and enhancing the language processing functionality provided for other languages within an existing framework and making use of external language resources where available. This paper begins by introducing the GATE NLP framework, which was used as the development platform for the WNLT. It then describes each of the core modules of the WNLT in turn, detailing the extensions and adaptations required for Welsh language processing. An evaluation of the WNLT is then reported. Following this, two demonstration applications are presented. The first is a simple text mining application that analyses wedding announcements. The second describes the development of a Twitter NLP application, which extends the core WNLT pipeline. As a relatively small-scale project, the WNLT makes use of existing external language resources where possible, rather than creating new resources. This approach of adaptation and reuse can provide a practical and achievable route to developing language resources for under-resourced languages

Aerial photography collected with a multirotor drone reveals impact of Eurasian beaver reintroduction on ecosystem structure

doi: 10.1139/juvs-2015-0005Copyright © 2015 Canadian Science PublishingBeavers are often described as ecological engineers with an ability to modify the structure and flow of fluvial systems and create complex wetland environments with dams, ponds and canals. Consequently, beaver activity has implications for a wide range of environmental ecosystem services including biodiversity, flood risk mitigation, water quality and sustainable drinking water provision. With the current debate surrounding the reintroduction of beavers into the United Kingdom, it is critical to be able to monitor the impact of beavers upon the environment. This study presents the first proof of concept results showing how a lightweight hexacopter fitted with a simple digital camera can be used to derive orthophoto and digital surface model (DSM) data products at a site where beavers have recently been reintroduced. Early results indicate that analysis of the fine-scale (0.01 m) orthophoto and DSM can be used to identify impacts on the ecosystem structure including the extent of dams and associated ponds, and changes in vegetation structure due to beaver tree felling activity. Unmanned aerial vehicle data acquisition offers an effective toolkit for regular repeat monitoring at fine spatial resolution which is a critical attribute for monitoring rapidly-changing and difficult to access beaver-impacted ecosystems

Linking the Conservation of Culture and Nature: A Case Study of Sacred Forests in Zimbabwe

This paper examines the role of traditional religious beliefs and traditional leaders in conserving remnant patches of a unique type of dry forest in the Zambezi Valley of northern Zimbabwe. We examined aerial photographs spanning more than three decades, interviewed and surveyed local residents, and met with communities to learn about the environmental history of the forests and the factors that have affected land use in the area. Our results show that forest loss is dramatically less in forests that are now considered sacred, or were in the past connected to sacred forests. This supports our hypothesis that traditional spiritual values have influenced human behavior affecting the forests, and have played a role in protecting them until now. We also found that rates of forest loss have been much higher in an area where traditional leaders are relatively disempowered within the post-independence political system compared to an area where traditional leaders have more power. These findings lead us to conclude that a strategy that links the conservation of culture and nature is likely to be more effective in conserving forests than a strategy that ignores traditional beliefs, values, and institutions

Eurasian beaver activity increases water storage, attenuates flow and mitigates diffuse pollution from intensively-managed grasslands

This is the final version of the article. Available from Elsevier via the DOI in this record.Beavers are the archetypal keystone species, which can profoundly alter ecosystem structure and function through their ecosystem engineering activity, most notably the building of dams. This can have a major impact upon water resource management, flow regimes and water quality. Previous research has predominantly focused on the activities of North American beaver (Castor canadensis) located in very different environments, to the intensive lowland agricultural landscapes of the United Kingdom and elsewhere in Europe. Two Eurasian beavers (Castor fiber) were introduced to a wooded site, situated on a first order tributary, draining from intensively managed grassland. The site was monitored to understand impacts upon water storage, flow regimes and water quality. Results indicated that beaver activity, primarily via the creation of 13 dams, has increased water storage within the site (holding ca. 1000m(3) in beaver ponds) and beavers were likely to have had a significant flow attenuation impact, as determined from peak discharges (mean 30±19% reduction), total discharges (mean 34±9% reduction) and peak rainfall to peak discharge lag times (mean 29±21% increase) during storm events. Event monitoring of water entering and leaving the site showed lower concentrations of suspended sediment, nitrogen and phosphate leaving the site (e.g. for suspended sediment; average entering site: 112±72mgl(-1), average leaving site: 39±37mgl(-1)). Combined with attenuated flows, this resulted in lower diffuse pollutant loads in water downstream. Conversely, dissolved organic carbon concentrations and loads downstream were higher. These observed changes are argued to be directly attributable to beaver activity at the site which has created a diverse wetland environment, reducing downstream hydrological connectivity. Results have important implications for beaver reintroduction programs which may provide nature based solutions to the catchment-scale water resource management issues that are faced in agricultural landscapes.The Devon Beaver Project is led by Devon Wildlife Trust, monitored by the University of Exeter, and funded by Devon Wildlife Trust and Westland Countryside Stewards

Hedgehog signalling acts upstream of Laminin alpha1 transcription in the zebrafish paraxial mesoderm

Laminin-111 (α1β1γ1) is a member of the Laminin family of extra-cellular matrix proteins that comprises 16 members, components of basement membranes. Laminin-111, one of the first Laminin proteins synthesised during embryogenesis, is required for basement membrane deposition and has essential roles in tissue morphogenesis and patterning. Yet, the mechanisms controlling Laminin-111 expression are poorly understood. We generated a zebrafish transgenic reporter line that reproduces faithfully the expression pattern of lama1, the gene encoding Laminin α1, and we used this reporter line to investigate lama1 transcriptional regulation. Our findings established that lama1 expression is controlled by intronic enhancers, including an enhancer directing expression in the paraxial mesoderm, anterior spinal cord and hindbrain, located in intron 1. We show that Hedgehog signalling is necessary and sufficient for lama1 transcription in the paraxial mesoderm and identify putative Gli/Zic binding sites that may mediate this control. These findings uncover a conserved role for Hedgehog signalling in the control of basement membrane assembly via its transcriptional regulation of lama1, and provide a mechanism to coordinate muscle cell fate specification in the zebrafish embryo

Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer

<p>Abstract</p> <p>Background</p> <p>Breast cancer is a highly heterogeneous disease with respect to molecular alterations and cellular composition making therapeutic and clinical outcome unpredictable. This diversity creates a significant challenge in developing tumor classifications that are clinically reliable with respect to prognosis prediction.</p> <p>Results</p> <p>This paper describes an unsupervised context analysis to infer context-specific gene regulatory networks from 1,614 samples obtained from publicly available gene expression data, an extension of a previously published methodology. We use the context-specific gene regulatory networks to classify the tumors into clinically relevant subgroups, and provide candidates for a finer sub-grouping of the previously known intrinsic tumors with a focus on Basal-like tumors. Our analysis of pathway enrichment in the key contexts provides an insight into the biological mechanism underlying the identified subtypes of breast cancer.</p> <p>Conclusions</p> <p>The use of context-specific gene regulatory networks to identify biological contexts from heterogenous breast cancer data set was able to identify genomic drivers for subgroups within the previously reported intrinsic subtypes. These subgroups (contexts) uphold the clinical relevant features for the intrinsic subtypes and were associated with increased survival differences compared to the intrinsic subtypes. We believe our computational approach led to the generation of novel rationalized hypotheses to explain mechanisms of disease progression within sub-contexts of breast cancer that could be therapeutically exploited once validated.</p