GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Use of solvents and environmental friendly materials for applications in Green Chemistry

The present Thesis studies three alternative solvent groups as sustainable replacement of traditional organic solvents. Some aspects of fluorinated solvents, supercritical fluids and ionic liquids, have been analysed with a critical approach and their effective “greenness” has been evaluated from the points of view of the synthesis, the properties and the applications. In particular, the attention has been put on the environmental and human health issues, evaluating the eco-toxicity, the toxicity and the persistence, to underline that applicability and sustainability are subjects with equal importance. The “green” features of fluorous solvents and supercritical fluids are almost well-established; in particular supercritical carbon dioxide (scCO2) is probably the “greenest” solvent among the alternative solvent systems developed in the last years, enabling to combine numerous advantages both from the point of view of industrial/technological applications and eco-compatibility. In the Thesis the analysis of these two classes of alternative solvents has been mainly focused on their applicability, rather than the evaluation of their environmental impact. Specifically they have been evaluated as alternative media for non-aqueous biocatalysis. For this purpose, the hydrophobic ion pairing (HIP), which allows solubilising enzymes in apolar solvents by an ion pairing between the protein and a surfactant, has been investigated as effective enzymatic derivatisation technique to improve the catalytic activity under homogeneous conditions in non conventional media. The results showed that the complex enzyme-surfactant was much more active both in fluorous solvents and in supercritical carbon dioxide than the native form of the enzyme. Ionic liquids, especially imidazolium salts, have been proposed some years ago as “fully green” alternative solvents; however this epithet does not take into account several “brown” aspects such as their synthesis from petro-chemical starting materials, their considerable eco-toxicity, toxicity and resistance to biodegradation, and the difficulty of clearly outline applications in which ionic liquids are really more advantageous than traditional solvents. For all of these reasons in this Thesis a critical analysis of ionic liquids has been focused on three main topics: i) alternative synthesis by introducing structural moieties which could reduce the toxicity of the most known liquid salts, and by using starting materials from renewable resources; ii) on the evaluation of their environmental impact through eco-toxicological tests (Daphnia magna and Vibrio fischeri acute toxicity tests, and algal growth inhibition), toxicity tests (MTT test, AChE inhibition and LDH release tests) and fate and rate of aerobic biodegradation in soil and water; iii) and on the demonstration of their effectiveness as reaction media in organo-catalysis and as extractive solvents in the recovery of vegetable oil from terrestrial and aquatic biomass. The results about eco-toxicity tests with Daphnia magna, Vibrio fischeri and algae, and toxicity assay using cultured cell lines, clearly indicate that the difference in toxicity between alkyl and oxygenated cations relies in differences of polarity, according to the general trend of decreasing toxicity by decreasing the lipophilicity. Independently by the biological approach in fact, all the results are in agreement, showing a lower toxicity for compounds with oxygenated lateral chains than for those having purely alkyl lateral chains. These findings indicate that an appropriate choice of cation and anion structures is important not only to design the IL with improved and suitable chemico-physical properties but also to obtain safer and eco-friendly ILs. Moreover there is a clear indication that the composition of the abiotic environment has to be taken into account when the toxicity of ILs in various biological test systems is analysed, because, for example, the data reported in the Thesis indicate a significant influence of salinity variations on algal toxicity. Aerobic biodegradation of four imidazolium ionic liquids, two alkylated and two oxygenated, in soil was evaluated for the first time. Alkyl ionic liquids were shown to be biodegradable over the 6 months test period, and in contrast no significant mineralisation was observed with oxygenated derivatives. A different result was observed in the aerobic biodegradation of alkylated and oxygenated pyridinium ionic liquids in water because all the ionic liquids were almost completely degraded after 10 days, independently by the number of oxygen in the lateral chain of the cation. The synthesis of new ionic liquids by using renewable feedstock as starting materials, has been developed through the synthesis of furan-based ion pairs from furfural. The new ammonium salts were synthesised in very good yields, good purity of the products and wide versatility, combining low melting points with high decomposition temperatures and reduced viscosities. Regarding the possible applications as surfactants and biocides, furan-based salts could be a valuable alternative to benzyltributylammonium salts and benzalkonium chloride that are produced from non-renewable resources. A new procedure for the allylation of ketones and aldehydes with tetraallyltin in ionic liquids was developed. The reaction afforded high yields both in sulfonate-containing ILs and in ILs without sulfonate upon addition of a small amount of sulfonic acid. The checked reaction resulted in peculiar chemoselectivity favouring aliphatic substrates towards aromatic ketones and good stereoselectivity in the allylation of levoglucosenone. Finally ILs-based systems could be easily and successfully recycled, making the described procedure environmentally benign. The potential role of switchable polarity solvents as a green technology for the extraction of vegetable oil from terrestrial and aquatic biomass has been investigated. The extraction efficiency of terrestrial biomass rich in triacylglycerols, as soy bean flakes and sunflower seeds, was comparable to those of traditional organic solvents, being the yield of vegetable oils recovery very similar. Switchable polarity solvents as been also exploited for the first time in the extraction of hydrocarbons from the microalga Botryococcus braunii, demonstrating the efficiency of the process for the extraction of both dried microalgal biomass and directly of the aqueous growth medium. The switchable polarity solvents exhibited better extraction efficiency than conventional solvents, both with dried and liquid samples. This is an important issue considering that the harvest and the dewatering of algal biomass have a large impact on overall costs and energy balance.

Partnership fra terzo Settore e Istituzioni Locali nelle Politiche Family Friendly: Il "Distretto famiglia"

L’idea fondamentale da cui prende avvio la presente tesi di dottorato è che sia possibile parlare di una svolta nel modo di concettualizzare e implementare le politiche sociali, il cui fuoco diviene sempre più la costruzione di reti di partnership fra attori pubblici e privati, in cui una serie di soggetti sociali plurimi (stakeholders) attivano fra loro una riflessività relazionale. L’ipotesi generale della ricerca è che, dopo le politiche improntate a modelli statalisti e mercatisti, o un loro mix, nella politica sociale italiana emerga l’esigenza di una svolta riflessiva e relazionale, verso un modello societario, sussidiario e plurale, e che di fatto – specie a livello locale – stiano sorgendo molte iniziative in tal senso. Una delle idee più promettenti sembra essere la creazione di distretti sociali per far collaborare tra loro attori pubblici, privati e di Terzo settore al fine di creare forme innovative di servizi per la famiglia e la persona. La presente tesi si focalizza sul tentativo della Provincia di Trento di distrettualizzare le politiche per la famiglia. Tramite l’analisi del progetto “Trentino – Territorio Amico della Famiglia” e di una sua verticalizzazione, il Distretto Famiglia, si è studiato l’apporto delle partnership pubblico-privato nella formazione di strumenti innovativi di governance che possano determinare una svolta morfogenetica nell’elaborazione di politiche per la famiglia. Le conclusioni del lavoro, attraverso una comparazione tra esperienze territoriali, presentano la differenziazione delle partnership sociali, in base ad alcuni variabili (pluralità di attori, pluralità di risorse, shared project, capitale sociale, decision making, mutual action, logiche di lavoro relazionale, sussidiarietà). Le diverse modalità di gestione delle partnership (capacitante, professionale e generativa) sintetizzano i portati culturali, strutturali e personali coinvolti nelle singole costruzioni. Solo le partnership che interpretano il loro potenziale regolativo e promozionale secondo la riflessività relazionale tendono a generare beni comuni nel contesto sociale.

New eco-friendly polyesters from renewable resources

Nowadays the development of sustainable polymers, with convenient properties to substitute the traditional petroleum-based materials, is one of the major issues for material science. The utilization of renewable resources as feedstock for biopolyesters is a challenging target.The research work described in the present thesis is strictly connected to these urgent necessities and is focused mainly in finding new biopolymers, in particular biopolyesters, which are obtainable from biomass and characterized by a wide range of properties, in order to potentially substitute polyolefins and aromatic polyesters (for example, poly(ethylene terephthalate))

Logiche modali e logiche independence friendly

Analisi di logiche modali con quantificatori parzialmente ordinati.

A multi-regional view on aging societies accounting for the existence of non-tradable goods

This thesis assesses the question, whether accounting for non-tradable goods sectors in a calibrated Auerbach-Kotlikoff multi-regional overlapping-generations-model significantly affects this model’s results when simulating the economic impact of demographic change. Non-tradable goods constitute a major part of up to 80 percent of GDP of modern economies. At the same time, multi-regional overlapping-generations-models presented by literature on demographic change so far ignored their existence and counterfactually assumed perfect tradability between model regions. Moreover, this thesis introduces the assumption of an increasing preference share for non-tradable goods of old generations. This fact-based as-sumption is also not part of models in relevant literature. rnThese obvious simplifications of common models vis-à-vis reality notwithstanding, this thesis concludes that differences in results between a model featuring non-tradable goods and a common model with perfect tradability are very small. In other words, the common simplifi-cation of ignoring non-tradable goods is unlikely to lead to significant distortions in model results. rnIn order to ensure that differences in results between the ‘new’ model, featuring both non-tradable and tradable goods, and the common model solely reflect deviations due to the more realistic structure of the ‘new’ model, both models are calibrated to match exactly the same benchmark data and thus do not show deviations in their respective baseline steady states.rnA variation analysis performed in this thesis suggests that differences between the common model and a model with non-tradable goods can theoretically be large, but only if the bench-mark tradable goods sector is assumed to be unrealistically small.rnFinally, this thesis analyzes potential real exchange rate effects of demographic change, which could occur due to regional price differences of non-tradable goods. However, results show that shifts in real exchange rate based on these price differences are negligible.rn

Bex: un ambiente user-friendly per esplorare articoli scientifici e bibliografie

Un'applicazione web user-friendly di supporto ai ricercatori per l'esecuzione efficiente di specifici tasks di ricerca e analisi di articoli scientifici

Current state of musculoskeletal ultrasound training and implementation in Europe: results of a survey of experts and scientific societies

To document the current state of musculoskeletal US (MSUS) training and extent of implementation among rheumatologists in the member countries of EULAR.

Extremely Violent Societies: Mass Violence in the Twentieth Century World

In this groundbreaking book Christian Gerlach traces the social roots of the extraordinary processes of human destruction involved in mass violence throughout the twentieth century. He argues that terms such as 'genocide' and 'ethnic cleansing' are too narrow to explain the diverse motives and interests that cause violence to spread in varying forms and intensities. From killings and expulsions to enforced hunger, collective rape, strategic bombing, forced labour and imprisonment he explores what happened before, during, and after periods of widespread bloodshed in countries such as Armenia, Indonesia, Bangladesh, Nazi-occupied Greece and in anti-guerilla wars worldwide in order to highlight the crucial role of socio-economic pressures in the generation of group conflicts. By focussing on why so many different people participated in or supported mass violence, and why different groups were victimized, he offers us a new way of understanding one of the most disturbing phenomena of our times.