Modelling multivariate data using product copulas and minimum distance estimators: an exemplary application to ecological traits

Modelling and applying multivariate distributions is an important topic in ecology. In particular in plant ecology, the multidimensional nature of plant traits comes with challenges such as wide ranges in observations as well as correlations between several characteristics. In other disciplines (e.g., finances and economics), copulas have been proven as a valuable tool for modelling multivariate distributions. However, applications in ecology are still rarely used. Here, we present a copula-based methodology of fitting multivariate distributions to ecological data. We used product copula models to fit multidimensional plant traits, on example of observations from the global trait database TRY. The fitting procedure is split into two parts: fitting the marginal distributions and fitting the copula. We found that product copulas are well suited to model ecological data as they have the advantage of being asymmetric (similar to the observed data). Challenges in the fitting were mainly addressed to limited amount of data. In view of growing global databases, we conclude that copula modelling provides a great potential for ecological modelling.

arakno - An R package for effective spider nomenclature, distribution and trait data retrieval from online resources

Online open databases are increasing in number, usefulness, and ease of use. There are currently two main global databases exclusive for spiders, the World Spider Catalogue (WSC) and the World Spider Trait (WST) database. Both are regularly used by thousands of researchers. Computational tools that allow effective processing of large data are now part of the workflow of any researcher and R is becoming a de facto standard for data manipulation, analysis, and presentation. Here we present an R package, arakno, that allows interface with the two databases. Implemented tools include checking species names against nomenclature of the WSC, obtaining and mapping data on distribution of species from both WST and the Global Biodiversity Information Facility (GBIF), and downloading trait data from the WST. A set of tools are also provided to prepare data for further statistical analysis.

Сравнение глобальных моделей гравитационного поля на территории Магаданской области

The global databases of gravity anomalies, currently available to researchers, provide a new informative tool for constructing density models of the deep structure of the earth's crust for individual regions. Currently, there are six models of gravitational anomalies, presented as a series of spherical harmonics up to 2190 degrees, which corresponds to about 10 km on the earth's surface. Different methods of processing terrestrial, marine, aerial, and satellite gravimetric data, available to their authors, determine the differences between these models, both on a global scale and within specific regions. We have performed a comparison of the EGM2008, GECO, EIGEN-6C4, and WGM2012 models with the Gravimag database on the Magadan Oblast territory. The comparison showed that free air anomalies for the EGM2008, GECO, EIGEN-6C4, and WGM2012 models in the selected area almost coincide. Bouguer anomalies of the WGM2012 model can be used in regional density modeling for adjacent regions where there are no conventional ground gravity data; however, within Magadan Oblast the Gravimag database has the best data quality.

Molecular Epidemiology of Azole-Resistant Aspergillus fumigatus in France Shows Patient and Healthcare Links to Environmentally Occurring Genotypes

Resistance of the human pathogenic fungus Aspergillus fumigatus to antifungal agents is on the rise. However, links between patient infections, their potential acquisition from local environmental sources, and links to global diversity remain cryptic. Here, we used genotyping analyses using nine microsatellites in A. fumigatus, in order to study patterns of diversity in France. In this study, we genotyped 225 local A. fumigatus isolates, 112 azole susceptible and 113 azole resistant, collected from the Bourgogne-Franche-Comté region (Eastern France) and sampled from both clinical (n = 34) and environmental (n = 191) sources. Azole-resistant clinical isolates (n = 29) were recovered mainly from cystic fibrosis patients and environmental isolates (n = 84) from market gardens and sawmills. In common with previous studies, the TR34/L98H allele predominated and comprised 80% of resistant isolates. The genotypes obtained for these local TR34/L98H isolates were integrated into a broader analysis including all genotypes for which data are available worldwide. We found that dominant local TR34/L98H genotypes were isolated in different sample types at different dates (different patients and types of environments) with hospital air and patient’s isolates linked. Therefore, we are not able to rule out the possibility of some nosocomial transmission. We also found genotypes in these same environments to be highly diverse, emphasizing the highly mixed nature of A. fumigatus populations. Identical clonal genotypes were found to occur both in the French Eastern region and in the rest of the world (notably Australia), while others have not yet been observed and could be specific to our region. Our study demonstrates the need to integrate patient, healthcare, and environmental sampling with global databases in order to contextualize the local-scale epidemiology of antifungal resistant aspergillosis.

Does pollen limitation limit plant ranges? Evidence and implications

Range limits often involve declines in sexual reproduction, reducing fitness, dispersal, and adaptive potential at range edges. For plants, sexual reproduction is frequently limited by inadequate pollination. While case studies show that pollen limitation can limit plant distributions, the extent to which pollination commonly declines toward plant range edges is unknown. Here, we leverage global databases of pollen-supplementation experiments and plant occurrence data to test whether pollen limitation increases toward plant range edges, using a phylogenetically controlled meta-analysis. While there was significant pollen limitation across studies, we found little evidence that pollen limitation increases toward plant range edges. Pollen limitation was not stronger toward the tropics, nor at species' equatorward vs poleward range limits. Meta-analysis results are consistent with results from targeted experiments, in which pollen limitation increased significantly toward only 14% of 14 plant range edges, suggesting that pollination contributes to range limits less often than do other interactions. Together, these results suggest pollination is one of the rich variety of potential ecological factors that can contribute to range limits, rather than a generally important constraint on plant distributions.

On the role of internal stakeholders in place branding

Purpose Although place branding (PB) has been researched and practised for several years, the number of studies examining the role of internal stakeholders is still limited. The purpose of this paper is to identify the internal stakeholders associated with PB and particularly, the roles they play in such a process. Design/methodology/approach Through a systematic literature review in four major global databases, 55 qualified research studies on PB were identified and thoroughly reviewed. Selected studies were examined, analysed and classified according to five categories: bibliographic data, methodologies adopted, conceptual frameworks, empirical foundation and stakeholders’ relevance. Findings This study shows no existing consensus over the type/role of internal stakeholders in PB research. The findings indicate different methodologies, conceptual frameworks and branding approaches, as well as various empirical foundations in the reviewed studies. The results highlight the significance of internal stakeholders’ influence over PB and their roles in the process. The findings also underline the need for strategies that prioritise stakeholders’ social interactions, collective experiences and affective engagement to develop an inclusive place brand. Practical implications This study provides an alternative perspective that underlines the development of inclusive PB frameworks by providing stakeholders with motivational and emotional incentives, capturing their creativity and imagination and encouraging them to participate in the process. Such frameworks entail a transdisciplinary approach to PB as a dynamic process that depends on all internal stakeholders’ active engagement. Originality/value This review offers an in-depth perspective on relevant internal stakeholders and their roles in PB. The study further scrutinises the three most related research topics on internal stakeholders, including co-creation, internal branding and participatory PB.

Phytoplankton Photophysiology Utilities: A Python Toolbox for the Standardization of Processing Active Chlorophyll-a Fluorescence Data

The uptake and application of single turnover chlorophyll fluorometers to the study of phytoplankton ecosystem status and microbial functions has grown considerably in the last two decades. However, standardization of measurement protocols, processing of fluorescence transients and quality control of derived photosynthetic parameters is still lacking and makes community goals of large global databases of high-quality data unrealistic. We introduce the Python package Phytoplankton Photophysiology Utilities (PPU), an adaptable and open-source interface between Fast Repetition Rate and Fluorescence Induction and Relaxation instruments and python. The PPU package includes a variety of functions for the loading, processing and quality control of single turnover fluorescence transients from many commercially available instruments. PPU provides the user with greater flexibility in the application of the Kolber-Prasil-Falkowski model; tools for plotting, quality control, correcting instrument biases and high-throughput processing with ease; and a greater appreciation for the uncertainties in derived photosynthetic parameters. Using data from three research cruises across different biogeochemical regimes, we provide example applications of PPU to fit raw active chlorophyll-a fluorescence data from three commercial instruments and demonstrate tools which help to reduce uncertainties in the final fitted parameters.

Optimising Multi-stakeholder Practices in Patient Engagement: A Gap Analysis to Enable Focused Evolution of Patient Engagement in the Development and Lifecycle Management of Medicines

Background The PARADIGM consortium aimed to make patient engagement in the development and lifecycle management of medicines easier and more effective for all, with the development of new tools that fulfil robustly defined gaps where engagement is suboptimal. Aims To generate an inventory of gaps in patient engagement practices and process from existing global examples. Methods A large set of criteria for effective patient engagement previously defined via a multi-stakeholder Delphi method, were mapped under fourteen overarching themes. A gap analysis was then performed by twenty-seven reviewers against the resulting forty-six mapped criteria, on a sample of seventy initiatives from global databases. Results An inventory of gaps was identified including contextual information as to why the gaps exist. Our work identified general patterns where patient engagement was suboptimal—defined as; fragmented reporting and dissemination of patient engagement activities, and the fundamental principles defined in frameworks or guidance being poorly adhered to in actual practice. Specific gaps were identified for sixteen criteria. Additionally, it was also common to observe primary aspects of a process were addressed for a given criteria (i.e. training for roles and responsibilities) but a secondary context element was lacking (i.e. making training material accessible/understandable/meaningful to all participants). Conclusion The results show that the evolution towards meaningful and systematic patient engagement is occurring, yet more importantly they provide clear directional insights to help enhance collaborative practices and co-design solutions. This targeted impact to catalyse a needs-oriented health system that integrates patient engagement at its core is essential.

Differential Sensitivities of Electricity Consumption to Global Warming Across Regions of Argentina

The description of the relationship between temperature (T) and electricity consumption (EC) is key to improve our understanding of a potential climate change amplification feedback and, thus, energy planning. We sought to characterize the relationship between the EC and daily T of different regions of Argentina and use these historical relationships to estimate expected EC under T future scenarios. We used a time series approach to model, remove trends and seasonality of EC accounting for breaks and discontinuities. EC and T data were obtained from Argentine Wholesale Market Administrator Company and global databases, respectively. We evaluated the T-EC model for the period between 1997 and 2014 and two sub-periods: 1997–2001 and 2011–2014. We used modelled temperature projections for the 2027–2044 period based on the Representative Pathway Concentration 4.5 together with our region specific T-EC models to predict changes in EC due to T changes. The shape of the T-EC relationships was quite stable between periods and regions but varied according to the temperature gradient. We found large increases in EC in warm days (from 40 to 126 Wh/cap/ºC) and a region specific response to cold days (from flat to steep responses). The T at which EC was minimum varied between 14 and 20°C and increased in time as mean daily T also increased. Estimated temperature projections translate into an average increase factor of 7.2 in EC with contrasting relative importance between regions of Argentina. Results highlight potential sensitivity of EC to T in the developing countries.

Fatalities caused by floods: a comparison between global databases and country scale historical research

<p>Datasets supporting the study of natural disasters and allowing spatial/temporal analyses of phenomena and their interactions with human societies is rapidly growing, due to the efforts of insurance companies, universities and humanitarian organizations. At the global scale, several disasters catalogues are available, even if some are only partially accessible. Generally, the focus is on the complete impact of disasters, in terms of areas affected and economic damage. Each record is a natural disaster, while database fields contain parameters assessing disaster magnitude. One of this parameter is the number of fatalities.</p><p>In Australia and USA, databases of fatalities caused by specific kinds of natural disasters are available, while, for Europe, natural disasters mortality is often investigated using global databases.</p><p>The present research focus on floods and their effects on people mortality. We named “flood fatalities” (FFs) people killed by direct impact of flood events due to the following short-term clinical causes: 1) Drowning; 2) Collapse/Heart attack; 3) Poly-trauma; 4) Poly-trauma and Suffocation; 5) Hypothermia; 6) Suffocation; 7) Electrocution.</p><p>For a 40-years study period and for 9 European study areas, we performed a survey of FFs reported in four of the widely known global databases. Then we compared figures with the results of a very specific research carried out for the same study areas and study period at a country scale, and focusing on a very restricted field: fatalities caused by floods.</p><p>The comparison highlights as the use of global databases can supply figures of FFs not correctly estimated, either underestimated or overestimated.</p><p>Underestimation depends on the fact that collecting data at the global scale needs some severity threshold of floods to be included in the database. Thus, local events causing a few FFs, as i.e. flash flooding, are systematically excluded, even if the majority of floods that occur in developed countries kill less than 10 people. This results in an underestimation of FFs, which is going to increase due to the increasing frequency of localized floods or flash floods related to climate change. Overestimation, instead, can happen due to the classification of fatalities occurred at the same time of the flood, even if they are caused by other phenomena (i.e., landslides, debris flows and wind).</p><p>This work aims to demonstrate how a database of flood fatalities realized at a country scale can supply realistic figures of fatalities in European countries, providing information that can reduce flood fatalities in the future. Our database is available for the period 1980-2018 (Petrucci et al., 2019). We encourage researchers working in European countries to collaborate with us to increase spatial coverage of the database and promote its common use in studies on flood mortality.</p><p>Petrucci O., Aceto, L., Bianchi, C., Bigot, V., Brázdil, R., Pereira, S., Kahraman, A., Kılıç, O., Kotroni, V., Llasat, M.C., Llasat-Botija, M., Papagiannaki, K., Pasqua. A.A., Řehoř J., Rossello Geli, J. Salvati, P., Vinet, F., Zêzere, J.L. (2019). Flood Fatalities in Europe, 1980–2018: Variability, Features, and Lessons to Learn. Water, 11(8), 1682.</p>