Extent, accuracy and repeatability of bare sand and vegetation cover in dunes mapped from aerial imagery is highly variable

Vegetation cover on coastal sand dunes has been increasing worldwide since at least the 1940s. Analysis of aerial and satellite imagery has been the principal source used to measure this change, however no studies have systematically evaluated the accuracy of remotely sensed estimates. Using established land cover classification methods and in-situ field measurements, we show that both the extent and accuracy of remotely sensed areas of bare sand and vegetation in dunes varies with image resolution and classification method. We found that supervised methods of classification (semi-automatic), whilst mapping a greater extent of bare sand and being more accurate than manual digitisation, had poor repeatability, exhibiting a relatively large range of bare sand and vegetation extent between classifications replicated under the same conditions. In contrast, areas of bare sand and vegetation classified by manual digitisation had high repeatability but a relatively low percentage of observed agreement with data collected in the field. For all classification methods, observed agreement with field data generally increased with image resolution. Our results demonstrate that users of land classification data in dunes should be cautious when interpreting trends of bare sand and vegetation cover due to substantial repeatability error in supervised classification methods, and relatively poor observed agreement with field data of manual classification. We recommend that analysis of bare sand and vegetation cover in dunes should be based on multiple replicates using supervised classification, employing the highest resolution imagery available and that all results presented should also include the range measured by multiple replicates

Aeolian dynamics of beach scraped ridge and dyke structures

Where urban areas are situated close to a beach, sand dunes act as protection from flooding and erosion.When a dune has been removed or damaged by erosion, dune, ridge or dyke re-building using heavymachinery, a process known as beach scraping, is a common method of restoration. Following construction, natural accretion of sediment on the backshore is preferable as it facilitates sustained natural dune building, growth of vegetation, and habitat creation and reduces the need for further beach scraping. This study investigates the near surface flowand transport potential for three artificial structure designs: a single ridge, a double ridge and a dyke. The three shapes contained an identical volume of sand and were preceded by 50mof beach at an angle of 3°. A computational fluid dynamic model (CFD)was created for each scenario to calculatewind flowand shear velocity from 4 differentwind directions at 22.5° intervals from 0° (onshore) to 67.5°. From this data sediment flux was predicted along a two dimensional transect for each of the scenarios. For all structures, shear velocity on the beach and stoss slope decreased as incident wind direction became more oblique; conversely shear velocity in the lee of the crest increased. A reduction in shear velocity at the foot of each structure also occurred and appears related to stoss slope,with the greatest reduction at the toe of the dyke structure (stoss slope 34°) and the least before the single ridge (stoss slope 17°). Specifically the results suggest that the double ridge structure is the most resilient to aeolian erosion. Shear velocity reduction on the back beach is comparable to the dyke and sediment flux fromthe stoss slope of the double ridge structure may become trapped in the swale between the two ridges encouraging sediment deposition, thus reducing sediment transport beyond the dunes and backshore. Although the dyke structure underwent the greatest reduction in shear velocity on the back beach it experienced substantial sediment flux at the crest and along the top of the structure, making it susceptible to erosion during a strongwind event. The highest sediment transport rate was calculated at the crest of the single ridge, and the single ridge structure also created the smallest reduction of shear velocity on the back beach, thus making it less desirable than the double ridge

D-MaPs - DNA-microarray projects: Web-based software for multi-platform microarray analysis

The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core

Scale-dependent perspectives on the geomorphology and evolution of beachdune systems

Despite widespread recognition that landforms are complex Earth systems with process-response linkages that span temporal scales from seconds to millennia and spatial scales from sand grains to landscapes, research that integrates knowledge across these scales is fairly uncommon. As a result, understanding of geomorphic systems is often scale-constrained due to a host of methodological, logistical, and theoretical factors that limit the scope of how Earth scientists study landforms and broader landscapes. This paper reviews recent advances in understanding of the geomorphology of beach-dune systems derived from over a decade of collaborative research from Prince Edward Island (PEI), Canada. A comprehensive summary of key findings is provided from short-term experiments embedded within a decade-long monitoring program and a multi-decadal reconstruction of coastal landscape change. Specific attention is paid to the challenges of scale integration and the contextual limitations research at specific spatial and/or temporal scales imposes. A conceptual framework is presented that integrates across key scales of investigation in geomorphology and is grounded in classic ideas in Earth surface sciences on the effectiveness of formative events at different scales. The paper uses this framework to organize the review of this body of research in a 'scale aware' way and, thereby, identifies many new advances in knowledge on the form and function of subaerial beach-dune systems. Finally, the paper offers a synopsis of how greater understanding of the complexities at different scales can be used to inform the development of predictive models, especially those at a temporal scale of decades to centuries, which are most relevant to coastal management issues. Models at this (landform) scale require an understanding of controls that exist at both ‘landscape’ and ‘plot’ scales. Landscape scale controls such as sea level change, regional climate, and the underlying geologic framework essentially provide bounding conditions for independent variables such as winds, waves, water levels, and littoral sediment supply. Similarly, an holistic understanding of the range of processes, feedbacks, and linkages at the finer plot scale is required to inform and verify the assumptions that underly the physical modelling of beach-dune interaction at the landform scale

Definition, diagnosis and treatment of oligometastatic oesophagogastric cancer: A Delphi consensus study in Europe.

Local treatment improves the outcomes for oligometastatic disease (OMD, i.e. an intermediate state between locoregional and widespread disseminated disease). However, consensus about the definition, diagnosis and treatment of oligometastatic oesophagogastric cancer is lacking. The aim of this study was to develop a multidisciplinary European consensus statement on the definition, diagnosis and treatment of oligometastatic oesophagogastric cancer. In total, 65 specialists in the multidisciplinary treatment for oesophagogastric cancer from 49 expert centres across 16 European countries were requested to participate in this Delphi study. The consensus finding process consisted of a starting meeting, 2 online Delphi questionnaire rounds and an online consensus meeting. Input for Delphi questionnaires consisted of (1) a systematic review on definitions of oligometastatic oesophagogastric cancer and (2) a discussion of real-life clinical cases by multidisciplinary teams. Experts were asked to score each statement on a 5-point Likert scale. The agreement was scored to be either absent/poor (<50%), fair (50%-75%) or consensus (≥75%). A total of 48 experts participated in the starting meeting, both Delphi rounds, and the consensus meeting (overall response rate: 71%). OMD was considered in patients with metastatic oesophagogastric cancer limited to 1 organ with ≤3 metastases or 1 extra-regional lymph node station (consensus). In addition, OMD was considered in patients without progression at restaging after systemic therapy (consensus). For patients with synchronous or metachronous OMD with a disease-free interval ≤2 years, systemic therapy followed by restaging to consider local treatment was considered as treatment (consensus). For metachronous OMD with a disease-free interval >2 years, either upfront local treatment or systemic treatment followed by restaging was considered as treatment (fair agreement). The OMEC project has resulted in a multidisciplinary European consensus statement for the definition, diagnosis and treatment of oligometastatic oesophagogastric adenocarcinoma and squamous cell cancer. This can be used to standardise inclusion criteria for future clinical trials

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Using Computational Fluid Dynamics (CFD) to investigate airflow and sand transport on a human-made coastal foredune dominated by offshore wind:Impact of the shape variability.

Foredunes provide many environmental and ecosystem services including protection from wave erosion and flooding hazards during storm events. While the impact of human interventions on the short-term evolution of coastal dunes is reasonably well understood, less is known about their contemporary influence on current wind and sediment dynamics several decades after implementation. The coastal dunes in Leucate (SE, France) have been anthropogenically constructed and are dominated by offshore wind conditions. Since their construction 20 years ago, a distinct variation in their longshore morphology has developed that is inherited from its original construction. The northern part of the dune has a symmetrical profile with a 28° degree stoss slope, 30° lee slope and a single crest. The southern part is asymmetric, with a gentler stoss slope (12°), 26° lee slope, and a double crest. To explore the potential geomorphic impacts of this distinct difference in morphology, several numerical simulations with varying wind speeds and direction were conducted. We used Computational Fluid Dynamics (CFD) to explore the spatial variations of the near surface wind flow, shear stress and aeolian sediment transport. Results: show that for each scenario, near surface wind speed accelerated toward the dune crest on the windward slope of the dune. The maximum wind speed varied with incident wind direction, the highest speeds occurring when incident wind flow was perpendicular to the dune crest. The double crest in the southern section of the dune affected the wind flow by inducing two consecutive speeds-up zones, with a greater maximum wind speed than on the single crested dune. Wind flow separation was observed where a steep lee slope was present (single crested dune), and only during perpendicular winds. This suggests that the shape of the dune and the direction of the wind are key parameters rather than wind speed. The area affected by reversed separated flow was spatially limited and did not extend beyond the dune toe but was below the threshold for aeolian sediment transport. Elsewhere in the lee of the dune, the wind was only deflected by an order of 15° for the oblique winds (310 and 330°), and less than 10° for the perpendicular wind (290°) on the southern part. In these locations, the shear velocity exceeded the threshold, notably on the southern dune, which coincided with the formation of undulating aeolian deposits in the lee of vegetation on the dune crest. The spatial differences observed in wind flow and aeolian sediment transport processes on this human-made dune were directly inherited from differences in their construction two decades ago. These results demonstrate the importance of the constructed dune profile, due to its potential impact on the long-term evolution of the landscape and the sediment budget of the system.</p