The Westerly Index as complementary indicator of the North Atlantic oscillation in explaining drought variability across Europe

This paper analyses the influence of different atmospheric circulation indices on the multi-scalar drought variability across Europe by using the Standardized Precipitation Evapotranspiration Index (SPEI). The monthly circulation indices used in this study include the North Atlantic oscillation (NAO), the East Atlantic (EA), the Scandinavian (SCAN) and the East Atlantic-Western Russia (EA-WR) patterns, as well as the recently published Westerly Index (WI), defined as the persistence of westerly winds over the eastern north Atlantic region. The results indicate that European drought variability is better explained by the station-based NAO index and the WI than by any other combination of circulation indices. In northern and central Europe the variability of drought severity for different seasons and time-scales is strongly associated with the WI. On the contrary, the influence of the NAO on southern Europe droughts is stronger than that exerted by the WI. The correlation patterns of the NAO and WI with the SPEI show a spatial complementarity in shaping drought variability across Europe. Lagged correlations of the NAO and WI with the SPEI also indicate enough skill of both indices to anticipate drought severity several months in advance. As long as instrumental series of the NAO and WI are available, their combined use would allow inferring European drought variability for the last two centuries and improve the calibration and interpretation of paleoclimatic proxies associated with drought.

Addressing wildfire risk in forest management with a wildfire resistance indicator

Mestrado Mediterranean Forestry and Natural Resources Management - Instituto Superior de Agronomia - UL

Using niche modelling of indicator species to predict the distribution of xerophitic shrub dune communities in South-Western Portugal

Inland sand dune systems are amongst the most threatened habitat types of Europe. Affected by severe conditions, these habitats present distinct community compositions, which makes them excellent for studying possible interactions among their integrating species and the environment. We focus on understanding the distribution and cooccurrence of the species from dune plant assemblages as a key step for the adequate protection of these habitats. Using data from an extensive survey we identified the shrub species that could be considered indicators of the different xerophytic scrub dune communities in South West Portugal. Then, we modelled the responses of these species to the environmental conditions using Ecological Niche Factor Analysis. We present some preliminary results elucidating whether using species distribution models of indicator species at a regional scale is a valid approach to predict the distribution of the different types of communities inhabiting these endangered habitats.

Can we use niche models of indicator species to predict the distribution of endangered communities?

European-wide conservation policies are based on the identification of priority habitats. However, research on conservation biogeography often relies on the results and projections of species distribution models to assess species' vulnerability to global change. We assess whether the distribution and structure of threatened communities can be predicted by the suitability of the environmental conditions for their indicator species. We present some preliminary results elucidating if using species distribution models of indicator species at a regional scale is a valid approach to predict these endangered communities. Dune plant assemblages, affected by severe conditions, are excellent models for studying possible interactions among their integrating species and the environment. We use data from an extensive survey of xerophytic inland sand dune scrub communities from Portugal, one of the most threatened habitat types of Europe. We identify indicator shrub species of different types of communities, model their geographical response to the environment, and evaluate whether the output of these niche models are able to predict the distribution of each type of community in a different region.

Cord Blood Alkaline Phosphatase as an Indicator of Neonatal Jaundice

Background: Management of hyperbilirubinemia remains a challenge for neonatal medicine because of the risk of neurological complications related to the toxicity of severe hyperbilirubinemia. Objectives: The purpose of this study was to examine the validity of cord blood alkaline phosphatase level for predicting neonatal hyperbilirubinemia. Patients and Methods: Between October and December 2013 a total of 102 healthy term infants born to healthy mothers were studied. Cord blood samples were collected for measurement of alkaline Phosphatase levels immediately after birth. Neonates were followed-up for the emergence of jaundice. Newborns with clinical jaundice were recalled and serum bilirubin levels measured. Appropriate treatment based on serum bilirubin level was performed. Alkaline phosphatase levels between the non-jaundiced and jaundiced treated neonates were compared. Results: The incidence of severe jaundice that required treatment among followed-up neonates was 9.8%. The mean alkaline phosphatase level was 309.09 ± 82.51 IU/L in the non-jaundiced group and 367.80 ± 73.82 IU/L in the severely jaundiced group (P = 0.040). The cutoff value of 314 IU/L was associated with sensitivity 80% and specificity 63% for predicting neonatal hyperbilirubinemia requiring treatment. Conclusions: The cord blood alkaline phosphatase level can be used as a predictor of severe neonatal jaundice.

Hemolytic activity of alternative complement pathway as an indicator of innate immunity in pacu (Piaractus mesopotamicus)

The objective of this study was to evaluate the methodology to establish the hemolytic activity of alternative complement pathway as an indicator of the innate immunity in Brazilian fish pacu (Piaractus mesopotamicus), in addition to verifying the influence of β-glucan as an immunostimulant. Fish were fed with diets containing 0, 0.1 and 1% β-glucan, during seven days, and then inoculated with Aeromonas hydrophila. Seven days after the challenge, they were bled for serum extraction. The methodology consisted of a kinetic assay that allows calculating the required time for serum proteins of the complement to promote 50% lysis of a rabbit red blood cell suspension. The method developed in mammals was successfully applied for pacu and determined that the hemolytic activity of the proteins of the complement system (alternative pathway) increased after the pathogen challenge, but was not influenced by the β-glucan treatment.

SYSTEM DYNAMICS MODELING AS A QUANTITATIVE-QUALITATIVE FRAMEWORK FOR SUSTAINABLE WATER RESOURCES MANAGEMENT: INSIGHTS FOR WATER QUALITY POLICY IN THE GREAT LAKES REGION

Early water resources modeling efforts were aimed mostly at representing hydrologic processes, but the need for interdisciplinary studies has led to increasing complexity and integration of environmental, social, and economic functions. The gradual shift from merely employing engineering-based simulation models to applying more holistic frameworks is an indicator of promising changes in the traditional paradigm for the application of water resources models, supporting more sustainable management decisions. This dissertation contributes to application of a quantitative-qualitative framework for sustainable water resources management using system dynamics simulation, as well as environmental systems analysis techniques to provide insights for water quality management in the Great Lakes basin. The traditional linear thinking paradigm lacks the mental and organizational framework for sustainable development trajectories, and may lead to quick-fix solutions that fail to address key drivers of water resources problems. To facilitate holistic analysis of water resources systems, systems thinking seeks to understand interactions among the subsystems. System dynamics provides a suitable framework for operationalizing systems thinking and its application to water resources problems by offering useful qualitative tools such as causal loop diagrams (CLD), stock-and-flow diagrams (SFD), and system archetypes. The approach provides a high-level quantitative-qualitative modeling framework for "big-picture" understanding of water resources systems, stakeholder participation, policy analysis, and strategic decision making. While quantitative modeling using extensive computer simulations and optimization is still very important and needed for policy screening, qualitative system dynamics models can improve understanding of general trends and the root causes of problems, and thus promote sustainable water resources decision making. Within the system dynamics framework, a growth and underinvestment (G&U) system archetype governing Lake Allegan's eutrophication problem was hypothesized to explain the system's problematic behavior and identify policy leverage points for mitigation. A system dynamics simulation model was developed to characterize the lake's recovery from its hypereutrophic state and assess a number of proposed total maximum daily load (TMDL) reduction policies, including phosphorus load reductions from point sources (PS) and non-point sources (NPS). It was shown that, for a TMDL plan to be effective, it should be considered a component of a continuous sustainability process, which considers the functionality of dynamic feedback relationships between socio-economic growth, land use change, and environmental conditions. Furthermore, a high-level simulation-optimization framework was developed to guide watershed scale BMP implementation in the Kalamazoo watershed. Agricultural BMPs should be given priority in the watershed in order to facilitate cost-efficient attainment of the Lake Allegan's TP concentration target. However, without adequate support policies, agricultural BMP implementation may adversely affect the agricultural producers. Results from a case study of the Maumee River basin show that coordinated BMP implementation across upstream and downstream watersheds can significantly improve cost efficiency of TP load abatement.

Antimicrobial resistance in indicator Escherichia coli isolates from free-ranging livestock and sympatric wild ungulates in a natural environment (Northeastern Spain)

Antimicrobial resistance was assessed in indicator Escherichia coli isolates from free-ranging livestock and sympatric wild boar (Sus scrofa) and Iberian ibex (Capra pyrenaica) in a National Game Reserve in northeastern Spain. The frequency of antimicrobial resistance was low (0% to 7.9%). However, resistance to an extended-spectrum cephalosporin and fluoroquinolones was detected.

Autoinducer-2 plays a crucial role in gut colonization and probiotic functionality of Bifidobacterium breve UCC2003

In the present study we show that luxS of Bifidobacterium breve UCC2003 is involved in the production of the interspecies signaling molecule autoinducer-2 (AI-2), and that this gene is essential for gastrointestinal colonization of a murine host, while it is also involved in providing protection against Salmonella infection in Caenorhabditis elegans. We demonstrate that a B. breve luxS-insertion mutant is significantly more susceptible to iron chelators than the WT strain and that this sensitivity can be partially reverted in the presence of the AI-2 precursor DPD. Furthermore, we show that several genes of an iron starvation-induced gene cluster, which are downregulated in the luxS-insertion mutant and which encodes a presumed iron-uptake system, are transcriptionally upregulated under in vivo conditions. Mutation of two genes of this cluster in B. breve UCC2003 renders the derived mutant strains sensitive to iron chelators while deficient in their ability to confer gut pathogen protection to Salmonella-infected nematodes. Since a functional luxS gene is present in all tested members of the genus Bifidobacterium, we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition.

Perceived Accessibility of Public Transport as a Potential Indicator of Social Inclusion

Perceived accessibility has been acknowledged as an important aspect of transport policy since the 70s. Nevertheless, very few empirical studies have been conducted in this field. When aiming to improve social inclusion, by making sus-tainable transport modes accessible to all, it is important to understand the factors driving perceived accessibility. Un-like conventional accessibility measures, perceived accessibility focuses on the perceived possibilities and ease of en-gaging in preferred activities using different transport modes. We define perceived accessibility in terms of how easy it is to live a satisfactory life with the help of the transport system, which is not necessarily the same thing as the objec-tive standard of the system. According to previous research, perceived accessibility varies with the subjectively-rated quality of the mode of transport. Thus, improvements in quality (e.g. trip planning, comfort, or safety) increase the per-ceived accessibility and make life easier to live using the chosen mode of transport. This study (n=750) focuses on the perceived accessibility of public transport, captured using the Perceived Accessibility Scale PAC (Lättman, Olsson, & Fri-man, 2015). More specifically, this study aims to determine how level of quality affects the perceived accessibility in public transport. A Conditional Process Model shows that, in addition to quality, feeling safe and frequency of travel are important predictors of perceived accessibility. Furthermore, elderly and those in their thirties report a lower level of perceived accessibility to their day-to-day activities using public transport. The basic premise of this study is that sub-jective experiences may be as important as objective indicators when planning and designing for socially inclusive transport systems.

Improving safety and establishing episomal maintenance of Adeno-associated viral vectors

Adeno-associated viral (AAV) vectors are among the most widely used gene transfer systems in basic and pre-clinical research and have been employed in more than 160 clinical trials. AAV vectors are commonly produced in producer cell lines like HEK293 by co-transfection with a so-called vector plasmid and one (in this work) or two so-called helper plasmids. The vector plasmid contains the transgene cassette of interest (TEC) flanked by AAV’s inverted terminal repeats (ITRs) which serve as packaging signals, whereas the helper plasmid provides the required AAV and helper virus functions in trans. A pivotal aspect of AAV vectorology is the manufacturing of AAV vectors free from impurities arising during the production process. These impurities include AAV vector preparations that contain capsids containing prokaryotic sequences, e.g. antibiotic resistance genes originating from the producer plasmids. In the first part of the thesis we aimed at improving the safety of AAV vectors. As we found that encapsidated prokaryotic sequences (using the ampicillin resistance gene as indicator) cannot be re-moved by standard purification methods we investigated whether the producer plasmids could be replaced by Minicircles (MCs). MCs are circular DNA constructs which contain no functional or coding prokaryotic sequences; they only consist of the TEC and a short sequence required for production and purification. MC counterparts of a vector plasmid encoding for enhanced green fluorescent (eGFP) protein and a helper plasmid encoding for AAV serotype 2 (AAV2) and helper Adenovirus (Ad) genes were designed and produced by PlasmidFactory (Bielefeld, Germany). Using all four possible combinations of plasmid and MCs, single-stranded AAV2 vectors (ssAAV) and self-complementary AAV vectors (scAAV) were produced and characterized for vector quantity, quality and functionality. The analyses showed that plasmids can be replaced by MCs without decreasing the efficiency of vector production and vector quality. MC-derived scAAV vector preparations even exceeded plasmid-derived preparations, as they displayed up to 30-fold improved transduction efficiencies. Using MCs as tools, we found that the vector plasmid is the main source of encapsidated prokaryotic sequences. Remarkably, we found that plasmid-derived scAAV vector preparations contained a much higher relative amount of prokaryotic sequences (up to 26.1 %, relative to TEC) compared to ssAAV vector preparations (up to 2.9 %). By replacing both plasmids by MCs the amount of functional prokaryotic sequences could be decreased to below the limit of quantification. Additional analyses for DNA impurities other than prokaryotic sequences showed that scAAV vectors generally contained a higher amount of non-vector DNA (e.g. adenoviral sequences) than ssAAV vectors. For both, ssAAV and scAAV vector preparations, MC-derived vectors tended to contain lower amounts of foreign DNA. None of the vectors tested could be shown to induce immunogenicity. In summary we could demonstrate that the quality of AAV vector preparations could be significantly improved by replacing producer plasmids by MCs. Upon transduction of a target tissue, AAV vector genomes predominantly remain in an episomal state, as duplex DNA circles or concatemers. These episomal forms mediate long-term transgene expression in terminally differentiated cells, but are lost in proliferating cells due to cell division. Therefore, in the second part of the thesis, in cooperation with Claudia Hagedorn and Hans J. Lipps (University Witten/Herdecke) an AAV vector genome was equipped with an autonomous replication element (Scaffold/matrix attachment region (S/MAR)). AAV-S/MAR encoding for eGFP and a blasticidin resistance gene and a control vector with the same TEC but lacking the S/MAR element (AAV-ΔS/MAR) were produced and transduced into highly proliferative HeLa cells. Antibiotic pressure was employed to select for cells stably maintaining the vector genome. AAV-S/MAR transduced cells yielded a higher number of colonies than AAV-ΔS/MAR-transduced cells. Colonies derived from each vector transduction were picked and cultured further. They remained eGFP-positive (up to 70 days, maximum cultivation period) even in the absence of antibiotic selection pressure. Interestingly, the mitotic stability of both AAV-S/MAR and control vector AAV-ΔS/MAR was found to be a result of episomal maintenance of the vector genome. This finding indicates that, under specific conditions such as the mild selection pressure we employed, “common” AAV vectors persist episomally. Thus, the S/MAR element increases the establishment frequency of stable episomes, but is not a prerequisite.

Analysis of size spectra off northwest Africa: a useful indicator in tropical areas?

Changes in the size spectra of demersal fish communities off Cape Verde (1988, 1994), Guinea (1985-1995), and Mauritania (1987-2001) were studied. Intercepts and slopes showed opposite trends for Guinea and Mauritania, but were relatively stable in spite of a strong increase in landings per unit area. For Cape Verde, there were marked changes in size structure, seemingly inconsistent with the more moderate fishing pressure there. Changes in size structure do not seem to be suitable indicators of the effects of fishing in areas characterized by faster growth rates, small sizes, high species diversity, and complex interrelationships, such as the tropics. (c) 2005 International Council for the Exploration of the Sea. Published by Elsevier Ltd. All rights reserved.

Is the human population a large-scale indicator of the species richness of ground beetles?

Aim Positive regional correlations between biodiversity and human population have been detected for several taxonomic groups and geographical regions. Such correlations could have important conservation implications and have been mainly attributed to ecological factors, with little testing for an artefactual explanation: more populated regions may show higher biodiversity because they are more thoroughly surveyed. We tested the hypothesis that the correlation between people and herptile diversity in Europe is influenced by survey effort

Assessing the ability of rural agrarian areas to provide cultural ecosystem services (CES): A multi scale social indicator framework (MSIF)

Assessing the ways in which rural agrarian areas provide Cultural Ecosystem Services (CES) is proving difficult to achieve. This research has developed an innovative methodological approach named as Multi Scale Indicator Framework (MSIF) for capturing the CES embedded into the rural agrarian areas. This framework reconciles a literature review with a transdisciplinary participatory workshop. Both of these sources reveal that societal preferences diverge upon judgemental criteria which in turn relate to different visual concepts that can be drawn from analyzing attributes, elements, features and characteristics of rural areas. We contend that it is now possible to list a group of possible multi scale indicators for stewardship, diversity and aesthetics. These results might also be of use for improving any existing European indicators frameworks by also including CES. This research carries major implications for policy at different levels of governance, as it makes possible to target and monitor policy instruments to the physical rural settings so that cultural dimensions are adequately considered. There is still work to be developed on regional specific values and thresholds for each criteria and its indicator set. In practical terms, by developing the conceptual design within a common framework as described in this paper, a considerable step forward toward the inclusion of the cultural dimension in European wide assessments can be made

Phenotypic and genotypic characterisation of antimicrobial resistance in Escherichia coli indicator of animal, food and human origin.

This thesis presents AMR phenotypic evaluation and whole genome sequencing analysis of 288 Escherichia coli strains isolated from different sources (livestock, companion animal, wildlife, food and human) in Italy. Our data reflects general resistance trends in Europe, reporting tetracycline, ampicillin, sulfisoxazole and aminoglycosides resistance as the most common phenotypic AMR profile among livestock, pets, wildlife and humans. Identification of human and animal (livestock and companion animal) AMR profiles in niches with a rare (fishery, mollusc) or absent (vegetable, wild animal, wild boar) direct exposure to antimicrobials, suggests widespread environmental pollution with ARGs conferring resistance to these antimicrobials. Phenotypic resistance to highest priority critically important antimicrobials was mainly observed in food-producing animals and related food such as rabbit, poultry, beef and swine. Discrepancies between AMR phenotypic pattern and genetic profile were observed. In particular, phenotypic aminoglycoside, cephalosporin, meropenem, colistin resistance and ESBL profile did not have a genetic explanation in different cases. This data could suggest the diffusion of new genetic variants of ARGs, associated to these antimicrobial classes. Generally, our collection shows a virulence profile typical of extraintestinal pathogenic Escherichia coli (ExPEC) pathotype. Different pandemic and emerging ExPEC lineages were identified, in particular in poultry meat (ST10; ST23; ST69, ST117; ST131). Rabbit was suggested as a source of ST20-ST40 potential hybrid pathogens. Wildlife carried a high average number (10) of VAGs (mostly associated to ExPEC pathotype) and different predominant ExPEC lineages (ST23, ST117, ST648), suggesting its possible involvement in maintenance and diffusion of virulence determinants. In conclusion, our study provides important knowledge related to the phenotypic/genetic AMR and virulence profiles circulating in E. coli in Italy. The role of different niches in AMR dynamics has been discussed. In particular, food-producing animals are worthy of continued investigation as a source of potential zoonotic pathogens, meanwhile wildlife might contribute to VAGs spread.