Assessing the use of very high resolution data to predict species distribution in a mountain environment

Nowadays, Species Distribution Models (SDMs) are a widely used tool. Using different statistical approaches these models reconstruct the realized niche of a species using presence data and a set of variables, often topoclimatic. There utilization range is quite large from understanding single species requirements, to the creation of nature reserve based on species hotspots, or modeling of climate change impact, etc... Most of the time these models are using variables at a resolution of 50km x 50km or 1 km x 1 km. However in some cases these models are used with resolutions below the kilometer scale and thus called high resolution models (100 m x 100 m or 25 m x 25 m). Quite recently a new kind of data has emerged enabling precision up to lm x lm and thus allowing very high resolution modeling. However these new variables are very costly and need an important amount of time to be processed. This is especially the case when these variables are used in complex calculation like models projections over large areas. Moreover the importance of very high resolution data in SDMs has not been assessed yet and is not well understood. Some basic knowledge on what drive species presence-absences is still missing. Indeed, it is not clear whether in mountain areas like the Alps coarse topoclimatic gradients are driving species distributions or if fine scale temperature or topography are more important or if their importance can be neglected when balance to competition or stochasticity. In this thesis I investigated the importance of very high resolution data (2-5m) in species distribution models using either very high resolution topographic, climatic or edaphic variables over a 2000m elevation gradient in the Western Swiss Alps. I also investigated more local responses of these variables for a subset of species living in this area at two precise elvation belts. During this thesis I showed that high resolution data necessitates very good datasets (species and variables for the models) to produce satisfactory results. Indeed, in mountain areas, temperature is the most important factor driving species distribution and needs to be modeled at very fine resolution instead of being interpolated over large surface to produce satisfactory results. Despite the instinctive idea that topographic should be very important at high resolution, results are mitigated. However looking at the importance of variables over a large gradient buffers the importance of the variables. Indeed topographic factors have been shown to be highly important at the subalpine level but their importance decrease at lower elevations. Wether at the mountane level edaphic and land use factors are more important high resolution topographic data is more imporatant at the subalpine level. Finally the biggest improvement in the models happens when edaphic variables are added. Indeed, adding soil variables is of high importance and variables like pH are overpassing the usual topographic variables in SDMs in term of importance in the models. To conclude high resolution is very important in modeling but necessitate very good datasets. Only increasing the resolution of the usual topoclimatic predictors is not sufficient and the use of edaphic predictors has been highlighted as fundamental to produce significantly better models. This is of primary importance, especially if these models are used to reconstruct communities or as basis for biodiversity assessments. -- Ces dernières années, l'utilisation des modèles de distribution d'espèces (SDMs) a continuellement augmenté. Ces modèles utilisent différents outils statistiques afin de reconstruire la niche réalisée d'une espèce à l'aide de variables, notamment climatiques ou topographiques, et de données de présence récoltées sur le terrain. Leur utilisation couvre de nombreux domaines allant de l'étude de l'écologie d'une espèce à la reconstruction de communautés ou à l'impact du réchauffement climatique. La plupart du temps, ces modèles utilisent des occur-rences issues des bases de données mondiales à une résolution plutôt large (1 km ou même 50 km). Certaines bases de données permettent cependant de travailler à haute résolution, par conséquent de descendre en dessous de l'échelle du kilomètre et de travailler avec des résolutions de 100 m x 100 m ou de 25 m x 25 m. Récemment, une nouvelle génération de données à très haute résolution est apparue et permet de travailler à l'échelle du mètre. Les variables qui peuvent être générées sur la base de ces nouvelles données sont cependant très coûteuses et nécessitent un temps conséquent quant à leur traitement. En effet, tout calcul statistique complexe, comme des projections de distribution d'espèces sur de larges surfaces, demande des calculateurs puissants et beaucoup de temps. De plus, les facteurs régissant la distribution des espèces à fine échelle sont encore mal connus et l'importance de variables à haute résolution comme la microtopographie ou la température dans les modèles n'est pas certaine. D'autres facteurs comme la compétition ou la stochasticité naturelle pourraient avoir une influence toute aussi forte. C'est dans ce contexte que se situe mon travail de thèse. J'ai cherché à comprendre l'importance de la haute résolution dans les modèles de distribution d'espèces, que ce soit pour la température, la microtopographie ou les variables édaphiques le long d'un important gradient d'altitude dans les Préalpes vaudoises. J'ai également cherché à comprendre l'impact local de certaines variables potentiellement négligées en raison d'effets confondants le long du gradient altitudinal. Durant cette thèse, j'ai pu monter que les variables à haute résolution, qu'elles soient liées à la température ou à la microtopographie, ne permettent qu'une amélioration substantielle des modèles. Afin de distinguer une amélioration conséquente, il est nécessaire de travailler avec des jeux de données plus importants, tant au niveau des espèces que des variables utilisées. Par exemple, les couches climatiques habituellement interpolées doivent être remplacées par des couches de température modélisées à haute résolution sur la base de données de terrain. Le fait de travailler le long d'un gradient de température de 2000m rend naturellement la température très importante au niveau des modèles. L'importance de la microtopographie est négligeable par rapport à la topographie à une résolution de 25m. Cependant, lorsque l'on regarde à une échelle plus locale, la haute résolution est une variable extrêmement importante dans le milieu subalpin. À l'étage montagnard par contre, les variables liées aux sols et à l'utilisation du sol sont très importantes. Finalement, les modèles de distribution d'espèces ont été particulièrement améliorés par l'addition de variables édaphiques, principalement le pH, dont l'importance supplante ou égale les variables topographique lors de leur ajout aux modèles de distribution d'espèces habituels.

Liquid transportation and distribution during (re)wetting : impact on coated papers in printing

In many industrial applications, such as the printing and coatings industry, wetting of porous materials by liquids includes not only imbibition and permeation into the bulk but also surface spreading and evaporation. By understanding these phenomena, valuable information can be obtained for improved process control, runnability and printability, in which liquid penetration and subsequent drying play important quality and economic roles. Knowledge of the position of the wetting front and the distribution/degree of pore filling within the structure is crucial in describing the transport phenomena involved. Although exemplifying paper as a porous medium in this work, the generalisation to dynamic liquid transfer onto a surface, including permeation and imbibition into porous media, is of importance to many industrial and naturally occurring environmental processes. This thesis explains the phenomena in the field of heatset web offset printing but the content and the analyses are applicable in many other printing methods and also other technologies where water/moisture monitoring is crucial in order to have a stable process and achieve high quality end products. The use of near-infrared technology to study the water and moisture response of porous pigmented structures is presented. The use of sensitive surface chemical and structural analysis, as well as the internal structure investigation of a porous structure, to inspect liquid wetting and distribution, complements the information obtained by spectroscopic techniques. Strong emphasis has been put on the scale of measurement, to filter irrelevant information and to understand the relationship between interactions involved. The near-infrared spectroscopic technique, presented here, samples directly the changes in signal absorbance and its variation in the process at multiple locations in a print production line. The in-line non-contact measurements are facilitated by using several diffuse reflectance probes, giving the absolute water/moisture content from a defined position in the dynamic process in real-time. The nearinfrared measurement data illustrate the changes in moisture content as the paper is passing through the printing nips and dryer, respectively, and the analysis of the mechanisms involved highlight the roles of the contacting surfaces and the relative liquid carrier properties of both non-image and printed image areas. The thesis includes laboratory studies on wetting of porous media in the form of coated paper and compressed pigment tablets by mono-, dual-, and multi-component liquids, and paper water/moisture content analysis in both offline and online conditions, thus also enabling direct sampling of temporal water/moisture profiles from multiple locations. One main focus in this thesis was to establish a measurement system which is able to monitor rapid changes in moisture content of paper. The study suggests that near-infrared diffuse reflectance spectroscopy can be used as a moisture sensitive system and to provide accurate online qualitative indicators, but, also, when accurately calibrated, can provide quantification of water/moisture levels, its distribution and dynamic liquid transfer. Due to the high sensitivity, samples can be measured with excellent reproducibility and good signal to noise ratio. Another focus of this thesis was on the evolution of the moisture content, i.e. changes in moisture content referred to (re)wetting, and liquid distribution during printing of coated paper. The study confirmed different wetting phases together with the factors affecting each phase both for a single droplet and a liquid film applied on a porous substrate. For a single droplet, initial capillary driven imbibition is followed by equilibrium pore filling and liquid retreat by evaporation. In the case of a liquid film applied on paper, the controlling factors defining the transportation were concluded to be the applied liquid volume in relation to surface roughness, capillarity and permeability of the coating giving the liquid uptake capacity. The printing trials confirmed moisture gradients in the printed sheet depending on process parameters such as speed, fountain solution dosage and drying conditions as well as the printed layout itself. Uneven moisture distribution in the printed sheet was identified to be one of the sources for waving appearance and the magnitude of waving was influenced by the drying conditions.

Isolation of bovine plasma albumin by liquid chromatography and its polymerization for use in immunohematology

The aim of the method described here is to remove hemoglobin, the major contaminant in the bovine plasma obtained from slaughterhouses, by adding a mixture of 19% cold ethanol and 0.6% chloroform, followed by fibrinogen and globulin precipitation by the Cohn method and nonspecific hemagglutinin by thermocoagulation. The experimental volume of bovine plasma was 2,000 ml per batch. Final purification was performed by liquid chromatography using the ion-exchange gel DEAE-Sepharose FF. The bovine albumin thus obtained presented > or = 99% purity, a yield of 25.0 ± 1.2 g/l plasma and >71.5% recovery. N-acetyl-DL-tryptophan (0.04 mmol/g protein) and sodium caprylate (0.04 mmol/g protein) were used as stabilizers and the final concentration of albumin was adjusted to 22.0% (w/v), pH 7.2 to 7.3. Viral inactivation was performed by pasteurization for 10 h at 60°C. The bovine albumin for the hemagglutination tests used in immunohematology was submitted to chemical treatment with 0.06% (w/v) glutaraldehyde and 0.1% (w/v) formaldehyde at 37°C for 12 h to obtain polymerization. A change in molecular distribution was observed after this treatment, with average contents of 56.0% monomers, 23.6% dimers, 12.2% trimers and 8.2% polymers. The tests performed demonstrated that this polymerized albumin enhances the agglutination of Rho(D)-positive red cells by anti-Rho(D) serum, permitting and improving visualization of the results.

Use of starter cultures isolated from native microbiota of artisanal sausage in the production of Italian sausage

The most promising microorganisms for use as starter cultures are those isolated from the native microbiota of traditional fermented products. The aim of this study was to evaluate the use of lactic acid bacteria selected from the native microbiota of sausages produced by spontaneous fermentation as starter cultures for the production of sausage. Strains of Lactobacillus plantarum 503 and 341 have the potential for use as starter cultures in the manufacture of Italian sausage type. The population of lactic acid bacteria in sausages was >8 log CFU.g-1 during fermentation, which caused the pH to decrease to <4.5. This decrease in pH and the water activity of < 0.90 of sausages ensures the safety and preservation of this product. Sausages produced with these lactic cultures fulfill the requirements for microbiological quality and composition of Italian sausage type. Our results suggest the possibility of using these starter cultures for the production of sausages with peculiar characteristics that contribute to the identity of the product.

Quantifying polynya ice production in the Laptev Sea with the COSMO model

Arctic flaw polynyas are considered to be highly productive areas for the formation of sea-ice throughout the winter season. Most estimates of sea-ice production are based on the surface energy balance equation and use global reanalyses as atmospheric forcing, which are too coarse to take into account the impact of polynyas on the atmosphere. Additional errors in the estimates of polynya ice production may result from the methods of calculating atmospheric energy fluxes and the assumption of a thin-ice distribution within polynyas. The present study uses simulations using the mesoscale weather prediction model of the Consortium for Small-scale Modelling (COSMO), where polynya area is prescribed from satellite data. The polynya area is either assumed to be ice-free or to be covered with thin ice of 10 cm. Simulations have been performed for two winter periods (2007/08 and 2008/09). When using a realistic thin-ice thickness of 10 cm, sea-ice production in Laptev polynyas amount to 30 km3 and 73 km3 for the winters 2007/08 and 2008/09, respectively. The higher turbulent energy fluxes of open-water polynyas result in a 50-70% increase in sea-ice production (49 km3 in 2007/08 and 123 km3 in 2008/09). Our results suggest that previous studies have overestimated ice production in the Laptev Sea.

Influence of package, type of apple juice and temperature on the production of patulin by Byssochlamys nivea and Byssochlamys fulva

Although the production of patulin in apple fruits is mainly by Penicillium expansum, there is no information on the ability of heat resistant moulds that may survive pasteurization to produce this mycotoxin in juice packages during storage and distribution. In this study, the production of patulin by Byssochlamys spp (Byssochlamys nivea FRR 4421, B. nivea ATCC 24008 and Byssochlamys fulva IOC 4518) in cloudy and clarified apple juices packaged in laminated paperboard packages or in polyethylene terephthalate bottles (PET) and stored at both 21 degrees C and 30 degrees C, was investigated. The three Byssochlamys strains were able to produce patulin in both cloudy and clarified apple juices. Overall, the lower the storage temperature, the lower the patulin levels and mycelium dry weight in the apple juices (p<0.05). The greatest variations in pH and degrees Brix were observed in the juices from which the greatest mycelium dry weights were recovered. The maximum levels of patulin recovered from the juices were ca. 150 mu g/kg at 21 degrees C and 220 mu g/kg at 30 degrees C. HPLC-UV, HPCL-DAD and mass spectrometry analyses confirmed the ability of B. fulva IOC 4518 to produce patulin. Due to the heat resistance of B. nivea and B. fulva and their ability to produce patulin either in PET bottles or in laminated paperboard packages, the control of contamination and the incidence of these fungi should be a matter of concern for food safety. Control measures taken by juice industries must also focus on controlling the ascospores of heat resistant moulds. (C) 2010 Elsevier B.V. All rights reserved.

Videography as production nexus : digital film cameras, media mangement and the distribution of creativity

This thesis is about new digital moving image recording technologies and how they augment the distribution of creativity and the flexibility in moving image production systems, but also impose constraints on how images flow through the production system. The central concept developed in this thesis is ‘creative space’ which links quality and efficiency in moving image production to time for creative work, capacity of digital tools, user skills and the constitution of digital moving image material. The empirical evidence of this thesis is primarily based on semi-structured interviews conducted with Swedish film and TV production representatives.This thesis highlights the importance of pre-production technical planning and proposes a design management support tool (MI-FLOW) as a way to leverage functional workflows that is a prerequisite for efficient and cost effective moving image production.

Production of fibrolytic enzymes by Aspergillus japonicus C03 using agro-industrial residues with potential application as additives in animal feed

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Isomaltulose production from Sucrose by Protaminobacter rubrum immobilized in calcium alginate

Different culture conditions for Protaminobacter rubrum and enzymatic reaction parameters were evaluated with the goal of improving isomaltulose production. P. rubrum was grown in a medium with 1% (w/v) cane molasses and 0.5% yeast extract and achieved a maximum cell yield Y(x/s) of 0.295 g of cells/g sucrose and a specific growth rate (mu) of 0.192 h(-1). The immobilization of P. rubrum cells was carried out with calcium alginate, glutaraldehyde and polyethyleneimine. Stabile immobilized cell pellets were obtained and used 24 times in batch processes. Enzymatic conversion was carried out at different sucrose concentrations and in pH 6 medium with 70% (w/v) sucrose at 30 degrees C an isomaltulose yield of 89-94% (w/v) was obtained. The specific activity of the P. rubrum immobilized pellets in calcium alginate at 30 degrees C ranged from 1.6 to 4.0 g isomaltulose g(-1) pellet h(-1), respectively with 70% and 65% sucrose solution, while in lower sucrose concentration had higher specific activities presumably due to substrate inhibition of the isomaltulose synthase in higher sucrose concentrations. (C) 2009 Elsevier Ltd. All rights reserved.

Ligninases production by Basidiomycetes strains on lignocellulosic agricultural residues and their application in the decolorization of synthetic dyes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cultivation of Rubrivivax gelatinosus in fish industry effluent for depollution and biomass production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ecological distribution of stream macroalgal communities from a drainage basin in the Serra da Canastra National Park, Minas Gerais, Southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Assessment of ALA-induced PpIX production in porcine skin pretreated with microneedles

Photodynamic therapy (PDT) is used for skin treatments of premalignant and cancer lesions and recognized as a non-invasive technique that combines tissue photosensitization and subsequent exposure to light to induce cell death. However, it is limited to the treatment of superficial lesions, mainly due to the low cream penetration. Therefore, the improvement of transdermal distribution of aminolevulinic acid (ALA) is needed. In this study, the kinetics and homogeneity of production of ALA-induced PpIX after the skin pre-treatment with microneedles rollers of 0.5, 1.0 and 1.5 mm length were investigated. An improvement in homogeneity and production of PpIX was shown in a porcine model. Widefield fluorescence imaging three hours after the topical application of ALA-cream in the combined treatment with microeedles rollers.

Ecological distribution of stream macroalgal communities from a drainage basin in the Serra da Canastra National Park, Minas Gerais, Southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Afghanistan connection : heroin production, distribution, and consumption

Heroin prices are a reflection of supply and demand, and similar to any other market, profits motivate participation. The intent of this research is to examine the change in Afghan opium production due to political conflict affecting Europe’s heroin market and government policies. If the Taliban remain in power, or a new Afghan government is formed, the changes will affect the heroin market in Europe to a certain degree. In the heroin market, the degree of change is dependent on many socioeconomic forces such as law enforcement, corruption, and proximity to Afghanistan. An econometric model that examines the degree of these socioeconomic effects has not been applied to the heroin trade in Afghanistan before. This research uses a two-stage least squares econometric model to reveal the supply and demand of heroin in 36 different countries from the Middle East to Western Europe in 2008. An application of the two-stage least squares model to the heroin market in Europe will attempt to predict the socioeconomic consequences of Afghanistan opium production.