Discovering Frequent Poly-Regions in DNA Sequences

The problem of discovering frequent arrangements of regions of high occurrence of one or more items of a given alphabet in a sequence is studied, and two efficient approaches are proposed to solve it. The first approach is entropy-based and uses an existing recursive segmentation technique to split the input sequence into a set of homogeneous segments. The key idea of the second approach is to use a set of sliding windows over the sequence. Each sliding window keeps a set of statistics of a sequence segment that mainly includes the number of occurrences of each item in that segment. Combining these statistics efficiently yields the complete set of regions of high occurrence of the items of the given alphabet. After identifying these regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a region). An efficient algorithm for mining frequent arrangements of temporal intervals on a single sequence is applied on the converted sequence to discover frequently occurring arrangements of these regions. The proposed algorithms are tested on various DNA sequences producing results with significant biological meaning.

Engineering of Vis-NIR Metamaterials towards Revolutionary Ultrasensitive and Versatile Plasmonic Biosensors

By enabling subwavelength light localization and strong electromagnetic field enhancement, plasmonic biosensors have opened up a new realm of possibilities for a broad range of chemical and biological sensing applications owing to their label-free and real-time attributes. Although significant progress has been made, many fundamental and practical challenges still remain to be addressed. For instance, the plasmonic biosensors are nonselective sensing platforms; they are not well-suited to provide information regarding conformation or chemical fingerprint of unknown biomolecules. Furthermore, tunability of the plasmonic resonance in visible frequency regime is still limited; this will prevent their efficient and reproducible exploitation in single-molecule sensitivity. Here, we show that by engineering geometry of plasmonic metamaterials,1 consisting of periodic arrays of artificial split-ring resonators (SRRs), the plasmonic resonance of metamaterials could be tuned to visible-near infrared regimes (Vis-NIR) such that it allows parallel acquisition of optical transmission and highly surface-enhanced Raman (SERS) spectra from large functionalized SRR arrays. The Au SRRs were designed in form of alphabet letters (U, V, S, H, Y) with various line width (from 80 to 30 nm). By tailoring their size and shape, plasmonic resonance wavelength of the SRRs could be actively tuned so that it gives the strongest SERS effect under given excitation energy and polarization for biological and organic molecules. On the other hand, the plasmonic tunability was also achieved for a given SRR pattern by tuning the laser wavelength to obtain the highest electromagnetic field enhancement. The geometry- and laser-tunable channels typically provide an electromagnetic field enhancement as high as 20 times. This will provide the basis of versatile and multichannel devices for identification of different conformational states of Guanine-rich DNA, detection of a cancer biomarker nucleolin, and femtomolar sensitivity detection of food and drink additives. These results show that the tunable Vis-IR metamaterials are very versatile biosensing platforms and suggest considerable promise in genomic research, disease diagnosis, and food safety analysis.

Molecular Medicine and Molecular Pathology for Haematologists:I. Gene Speak made Easy: An Overview of Genes and Gene Expression

Molecular Medicine and Molecular Pathology are integral parts of Haematology as we enter the new millennium. Their origins can be linked to fundamental developments in the basic sciences, particularly genetics, chemistry and biochemistry. The structure of DNA and the genetic code that it encrypts are the critical starting points to our understanding of these new disciplines. The genetic alphabet is a simple one, consisting of just 4 letters, buts its influence is crucial to human development and differentiation. The concept of a gene is not a new one but the Human Genome Project (a joint world-wide effort to characterise our entire genetic make-up) is providing an invaluable understanding of how genes function in normal cellular processes and pinpointing how disruption of these processes can lead to disease. Transcription and translation are the key events by which our genotype is converted to our phenotype (via a messenger RNA intermediate), producing the myriad proteins and enzymes which populate the cellular factory of our body. Unlike the bacterial or prokaryotic genome, the human genome contains a large amount of non coding DNA (less than 1% of our genome codes for proteins), and our genes are interrupted, with the coding regions or exons separated by non coding introns. Precise removal of the intronic material after transcription (though a process called splicing) is critical for efficient translation to occur. Incorrect splicing can lead to the generation of mutant proteins, which can have a dilaterious effect on the phenotype of the individual. Thus the 100,000-200,000 genes which are present in each cell in our body have a defined control mechanism permitting efficient and appropriate expression of proteins and enzymes and yet a single base change in just one of those genes can lead to diseases such as haemophilia or fanconis anaemia.

Specifying and analysing networks of processes in CSPt (or in search of associativity)

In proposing theories of how we should design and specify networks of processes it is necessary to show that the semantics of any language we use to write down the intended behaviours of a system has several qualities. First in that the meaning of what is written on the page reflects the intention of the designer; second that there are no unexpected behaviours that might arise in a specified system that are hidden from the unsuspecting specifier; and third that the intention for the design of the behaviour of a network of processes can be communicated clearly and intuitively to others. In order to achieve this we have developed a variant of CSP, called CSPt, designed to solve the problems of termination of parallel processes present in the original formulation of CSP. In CSPt we introduced three parallel operators, each with a different kind of termination semantics, which we call synchronous, asynchronous and race. These operators provide specifiers with an expressive and flexible tool kit to define the intended behaviour of a system in such a way that unexpected or unwanted behaviours are guaranteed not to take place. In this paper we extend out analysis of CSPt and introduce the notion of an alphabet diagram that illustrates the different categories of events that can arise in the parallel composition of processes. These alphabet diagrams are then used to analyse networks of three processes in parallel with the aim of identifying sufficient constraints to ensure associativity of their parallel composition. Having achieved this we then proceed to prove associativity laws for the three parallel operators of CSPt. Next, we illustrate how to design and construct a network of three processes that satisfy the associativity law, using the associativity theorem and alphabet diagrams. Finally, we outline how this could be achieved for more general networks of processes.

Successful termination in timed CSP

In proposing theories of how we should design and specify networks of processes it is necessary to show that the semantics of any language we use to write down the intended behaviours of a system has several qualities. First in that the meaning of what is written on the page reflects the intention of the designer; second that there are no unexpected behaviours that might arise in a specified system that are hidden from the unsuspecting specifier; and third that the intention for the design of the behaviour of a network of processes can be communicated clearly and intuitively to others. In order to achieve this we have developed a variant of CSP, called CSPt, designed to solve the problems of termination of parallel processes present in the original formulation of CSP. In CSPt we introduced three parallel operators, each with a different kind of termination semantics, which we call synchronous, asynchronous and race. These operators provide specifiers with an expressive and flexible tool kit to define the intended behaviour of a system in such a way that unexpected or unwanted behaviours are guaranteed not to take place. In this paper we extend out analysis of CSPt and introduce the notion of an alphabet diagram that illustrates the different categories of events that can arise in the parallel composition of processes. These alphabet diagrams are then used to analyse networks of three processes in parallel with the aim of identifying sufficient constraints to ensure associativity of their parallel composition. Having achieved this we then proceed to prove associativity laws for the three parallel operators of CSPt. Next, we illustrate how to design and construct a network of three processes that satisfy the associativity law, using the associativity theorem and alphabet diagrams. Finally, we outline how this could be achieved for more general networks of processes.

Fractional dynamics in DNA

This paper addresses the DNA code analysis in the perspective of dynamics and fractional calculus. Several mathematical tools are selected to establish a quantitative method without distorting the alphabet represented by the sequence of DNA bases. The association of Gray code, Fourier transform and fractional calculus leads to a categorical representation of species and chromosomes.

Analysis and visualization of chromosome information

This paper analyzes the DNA code of several species in the perspective of information content. For that purpose several concepts and mathematical tools are selected towards establishing a quantitative method without a priori distorting the alphabet represented by the sequence of DNA bases. The synergies of associating Gray code, histogram characterization and multidimensional scaling visualization lead to a collection of plots with a categorical representation of species and chromosomes.

The rebirth of an old language: issues of gender equality in Kazakhsstan

The existing language situation in Kazakhstan, while peaceful, is not without some tension. We propose to analyze here some questions we consider relevant in the frame of cultural globalization and gender equality, such as: free from Russian imperialism, could Kazakhstan become an easy prey of Turkey’s “imperialist dream”? Could these traditionally Muslim people be soon facing the end of religious tolerance and gender equality, becoming this new old language an easy instrument for the infiltration in the country of fundamentalism (it has already crossed the boarders of Uzbekistan), leading to a gradual deterioration of its rich multicultural relations? The present structure of the language is still very fragile: there are three main dialects and many academics defend the re-introduction of the Latin alphabet, thus enlarging the possibility of cultural “contamination” by making the transmission of fundamentalist ideas still easier through neighbour countries like Azerbaijan, Uzbekistan and Turkmenistan (their languages belong to the same sub-group of Common Turkic), where the Latin alphabet is already in use, and where the ground for such ideas shown itself very fruitful.

Laboratório de criação a partir de Macbeth de William Shakespeare: relatório de estágio

Relatório de Estágio submetido à Escola Superior de Teatro e Cinema para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Teatro - especialização em Encenação.

Papias, Vocabularium.

Abbaye Saint-Maur-des-Fossés ; cf. B. de Montfaucon, Bibliotheca bibliothecarum, II, 1739, p.1141-1143 : "73. 1095. Dictionarium amplissimum". Ex-libris : F. 1 : "Sti Germani a Pratis". Paris.

« Extraicts et mémoires concernans l'Ordre du Sainct-Esprit ».

Contient : « Extraict des statuts de l'Ordre du Sainct-Esprit, rédigé suivant l'ordre de l'alphabet » ; « Extraicts et copies des Registres de l'Ordre du Sainct-Esprit » ; « Noms de tous les officiers de l'Ordre qui ont exercé les charges, depuis la création dudict Ordre jusques à présent, 1662 » ; « Enregistrement de tout ce qui a concerné la promotion des commandeurs de l'Ordre du Sainct-Esprit, faicte le premier janvier 1662... » ; « Table alphabétique des extraicts et copies des Registres de l'Ordre du Sainct-Esprit » [cf. f. 21] ; « Lettre du maréchal de Fabert... au Roy, refusant la qualité de chevallier de l'Ordre de Sa Majesté », décembre 1661 ; « Discours sur les contraventions aux statuts de l'Ordre du Saint Esprit, faites par les officiers dudit Ordre. Ensemble sur la protestation du sieur marquis de Sourdis, chevalier de l'Ordre du S. Esprit, pour tous les chevaliers, signifiée ausdits officiers le deuxiesme janvier mil six cens cinquante sept », in-4°, impr ; « Responce à l'escrit publié contre les grâces et les priviléges accordez par nos rois Très-chrestiens aux officiers de leurs Ordres », in-4°, impr

« Les oeuvres de CHRISTOPHLE, parisien, très exsellant philosophe, corrigées de toute superfluité, traduite[s] d'italien en françoys, au mois de janvier 1584, par EA. D. M. ».

Contient : « Medul[l]a artis » ; « La Pierre végétable de Christophle, parisien, comme elle se contient dans son Alphabet » ; « Icy commence la Sommette du très excellant Christophle, parisien, de la composition de la grande pierre des philosophes », traité divisé en deux parties principales, dont la première comprend 17 chapitres, cotés de 7 à 23, et suivi (fol. 67 v°) de l' « Alphabet de la présente Sommette » ; Traité intitulé « Violete », en deux parties, suivi (fol. 99 v°) de l'« Alphabet de nostre susdite Violete » ; « Lucidaire, ou Somme majeur de l'art transmutatoire des corps des métaulx », en deux parties principales, suivi (fol. 216) de l'« Alp[h]abet dudict Lucidaire » ; Traité intitulé « La Pratique de nostre oeuvre », traité à la suite duquel se lisent les dates 1466 et 1476 ; « L'extraction et exubération de la très excellente quinte essence de l'estoille de la mer antienne » ; On a ajouté, d'une autre main, un « Abbrégé des euvres practicales [de] Christofle, parisien » ; Notes diverses d'un des possesseurs du volume, parmi lesquelles on remarque : « Monsieur Bongard [Jacques Bongars ?] est honest home et de mes bons amys ; Dieu le vueille conserver et tous les ciens par sa grâce et miséricorde infinie »

Recueil sur l'Alchimie, en vers et en prose ; traités ou poèmes de RAYMOND LULLE, de Jean DE LA FONTAINE, de Nicolas FLAMEL, de JEAN DE MEUNG, de Christofle DE GAMON.

Contient : « Dictionnaire des mots et termes plus usitez et cachez en l'art spagirique, desquels les philosophes chimiques ont accoutumé de se servir, suivant les lettres de l'alphabet : Acetum philosophorum- » ; inachevé ; « Recueil de plusieurs secretz et pièces curieuses, exactement recherché ; le tout aprouvé pour estre bon et avoir esté esprouvé ; faict par moy, G. D. R., à Paris, ce 30e juillet 1666 » ; Recettes diverses ; « Le débat et question sur la grande oeuvre, entre Aaron et Marie la prophétesse » ; « Le Vade mecum, ou abrégé de l'art chimique, touchant la transmutation des mestaux et vraye pierre des philosophes, extraict des oeuvres du très docte et très vénérable RAYMOND LULLE, traduict fidellement du latin en françois, en faveur des amateurs de la philosophie hermétique... Le livre de l'art compendieuse de Raymond Lulle, qu'il a nommé Vade mecum : La teinture du feu est la plus excellente... » ; l'ouvrage ici traduit est celui qui est imprimé dans la Bibliotheca chemica curiosa de J.-J. Manget, t. I, pp. 849-852, sous le titre : Raymundi Lullii liber Artis compendiosae, quem Vade mecum nuncupavit ; n° CXI de la notice de l'Histoire littéraire de la France, t. XXIX, p. 280 ; « Claviculles de RAYMOND LULLE ; Raymondi Lullii clavicula. Chers enfans, qui voulez estre de nostre doctrine... ; et pour ce que sans ce petit livre et clavicule... » ; traduction et extraits, avec de notables différences, de l'ouvrage imprimé dans la Bibliotheca chemica curiosa de J.-J. Manget, t. I, pp. 872-875, sous le titre : Clavicula Raymundi Lullii..., quae et Apertorium dicitur ; Hist. littér., ibid., p. 284, n° CXVII ; Traités d'alchimie, en vers, probablement copie du recueil publié à Paris, en 1561, sous le titre : De la transformation métallique, trois anciens traités en rithme françoise, et comprenant : La Fontaine des amoureux de science, par Jean DE LA FONTAINE, de Valenciennes (fol. 106), — le Sommaire philosophique, de Nicolas FLAMEL (fol. 117), — et les Remontrances de Nature à l'alchimiste errant, par JEAN DE MEUNG (fol. 120 v°) ; « Du traité de Terra terrarum » ; « Christofle DE GAMON à un singulier » ; poème de C. de Gamon sur l'alchimie, connu sous le titre de « Trésor des Trésors », avec partie du commentaire