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Re-Scaling the Socio-Ecological Italian Conflicts: Marginality as Arena of Practices  [PDF]
Alessandro Boldo, Raffaella Freschi
Open Journal of Social Sciences (JSS) , 2014, DOI: 10.4236/jss.2014.211022
Abstract: The progressive raising of socio-ecological conflicts in Italy and the ordinary abuse of “emergency regimes” are progressively contributing to the fragmentation of public sphere. In Italy, “territorial public action” has long since abandoned indeed the ability to arrange the goods according to the model of the Nation State and Welfare State: recent cases like ILVA in Taranto, the earthquake in L’Aquila, and the improper management of the “environmental regimes” testifying the growing of regional conflicts around distribution of bads and production of risks. Abusing of emergency regimes is becoming both a structural constraints and a strategy for Italian policies, forcing institutional rationality to set up umbrella concept—sustainable development for instance—, a body of international Law in its own right, but de facto proceed intentionally avoiding implementation processes, broadening space-temporal misfit, favoring negative cascade effects even on democracy spaces. Moreover, the vertical shift of political authority produces an enforcement of functional differentiations reducing the policy efforts for a multisectorial and multistakeholder approach, the occasions of citizenship and inclusion of public policies, enhancing on the opposite “territorial conflict” in collective resistance. The aim is not to test the validity of the best technique to solve territorial conflicts. Rather it is to show the right path of a counter-apparatus and the role of polycentric perspectives and micro-territorial practices enhancing cognitive processes on territorial policies and breaking up the organizational constraints of “emergentism”. Using small case studies stands out the role of marginality as “creative approaches” that increase the governance (and government) effectiveness of public action, turning on the interstices that link different functional domains. Those capabilities are not usual to public action itself, belonging rather to community of practices. We name these “caring practices”, able to foster opportunity to de-structuring consolidated bodies of knowledge and set an unusual interaction processes together with the institutions. These practices do not re-balance the conflicts, but are able to overturn territorial conflicts in a new “codex” of learning opportunities, helping to set up renewed political spaces widening the intensity of citizenship and generating territorial innovation.
A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment
Valerio Freschi and Alessandro Bogliolo
Evolutionary Bioinformatics , 2012, DOI: 10.4137/EBO.S9131
Abstract: In spite of the recognized importance of tandem duplications in genome evolution, commonly adopted sequence comparison algorithms do not take into account complex mutation events involving more than one residue at the time, since they are not compliant with the underlying assumption of statistical independence of adjacent residues. As a consequence, the presence of tandem repeats in sequences under comparison may impair the biological significance of the resulting alignment. Although solutions have been proposed, repeat-aware sequence alignment is still considered to be an open problem and new efficient and effective methods have been advocated. The present paper describes an alternative lossy compression scheme for genomic sequences which iteratively collapses repeats of increasing length. The resulting approximate representations do not contain tandem duplications, while retaining enough information for making their comparison even more significant than the edit distance between the original sequences. This allows us to exploit traditional alignment algorithms directly on the compressed sequences. Results confirm the validity of the proposed approach for the problem of duplication-aware sequence alignment.
As percep es docentes sobre a dimens o metodológica no processo ensino-aprendizagem
Márcio Freschi
Práxis Educativa , 2008,
Abstract: This article analyses the reports of Science and Maths’ teachers, who were students on a Master’s degree course in Sciences and Mathematics Education. The research aims at identifying the principles which underpin the pedagogic work of the teachers involved in the research. In order to identify these principles, an analysis was made of the texts written by the teachers answering questions related to their pedagogic practices. Among the several conclusions, the paper emphasises that it is necessary to diversify methodological procedures in the classroom, contextualizing the content, and departing from the students’ previous knowledge, aiming to guarantee them the development of more complex knowledge which contributes to the formation of critical citizens.
A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment
Valerio Freschi,Alessandro Bogliolo
Evolutionary Bioinformatics , 2012,
Abstract:
A Monte Carlo Method for Assessing the Quality of Duplication-Aware Alignment Algorithms
Valerio Freschi,Alessandro Bogliolo
Evolutionary Bioinformatics , 2011,
Abstract:
Where Do Phosphosites Come from and Where Do They Go after Gene Duplication?
Guillaume Diss,Luca Freschi,Christian R Landry
International Journal of Evolutionary Biology , 2012, DOI: 10.1155/2012/843167
Abstract: Gene duplication followed by divergence is an important mechanism that leads to molecular innovation. Divergence of paralogous genes can be achieved at functional and regulatory levels. Whereas regulatory divergence at the transcriptional level is well documented, little is known about divergence of posttranslational modifications (PTMs). Protein phosphorylation, one of the most important PTMs, has recently been shown to be an important determinant of the retention of paralogous genes. Here we test whether gains and losses of phosphorylated amino acids after gene duplication may specifically modify the regulation of these duplicated proteins. We show that when phosphosites are lost in one paralog, transitions from phosphorylated serines and threonines are significantly biased toward negatively charged amino acids, which can mimic their phosphorylated status in a constitutive manner. Our analyses support the hypothesis that divergence between paralogs can be generated by a loss of the posttranslational regulatory control on a function rather than by the complete loss of the function itself. Surprisingly, these favoured transitions cannot be reached by single mutational steps, which suggests that the function of a phosphosite needs to be completely abolished before it is restored through substitution by these phosphomimetic residues. We conclude by discussing how gene duplication could facilitate the transitions between phosphorylated and phosphomimetic amino acids. 1. Introduction Gene duplication is one of the most prominent mechanisms by which organisms acquire new functions [1]. Spectacular examples of such gains of function resulting from gene duplications are the evolution of trichromatic vision in primates [2], the evolution of human beta-globin genes that are involved in the oxygen transport at different developmental stages [3] as well as the expansion of the family of immunoglobulins and other immunity-related genes that shaped the vertebrate immune system [4, 5]. Because of the central role of gene duplication in evolution, there has been a profound interest for a better understanding of how these new functions evolve at the molecular level [6], for determining at what rate gene duplication occurs [7–9] and for testing whether the retention of paralogous genes necessarily requires the evolution of new functions [6, 10, 11]. One of the most important challenges has been to determine mechanistically how specific mutations translate into new functions, as establishing sequence-function relationships remains a difficult task [12]. After a gene
Unexpected Hypertensive Pneumothorax after Digestive Upper Endoscopy: A Case Report  [PDF]
Giovanni Zagli, Rosario Spina, Stefano Batacchi, Giancarlo Freschi, Manlio Acquafresca, Antonio Taddei, Adriano Peris
Open Journal of Anesthesiology (OJAnes) , 2012, DOI: 10.4236/ojanes.2012.24041
Abstract: We report an unexpected massive left pneumothorax at the end of a digestive upper endoscopy without evidences of perforation or airway over-pressure. The possible air passage through a diaphragmatic failing is discussed.
Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes
Luca Freschi,Mazid Osseni,Christian R. Landry
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004062
Abstract: Protein phosphorylation is a key mechanism to regulate protein functions. However, the contribution of this protein modification to species divergence is still largely unknown. Here, we studied the evolution of mammalian phosphoregulation by comparing the human and mouse phosphoproteomes. We found that 84% of the positions that are phosphorylated in one species or the other are conserved at the residue level. Twenty percent of these conserved sites are phosphorylated in both species. This proportion is 2.5 times more than expected by chance alone, suggesting that purifying selection is preserving phosphoregulation. However, we show that the majority of the sites that are conserved at the residue level are differentially phosphorylated between species. These sites likely result from false-negative identifications due to incomplete experimental coverage, false-positive identifications and non-functional sites. In addition, our results suggest that at least 5% of them are likely to be true differentially phosphorylated sites and may thus contribute to the divergence in phosphorylation networks between mouse and humans and this, despite residue conservation between orthologous proteins. We also showed that evolutionary turnover of phosphosites at adjacent positions (in a distance range of up to 40 amino acids) in human or mouse leads to an over estimation of the divergence in phosphoregulation between these two species. These sites tend to be phosphorylated by the same kinases, supporting the hypothesis that they are functionally redundant. Our results support the hypothesis that the evolutionary turnover of phosphorylation sites contributes to the divergence in phosphorylation profiles while preserving phosphoregulation. Overall, our study provides advanced analyses of mammalian phosphoproteomes and a framework for the study of their contribution to phenotypic evolution.
Models for Master-Slave Clock Distribution Networks with Third-Order Phase-Locked Loops
José Roberto Castilho Piqueira,Marcela de Carvalho Freschi
Mathematical Problems in Engineering , 2007, DOI: 10.1155/2007/18609
Abstract: The purpose of this work is to study the processing and transmission of clock signals in networks of geographically distributed nodes, in order to derive conditions for frequency and phase synchronization between the nodes. The focus is on the master-slave architecture, which presents a priority scheme of clock distribution. One-way master-slave (OWMS ) and two-way master-slave (TWMS) chains are studied, considering that the slave nodes are third-order phase-locked loops (PLLs). Third-order PLLs are chosen to improve the transient response but, if their parameters are not well adjusted, stability problems and chaotic behaviors appear, restricting the lock-in range of the network. Lock-in range for third-order PLLs with Sallen-Key filter is determined and it is verified whether this range is reduced when the PLLs are connected to a network. Numerical experiments show how chain size changes the lock-in ranges and the acquisition times.
Modulators of arginine metabolism support cancer immunosurveillance
Giusy Capuano, Nicolò Rigamonti, Matteo Grioni, Massimo Freschi, Matteo Bellone
BMC Immunology , 2009, DOI: 10.1186/1471-2172-10-1
Abstract: We report here that MDSC accumulate in the spleen and blood of mice irrespective of the mouse and tumor model used. Treatment of tumor-bearing mice with either the phosphodiesterase-5 inhibitor sildenafil or the nitric-oxide synthase (NOS) inhibitor L-NAME significantly restrained tumor growth and expanded the tumor-specific immune response.Our data emphasize the role of MDSC in modulating the endogenous tumor-specific immune response and underline the anti-neoplastic therapeutic potential of arginine metabolism modulators.An established tumor adopts several strategies to escape immunosurveillance and this complex phenomenon results in generation of a site of acquired immune privilege [1]. Over time, local suppression spreads systemically, thereby weakening immunological barriers that might protect against tumor metastasis. Tumor-specific suppression might explain why even immunotherapies that succeed in inducing systemic immune response are rarely of clinical effect on tumors.As reviewed in [2], impairment in tumor antigen expression or its processing and presentation by both tumor cells and antigen presenting cells (APC), release of immunouppressive cytokines and prostaglandins as well as pro-apoptotic mechanisms may directly and/or indirectly impair T cell function while favoring tumor cell growth. Finally, tumor cells may promote development and recruitment of regulatory T cells (Treg) and myeloid derived suppressor cells (MDSC). CD4+CD25+ Treg in particular, represent an essential mechanism of peripheral tolerance to self antigens [3]. They selectively express Foxp3, a forkhead/winged helix transcription factor that controls master genes in Treg development/function [3]. Several neoplasms associate with CD4+CD25+ Treg accumulation in the blood and/or in tumors, and this may inversely correlate with patients' survival [4].MDSC are a heterogeneous population of cells of myeloid origin [5], and include immature macrophages, granulocytes, dendritic cells (DC) and o
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