Delegation, Arbitration and High-Level Service Discovery as Key Elements of a Software Infrastructure for Pervasive Computing

The dream of pervasive computing is slowly becoming a reality. A number of projects around the world are constantly contributing ideas and solutions that are bound to change the way we interact with our environments and with one another. An essential component of the future is a software infrastructure that is capable of supporting interactions on scales ranging from a single physical space to intercontinental collaborations. Such infrastructure must help applications adapt to very diverse environments and must protect people's privacy and respect their personal preferences. In this paper we indicate a number of limitations present in the software infrastructures proposed so far (including our previous work). We then describe the framework for building an infrastructure that satisfies the abovementioned criteria. This framework hinges on the concepts of delegation, arbitration and high-level service discovery. Components of our own implementation of such an infrastructure are presented.

Analysis of the elements of catabolite repression in Clostridium acetobutylicum.

The ptsH gene, encoding the phosphotransferase protein HPr, from Clostridium acetobutylicum ATCC 824 was identified from the genome sequence, cloned and shown to complement a ptsH mutant of Escherichia coli. The deduced protein sequence shares significant homology with HPr proteins from other low-GC gram-positive bacteria, although the highly conserved sequence surrounding the Ser-46 phosphorylation site is not well preserved in the clostridial protein. Nevertheless, the HPr was phosphorylated in an ATP-dependent manner in cell-free extracts of C. acetobutylicum. Furthermore, purified His-tagged HPr from Bacillus subtilis was also a substrate for the clostridial HPr kinase/phosphorylase. This phosphorylation reaction is a key step in the mechanism of carbon catabolite repression proposed to operate in B. subtilis and other low-GC gram-positive bacteria. Putative genes encoding the HPr kinase/phosphorylase and the other element of this model, namely the catabolite control protein CcpA, were identified from the C. acetobutylicum genome sequence, suggesting that a similar mechanism of carbon catabolite repression may operate in this industrially important organism.

Determinação de cádmio e chumbo em brinquedos para crianças com idade inferior a 3 anos

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

The brand-orientated play-community: toxic play in the marketplace

This ethnographic study makes a number of original contributions to the consumer identity projects and the marketplace cultures dimensions of consumer culture theory research. This study introduces the notion of the brand-orientated play-community, a novel consumption community form, which displays, as locus, a desire to play. This contributes to our understanding of the fluid relationship between subcultures of consumption, consumer tribes, and brand community. It was found that the brand-orientated play-community’s prime celebration, conceptualised as the ‘branded carnival’, displays characteristics of the archetypal carnival. The community access carnivalistic life and a world-upside-down ethos via the use and misuse of marketplace resources. The branded carnival is further supported by the community’s enactment of ‘toxic play’, which entails abnormal alcohol consumption, black market illegal resources, edgework activities, hegemonic masculinity and upsetting the public. This play-community is discussed in terms of a hyper-masculine playpen, as the play enacted has a direct relationship with the enactment of strong masculine roles. It was found that male play-ground members enact the extremes of contrasting masculine roles as a means to subvert the calculated and sedate ‘man-of-action-hero’ synthesis. Carnivals are unisex, and hence, women have begun entering the play-ground. Female members have successfully renegotiated their role within the community, from playthings to players – they have achieved player equality, which within the liminoid zone is more powerful than gender equality. However, while toxic play is essential to the maintenance of collective identity within the culture so too is the more serious form of play: the toxic sport of professional beer pong. The author conceptualises beer pong as a ‘toxic sport’, as it displays the contradictory play foundations of agon and corrupt ilinx: this is understood as a milestone step in the emergence of the postmodern sport era, in which spontaneity and the carnivalesque will dominate.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Four-decade responses of soil trace elements to an aggrading old-field forest: B, Mn, Zn, Cu, and Fe.

In the ancient and acidic Ultisol soils of the Southern Piedmont, USA, we studied changes in trace element biogeochemistry over four decades, a period during which formerly cultivated cotton fields were planted with pine seedlings that grew into mature forest stands. In 16 permanent plots, we estimated 40-year accumulations of trace elements in forest biomass and O horizons (between 1957 and 1997), and changes in bioavailable soil fractions indexed by extractions of 0.05 mol/L HCl and 0.2 mol/L acid ammonium oxalate (AAO). Element accumulations in 40-year tree biomass plus O horizons totaled 0.9, 2.9, 4.8, 49.6, and 501.3 kg/ha for Cu, B, Zn, Mn, and Fe, respectively. In response to this forest development, samples of the upper 0.6-m of mineral soil archived in 1962 and 1997 followed one of three patterns. (1) Extractable B and Mn were significantly depleted, by -4.1 and -57.7 kg/ha with AAO, depletions comparable to accumulations in biomass plus O horizons, 2.9 and 49.6 kg/ha, respectively. Tree uptake of B and Mn from mineral soil greatly outpaced resupplies from atmospheric deposition, mineral weathering, and deep-root uptake. (2) Extractable Zn and Cu changed little during forest growth, indicating that nutrient resupplies kept pace with accumulations by the aggrading forest. (3) Oxalate-extractable Fe increased substantially during forest growth, by 275.8 kg/ha, about 10-fold more than accumulations in tree biomass (28.7 kg/ha). The large increases in AAO-extractable Fe in surficial 0.35-m mineral soils were accompanied by substantial accretions of Fe in the forest's O horizon, by 473 kg/ha, amounts that dwarfed inputs via litterfall and canopy throughfall, indicating that forest Fe cycling is qualitatively different from that of other macro- and micronutrients. Bioturbation of surficial forest soil layers cannot account for these fractions and transformations of Fe, and we hypothesize that the secondary forest's large inputs of organic additions over four decades has fundamentally altered soil Fe oxides, potentially altering the bioavailability and retention of macro- and micronutrients, contaminants, and organic matter itself. The wide range of responses among the ecosystem's trace elements illustrates the great dynamics of the soil system over time scales of decades.

VIRTUOSIC ELEMENTS IN THE COLLABORATIVE PIANIST’S REPERTOIRE: SELECTED SOLO, VOCAL, AND CHAMBER WORKS OF RACHMANINOFF AND RAVEL

This dissertation project explores some of the technical and musical challenges that face pianists in a collaborative role—specifically, those challenges that may be considered virtuosic in nature. The material was chosen from the works of Rachmaninoff and Ravel because of the technically and musically demanding yet idiomatic piano writing. This virtuosic piano writing also extends into the collaborative repertoire. The pieces were also chosen to demonstrate these virtuosic elements in a wide variety of settings. Solo piano pieces were chosen to provide a point of departure, and the programmed works ranged from vocal to two-piano, to sonatas and a piano trio. The recitals were arranged to demonstrate as much contrast as possible, while being grouped by composer. The first recital was performed on April 24, 2009. This recital featured five songs of Rachmaninoff, as well as three solo piano preludes and his Suite No. 2 for two pianos. The second recital occurred on November 16, 2010. This recital featured the music of both Rachmaninoff and Ravel, as well as a short lecture introducing the solo work “Ondine” from Gaspard de la nuit by Ravel. Following the lecture were the Cinq mélodies populaires grecques and the program closed with the substantial Rachmaninoff Sonata for Cello and Piano. The final program was given on October 10, 2011. This recital featured the music of Ravel, and it included his Sonata for Violin and Piano, the Debussy Nocturnes transcribed for two pianos by Ravel, and the Piano Trio. The inclusion of a transcription of a work by another composer highlights Ravel’s particular style of writing for the piano. All of these recitals were performed at the Gildenhorn Recital Hall in the Clarice Smith Performing Arts Center at the University of Maryland. The recitals are recorded on compact discs, which can be found in the Digital Repository at the University of Maryland (DRUM).

FOLK ELEMENTS IN TWENTIETH-CENTURY HUNGARIAN MUSIC

At the beginning of the twentieth century, composers Béla Bartók and Zoltán Kodály collected thousands of folksongs from the rural regions of Hungary. In an effort to preserve a part of their culture that they feared would be lost, they not only transcribed and catalogued these folksongs, but also incorporated the folk traditions they encountered into their own compositional style. This dissertation deals with violin music written by Bartók, Kodály and their Hungarian contemporaries that have in common the use of rhythms, modes, melodies, figurations and playing techniques sourced in folk traditions. The use of the Hungarian folk idiom in classical music was not exclusive to the twentieth century. From the late eighteenth century until the first decades of the twentieth century, composers utilized aspects of a popular eighteenth-century form of Hungarian folk music called verbunkos. What makes the use of folk music unique in the twentieth century is that, thanks to the work of Bartók and Kodály, composers found inspiration in the more authentic “peasant music.” Unlike the popular, urban verbunkos music, peasant music was the product of the more secluded village-music tradition, largely untouched by the influences of city life. In addition to stimulating a new focus on peasant music, Bartók and Kodály fully assimilated the folk idiom into their compositional toolkits, creating a new style of folk-inspired art music that influenced a generation of Hungarian composers. The new style included characteristic elements of both peasant music and the verbunkos tradition, such as ancient modes and scales, accompanimental and melodic rhythmic patterns, ornamentation, and phrase structures sourced in folk song. To demonstrate the implementation of the folk idiom by twentieth-century Hungarian composers, three recital programs were given at the University of Maryland that included works by Béla Bartók, Sándor Veress, Leo Weiner, Zoltán Kodály, Ernő Dohnányi, Zoltán Székely and György Kurtág. The works can be divided into two main categories: settings or transcriptions of folk material (e.g. Bartók’s Hungarian Folksongs) and compositions using classical forms that include the Hungarian folk idiom (e.g. Bartók’s Contrasts). Recital collaborators include Li-Tan Hsu, Evelyn Elsing, Elizabeth Brown, Shelby Sender and Samantha Angelo.

Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.

Conditions that impair protein folding in the Gram-negative bacterial envelope cause stress. The destabilizing effects of stress in this compartment are recognized and countered by a number of signal transduction mechanisms. Data presented here reveal another facet of the complex bacterial stress response, release of outer membrane vesicles. Native vesicles are composed of outer membrane and periplasmic material, and they are released from the bacterial surface without loss of membrane integrity. Here we demonstrate that the quantity of vesicle release correlates directly with the level of protein accumulation in the cell envelope. Accumulation of material occurs under stress, and is exacerbated upon impairment of the normal housekeeping and stress-responsive mechanisms of the cell. Mutations that cause increased vesiculation enhance bacterial survival upon challenge with stressing agents or accumulation of toxic misfolded proteins. Preferential packaging of a misfolded protein mimic into vesicles for removal indicates that the vesiculation process can act to selectively eliminate unwanted material. Our results demonstrate that production of bacterial outer membrane vesicles is a fully independent, general envelope stress response. In addition to identifying a novel mechanism for alleviating stress, this work provides physiological relevance for vesicle production as a protective mechanism.