A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence

Polycomb-like proteins 1-3 (PCL1-3) are substoichiometric components of the Polycomb-repressive complex 2 (PRC2) that are essential for association of the complex with chromatin. However, it remains unclear why three proteins with such apparent functional redundancy exist in mammals. Here we characterize their divergent roles in both positively and negatively regulating cellular proliferation. We show that while PCL2 and PCL3 are E2F-regulated genes expressed in proliferating cells, PCL1 is a p53 target gene predominantly expressed in quiescent cells. Ectopic expression of any PCL protein recruits PRC2 to repress the INK4A gene; however, only PCL2 and PCL3 confer an INK4A-dependent proliferative advantage. Remarkably, PCL1 has evolved a PRC2- and chromatin-independent function to negatively regulate proliferation. We show that PCL1 binds to and stabilizes p53 to induce cellular quiescence. Moreover, depletion of PCL1 phenocopies the defects in maintaining cellular quiescence associated with p53 loss. This newly evolved function is achieved by the binding of the PCL1 N-terminal PHD domain to the C-terminal domain of p53 through two unique serine residues, which were acquired during recent vertebrate evolution. This study illustrates the functional bifurcation of PCL proteins, which act in both a chromatin-dependent and a chromatin-independent manner to regulate the INK4A and p53 pathways.

Smartphone and GPS technology for freeroaming dog population surveillance -a methodological study (Studio metodologico sull’applicazione di smartphone e tecnologia GPS alla sorveglianza delle popolazioni di cani vaganti)

Free-roaming dogs (FRD) represent a potential threat to the quality of life in cities from an ecological, social and public health point of view. One of the most urgent concerns is the role of uncontrolled dogs as reservoirs of infectious diseases transmittable to humans and, above all, rabies. An estimate of the FRD population size and characteristics in a given area is the first step for any relevant intervention programme. Direct count methods are still prominent because of their non-invasive approach, information technologies can support such methods facilitating data collection and allowing for a more efficient data handling. This paper presents a new framework for data collection using a topological algorithm implemented as ArcScript in ESRI® ArcGIS software, which allows for a random selection of the sampling areas. It also supplies a mobile phone application for Android® operating system devices which integrates Global Positioning System (GPS) and Google Maps™. The potential of such a framework was tested in 2 Italian regions. Coupling technological and innovative solutions associated with common counting methods facilitate data collection and transcription. It also paves the way to future applications, which could support dog population management systems.

Ferroelectric Vortices and Related Configurations

This chapter discusses that the theoretical studies, using both atomistic and phenomenological approaches, have made clear predictions about the existence and behaviour of ferroelectric (FE) vortices. Effective Hamiltonians can be implemented within both Monte Carlo (MC) and molecular dynamics (MD) simulations. In contrast to the effective Hamiltonian method, which is atomistic in nature, the phase field method employs a continuum approach, in which the polarization field is the order parameter. Properties of FE nanostructures are largely governed by the existence of a depolarization field, which is much stronger than the demagnetization field in magnetic nanosystems. The topological patterns seen in rare earth manganites are often referred to as vortices and yet this claim never seems to be explicitly justified. By inspection, the form of a vortex structure is such that there is a continuous rotation in the orientation of dipole vectors around the singularity at the centre of the vortex.

Bicontactual hypermaps

Esta tese dedica-se ao estudo de hipermapas regulares bicontactuais, hipermapas com a propriedade que cada hiperface contacta só com outras duas hiperfaces. Nos anos 70, S. Wilson classificou os mapas bicontactuais e, em 2003, Wilson e Breda d’Azevedo classificaram os hipermapas bicontactuais no caso não-orientável. Quando esta propriedade é transferida para hipermapas origina três tipos de bicontactualidade, atendendo ao modo como as duas hiperfaces aparecem à volta de uma hiperface fixa: edge-twin, vertextwin and alternate (dois deles são o dual um do outro). Um hipermapa topológico é um mergulho celular de um grafo conexo trivalente numa superfície compacta e conexa tal que as células são 3-coloridas. Ou de maneira mais simples, um hipermapa pode ser visto como um mapa bipartido. Um hipermapa orientado regular é um triplo ordenado consistindo num conjunto finito e dois geradores, que são permutações (involuções) do conjunto tal que o grupo gerado por eles, chamado o grupo de monodromia, actua regularmente no conjunto. Nesta tese, damos uma classificação de todos os hipermapas orientados regulares bicontactuais e, para completar, reclassificamos, usando o nosso método algébrico, os hipermapas não-orientáveis bicontactuais.

A study of singular integral operators with shift

Nesta tese, consideram-se operadores integrais singulares com a acção extra de um operador de deslocacamento de Carleman e com coeficientes em diferentes classes de funções essencialmente limitadas. Nomeadamente, funções contínuas por troços, funções quase-periódicas e funções possuíndo factorização generalizada. Nos casos dos operadores integrais singulares com deslocamento dado pelo operador de reflexão ou pelo operador de salto no círculo unitário complexo, obtêm-se critérios para a propriedade de Fredholm. Para os coeficientes contínuos, uma fórmula do índice de Fredholm é apresentada. Estes resultados são consequência das relações de equivalência explícitas entre aqueles operadores e alguns operadores adicionais, tais como o operador integral singular, operadores de Toeplitz e operadores de Toeplitz mais Hankel. Além disso, as relações de equivalência permitem-nos obter um critério de invertibilidade e fórmulas para os inversos laterais dos operadores iniciais com coeficientes factorizáveis. Adicionalmente, aplicamos técnicas de análise numérica, tais como métodos de colocação de polinómios, para o estudo da dimensão do núcleo dos dois tipos de operadores integrais singulares com coeficientes contínuos por troços. Esta abordagem permite também a computação do inverso no sentido Moore-Penrose dos operadores principais. Para operadores integrais singulares com operadores de deslocamento do tipo Carleman preservando a orientação e com funções contínuas como coeficientes, são obtidos limites superiores da dimensão do núcleo. Tal é implementado utilizando algumas estimativas e com a ajuda de relações (explícitas) de equivalência entre operadores. Focamos ainda a nossa atenção na resolução e nas soluções de uma classe de equações integrais singulares com deslocamento que não pode ser reduzida a um problema de valor de fronteira binomial. De forma a atingir os objectivos propostos, foram utilizadas projecções complementares e identidades entre operadores. Desta forma, as equações em estudo são associadas a sistemas de equações integrais singulares. Estes sistemas são depois analisados utilizando um problema de valor de fronteira de Riemann. Este procedimento tem como consequência a construção das soluções das equações iniciais a partir das soluções de problemas de valor de fronteira de Riemann. Motivados por uma grande diversidade de aplicações, estendemos a definição de operador integral de Cauchy para espaços de Lebesgue sobre grupos topológicos. Assim, são investigadas as condições de invertibilidade dos operadores integrais neste contexto.

Smart design of scaffolds obtained by biofabrication for tissue engineering applications

A engenharia de tecidos é um domínio tecnológico emergente em rápido desenvolvimento que se destina a produzir substitutos viáveis para a restauração, manutenção ou melhoria da função dos tecidos ou órgãos humanos. Uma das estratégias mais predominantes em engenharia de tecidos envolve crescimento celular sobre matrizes de suporte (scaffolds), biocompatíveis e biodegradáveis. Estas matrizes devem possuir não só elevadas propriedades mecânicas e vasculares, mas também uma elevada porosidade. Devido à incompatibilidade destes dois parâmetros, é necessário desenvolver estratégias de simulação de forma a obter estruturas optimizadas. A previsão real das propriedades mecânicas, vasculares e topológicas das matrizes de suporte, produzidas por técnicas de biofabricação, é muito importante para as diversas aplicações em engenharia de tecidos. A presente dissertação apresenta o estado da arte da engenharia de tecidos, bem como as técnicas de biofabricação envolvidas na produção de matrizes de suporte. Para o design optimizado de matrizes de suporte foi adoptada uma metodologia de design baseada tanto em métodos de elementos finitos para o cálculo do comportamento mecânico, vascular e as optimizações topológicas, como em métodos analíticos para a validação das simulações estruturais utilizando dados experimentais. Considerando que as matrizes de suporte são estruturas elementares do tipo LEGO, dois tipos de famílias foram consideradas, superfícies não periódicas e as superfícies triplas periódicas que descrevem superfícies naturais. Os objectivos principais desta dissertação são: i) avaliar as técnicas existentes de engenharia de tecidos; ii) avaliar as técnicas existentes de biofabricação para a produção de matrizes de suporte; iii) avaliar o desempenho e comportamento das matrizes de suporte; iv) implementar uma metodologia de design de matrizes de suporte em variáveis tais como a porosidade, geometria e comportamento mecânico e vascular por forma a auxiliar o processo de design; e por fim, v) validar experimentalmente a metodologia adoptada.

Machine learning methods for quantitative structure-property relationship modeling

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome

Thesis (Ph.D.)--University of Washington, 2014

Critical autopoiesis and the materiality of law

Autopoietic theory is increasingly seen as a candidate for a radical theory of law, both in relation to its theoretical credentials and its relevance in terms of new and emerging forms of law. An aspect of the theory that has remained less developed, however, is its material side, and more concretely the theory’s accommodation of bodies, space, objects and their claim to legal agency. The present article reads Luhmann’s theory of autopoietic systems in a radical and material manner, linking it on the one hand to current post-structural theorisations of law and society, and on the other hand extending its ambit to accommodate the influx of material considerations that have been working their way through various other disciplines. The latter comprises both a materialisation of the theory itself and ways of conceptualising the legal system as material through and through. This I do by further developing what I have called Critical Autopoiesis, namely an acentric, topological, post-ecological and posthuman understanding of Luhmann’s theory, that draws on Deleuzian thought, feminist theory, geography, non-representational theory, and new material and object-oriented ontologies. These are combined with some well-rehearsed autopoietic concepts, such as distinction, environment and boundaries; Luhmann’s earlier work on materiality continuum; more recent work on bodies and space; as well as his work on form and medium in relation to art. The article concludes with five suggestions for an understanding of what critical autopoietic materiality might mean for law.

Cappadocia: where Greek prepositions come to die

The Cappadocian variety of Ulaghátsh is unique among the Greek-speaking world in having lost the inherited preposition ‘se’. The innovation is found with both locative and allative uses and has af-ected both syntactic contexts in which ‘se’ was originally found, that is, as a simple preposition (1) and as the left-occurring member of circumpositions of the type ‘se’ + NP + spatial adverb (2). (1) a. tránse ci [to meidán] en ávʝa see.PST.3SG COMP ART.DEF.SG.ACC yard.SG.ACC COP.3 game.PL.NOM ‘he saw that in the yard is some game’ (Dawkins 1916: 348) b. ta erʝó da qardáʃa évɣan [to qonáq] ART.DEF.PL.NOM two ART.DEF.PL.NOM friend.PL.NOM ascend.PST.3PL ART.DEF.SG.ACC house.SG.ACC ‘the two friends went up to the house’ (Dawkins 1916: 354) (2) émi [ta qonáca mésa], kiríʃde [to ʝasdɯ́q píso] enter.PST.3SG ART.DEF.PL.NOM house.PL.ACC inside hide.PST.3SG. ART.DEF.SG.ACC cushion.SG.ACC behind ‘he went into the houses and hid behind the cushions’ (Dawkins 1916: 348) In this paper, we set out to provide (a) a diachronic account of the loss of ‘se’ in Asia Minor Greek, and (b) a synchronic analysis of its ramifications for the encoding of the semantic and grammatical functions it had prior to its loss. The diachronic development of ‘se’ is traced by comparing the Ulaghátsh data with those obtained from Cappadocian varieties that have neither lost it nor do they show signs of losing it and, crucially, also from varieties in which ‘se’ is in the process of being lost. The comparative analysis shows that the loss first became manifest in circumpositions in which ‘se’ was preposed to the complement to which in turn a wide range of adverbs expressing topological relations were postposed (émi sa qonáca mésa > émi ta qonáca mésa). This finding is accounted for in terms of Sinha and Kuteva’s (1995) distributed spatial semantics framework, which accepts that the elements involved in the constructions under investigation—the verb (émi), ‘se’ and the spatial adverb (mésa)—all contribute to the expression of the spatial relational meaning but with differences in weighting. Of the three, ‘eis’ made the most minimal contribution, the bulk of it being distributed over the verb and the adverb. This allowed for it to be optionally dropped from circumpositions, a stage attested in Phlo-tá Cappadocian and Silliot, and to be later completely abandoned, originally in allative and subsequently in locative contexts (earlier: évɣan so qonáq > évɣan to qonáq; later: so meidán en ávʝa > to meidán en ávʝa). The earlier loss in allative contexts is also dealt with in distributed semantics terms as verbs of motion such as έβγαν are semantically more loaded than vacuous verbs like the copula and therefore the preposition could be left out in the former context more easily than in the latter. The analysis also addresses the possibility that the loss of ‘se’ may ultimately originate in substandard forms of Medieval Greek, which according to Tachibana (1994) displayed SPATIAL ADVERB + NP constructions. Applying the semantic map model (Croft 2003, Haspelmath 2003), the synchronic analysis of the varieties that retain ‘se’ reveals that—like many other allative markers crosslinguistically—it displays a pattern of multifunctionality in expressing nine different functions (among others allative, locative, recipient, addressee, experiencer), which can be mapped against four domains, viz. the spatiotemporal, the social, the mental and the logicotextual (cf. Rice & Kabata 2007). In Ulaghátsh Cappadocian, none of these functions is overtly marked as such. In cases like (1), the intended spatial relational meaning is arrived at through the combination of the syntax and the inherent semantics of the verb and the zero-marked NP as well as from the context. In environments of the type exemplified by (2), the adverb contributes further to the correct interpretation. The analysis additionally shows that, despite the loss of ‘se’, Ulaghátsh patterns with all other Cappadocian varieties in one important aspect: Goal and Location are expressed similarly (by zero in Ulaghátsh, by ‘se’ in the other varieties) whereas Source is being kept distinct (expressed by ‘apó’ in all varieties). Goal-Location polysemy is very common across the world’s languages and, most crucially, prevails over other possible polysemies in the tripartite distinction Source—Location—Goal (Lestrade 2010, Nikitina 2009). Taking into account this empirical observation, our findings suggest that the reor-anisation of spatial systems can have a local effect—in our case the loss of a member of the prepositional paradigm—but will keep the original global picture intact, thus conforming to crosslinguistically robust tendencies.  References Croft, W. 2001. Radical Construction Grammar: Syntactic Theory in Typological Perspective. Oxford: Oxford University Press. Dawkins, R. M. 1916. Modern Greek in Asia Minor: A Study of the Dialects of Sílli, Cappadocia and Phárasa with Grammar, Texts, Translations and Glossary. Cambridge: Cambridge University Press. Haspelmath, M. 2003. The geometry of grammatical meaning: semantic maps and cross-linguistic comparison. In M. Tomasello (Ed.), The New Psychology of Language, Volume 2. New York: Erlbaum, 211–243. Lestrade, S. 2010. The Space of Case. Doctoral dissertation. Radboud University Nijmegen. Nikitina, T. 2009. Subcategorization pattern and lexical meaning of motion verbs: a study of the source/goal ambiguity. Linguistics 47, 1113–1141. Rice, S. & K. Kabata. 2007. Cross-linguistic grammaticalization patterns of the allative. Linguistic Typology 11, 451–514. Sinha, C. & T. Kuteva. 1995. Distributed spatial semantics. Nordic Journal of Linguistics 18:2, 167–199. Tachibana, T. 1994. Syntactic structure of spatial expressions in the “Late Byzantine Prose Alexander Romance”. Propylaia 6, 35–51.

EU Criminal Law and Enlargement

Since creation of the European Communities the number of Member States has gradually increased from the original six to current twenty-eight. Enlargement has become an EU’s flagship external policy, demonstrating the EU’s ability to shape its neighbourhood and to serve as a catalyst of deep and multilayered reforms. The consecutive seven enlargement rounds went in parallel with widespread internal developments, culminating with the creation of the European Union and, most recently, entry into force of the Treaty of Lisbon. As this volume demonstrates, EU criminal law has evolved considerably from its early days under the legal framework laid down by the Treaty of Maastricht to its current post-Lisbon shape. On 1 December 2014, that is with expiry of a five year transitional regime for the jurisdiction of the Court of Justice, Police and Judicial Co-operation in Criminal Matters became a fully fledged EU policy, governed largely by the same modus operandi as other areas of EU competence and with compulsory jurisdiction of the Court of Justice. As EU criminal law developed internally, so did its external dimension, including the role it plays in the enlargement policy. In case of the latter the expiry of the same transitional period has brought to an end a rather anomalous situation whereby the European Union had more enforcement tools before and after accession vis-à-vis its future/new Member States than it could employ against the old ones. This bifurcation, quite rightly, triggered a lot of discussions about double standards used by the European Union in its pre-accession policy. This is exacerbated by the fact that some of those standards are neither defined in EU law, nor pursued vis-à-vis the existing EU’s Member States. The aim of this chapter is to demonstrate that evolution with particular emphasis on the role of EU Criminal Law in the policy currently employed by the European Union vis-à-vis candidate and potential candidate countries of the Western Balkans and to Turkey. Arguably, together with political conditionality, it has become one of the pillars of the enlargement process and, as the examples of accession negotiations with Montenegro and Serbia prove, its role is likely to increase as rapprochement of other candidates and potential candidates progresses to the next stages.

On the DNA of eleven mammals

This paper studies the DNA code of eleven mammals from the perspective of fractional dynamics. The application of Fourier transform and power law trendlines leads to a categorical representation of species and chromosomes. The DNA information reveals long range memory characteristics.

Complex order biped rhythms

Animal locomotion is a complex process, involving the central pattern generators (neural networks, located in the spinal cord, that produce rhythmic patterns), the brainstem command systems, the steering and posture control systems and the top layer structures that decide which motor primitive is activated at a given time. Pinto and Golubitsky studied an integer CPG model for legs rhythms in bipeds. It is a four-coupled identical oscillators' network with dihedral symmetry. This paper considers a new complex order central pattern generator (CPG) model for locomotion in bipeds. A complex derivative Dα±jβ, with α, β ∈ ℜ+, j = √-1, is a generalization of the concept of an integer derivative, where α = 1, β = 0. Parameter regions where periodic solutions, identified with legs' rhythms in bipeds, occur, are analyzed. Also observed is the variation of the amplitude and period of periodic solutions with the complex order derivative.

Fractional central pattern generators for bipedal locomotion

Locomotion has been a major research issue in the last few years. Many models for the locomotion rhythms of quadrupeds, hexapods, bipeds and other animals have been proposed. This study has also been extended to the control of rhythmic movements of adaptive legged robots. In this paper, we consider a fractional version of a central pattern generator (CPG) model for locomotion in bipeds. A fractional derivative D α f(x), with α non-integer, is a generalization of the concept of an integer derivative, where α=1. The integer CPG model has been proposed by Golubitsky, Stewart, Buono and Collins, and studied later by Pinto and Golubitsky. It is a network of four coupled identical oscillators which has dihedral symmetry. We study parameter regions where periodic solutions, identified with legs’ rhythms in bipeds, occur, for 0<α≤1. We find that the amplitude and the period of the periodic solutions, identified with biped rhythms, increase as α varies from near 0 to values close to unity.

Positive radial solutions of the Dirichlet problem for the Minkowski-Curvature equation in a ball

We study the existence and multiplicity of positive radial solutions of the Dirichlet problem for the Minkowski-curvature equation { -div(del upsilon/root 1-vertical bar del upsilon vertical bar(2)) in B-R, upsilon=0 on partial derivative B-R,B- where B-R is a ball in R-N (N >= 2). According to the behaviour off = f (r, s) near s = 0, we prove the existence of either one, two or three positive solutions. All results are obtained by reduction to an equivalent non-singular one-dimensional problem, to which variational methods can be applied in a standard way.