Leveraging the Grid to Provide a Global Platform for Ubiquitous Computing Research

The requirement for distributed systems support for Ubicomp has led to the development of numerous platforms, each addressing a subset of the overall requirements of ubiquitous systems. In contrast, many other scientific disciplines have embraced the vision of a global distributed computing platform, i.e. the Grid. We believe that the Grid has the potential to evolve into an ideal platform for building ubiquitous computing applications. In this paper we explore in detail the areas of synergy between Grid computing and ubiquitous computing and highlight a series of research challenges in this space

The simplicity project: easing the burden of using complex and heterogeneous ICT devices and services

As of today, to exploit the variety of different "services", users need to configure each of their devices by using different procedures and need to explicitly select among heterogeneous access technologies and protocols. In addition to that, users are authenticated and charged by different means. The lack of implicit human computer interaction, context-awareness and standardisation places an enormous burden of complexity on the shoulders of the final users. The IST-Simplicity project aims at leveraging such problems by: i) automatically creating and customizing a user communication space; ii) adapting services to user terminal characteristics and to users preferences; iii) orchestrating network capabilities. The aim of this paper is to present the technical framework of the IST-Simplicity project. This paper is a thorough analysis and qualitative evaluation of the different technologies, standards and works presented in the literature related to the Simplicity system to be developed

Mapping the effect of defect-induced strain disorder on the Dirac states of topological insulators

We provide a detailed microscopic characterization of the influence of defects-induced disorder onto the Dirac spectrum of three dimensional topological insulators. By spatially resolved Landau-levels spectroscopy measurements, we reveal the existence of nanoscale fluctuations of both the Dirac point energy as well as of the Dirac-fermions velocity which is found to spatially change in opposite direction for electrons and holes, respectively. These results evidence a scenario which goes beyond the existing picture based on chemical potential fluctuations. The findings are consistently explained by considering the microscopic effects of local stain introduced by defects, which our model calculations show to effectively couple to topological states, reshaping their Dirac-like dispersion over a large energy range. In particular, our results indicate that the presence of microscopic spatially varying stain, inevitably present in crystals because of the random distribution of defects, effectively couple to topological states and should be carefully considered for correctly describing the effects of disorder

Human Bocavirus – Insights into a Newly Identified Respiratory Virus

Human Bocavirus (HBoV) was discovered in 2005 using a molecular virus screening technique. It is often found in respiratory samples and is a likely cause for respiratory diseases in children. HBoV is distributed worldwide and has been found not only in respiratory samples, but also in feces, urine and serum. HBoV infections are mostly found in young children and coinfections with other respiratory viruses are often found, exacerbating the efforts to link HBoV to specific symptoms. The purpose of this review is to give an overview of recent HBoV research, highlighting some recent findings

Over-pressurized bioreactors : application to microbial cell cultures

In industrial biotechnology, microbial cultures are exposed to different local pressures inside bioreactors. Depending on the microbial species and strains, the increased pressure may have detrimental or beneficial effects on cellular growth and product formation. In this review, the effects of increased air pressure on various microbial cultures growing in bioreactors under moderate total pressure conditions (maximum, 15 bar) will be discussed. Recent data illustrating the diversity of increased air pressure effects at different levels in microbial cells cultivation will be presented, with particular attention to the effects of oxygen and carbon dioxide partial pressures on cellular growth and product formation, and the concomitant effect of oxygen pressure on antioxidant cellular defense mechanisms.The authors thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Project "BioInd-Biotechnology and Bioengineering for improved Industrial and Agro-Food processes, REF. NORTE-07-0124-FEDER-000028," cofunded by the Programa Operacional Regional do Norte (ON.2-O Novo Norte), QREN, FEDER. A special aknowledgement is given to FCT for the support to the improvement of infrastructures awarded by the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462)

Over-pressurized bioreactors : application to microbial cell cultures

In industrial biotechnology, microbial cultures are exposed to different local pressures inside bioreactors. Depending on the microbial species and strains, the increased pressure may have detrimental or beneficial effects on cellular growth and product formation. In this review, the effects of increased air pressure on various microbial cultures growing in bioreactors under moderate total pressure conditions (maximum, 15 bar) will be discussed. Recent data illustrating the diversity of increased air pressure effects at different levels in microbial cells cultivation will be presented, with particular attention to the effects of oxygen and carbon dioxide partial pressures on cellular growth and product formation, and the concomitant effect of oxygen pressure on antioxidant cellular defense mechanisms.The authors thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Project "BioInd-Biotechnology and Bioengineering for improved Industrial and Agro-Food processes, REF. NORTE-07-0124-FEDER-000028," cofunded by the Programa Operacional Regional do Norte (ON.2-O Novo Norte), QREN, FEDER. A special aknowledgement is given to FCT for the support to the improvement of infrastructures awarded by the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462)

An Integrated Approach for Finding Overlooked Genes in Shigella

Background: The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs) and small open reading frames (sORFs). In order to improve genome annotation, we aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery. Methodology/Principal Findings: We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based methods to search for sRNAs, followed by RT-PCR and northern blots, to identify nine sRNAs in Shigella flexneri strain 301 (Sf301) and 256 regions containing possible sRNA genes. We found 29 candidate sORFs using bioinformatic prediction, array hybridization and RT-PCR verification. We experimentally validated 557 (57.9%) DOOR operon predictions in the chromosomes of Sf301 and 46 (76.7%) in virulence plasmid.We found 40 additional co-expressed gene pairs that were not predicted by DOOR. Conclusions/Significance: We provide an updated and comprehensive annotation of the Shigella genome. Our study increased the expected numbers of sORFs and sRNAs, which will impact on future functional genomics and proteomics studies. Our method can be used for large scale reannotation of sRNAs and sORFs in any microbe with a known genom

Is Promiscuity Associated with Enhanced Selection on MHC-DQα in Mice (genus Peromyscus)?

Reproductive behavior may play an important role in shaping selection on Major Histocompatibility Complex (MHC) genes. For example, the number of sexual partners that an individual has may affect exposure to sexually transmitted pathogens, with more partners leading to greater exposure and, hence, potentially greater selection for variation at MHC loci. To explore this hypothesis, we examined the strength of selection on exon 2 of the MHC-DQα locus in two species of Peromyscus. While the California mouse (P. californicus) is characterized by lifetime social and genetic monogamy, the deer mouse (P. maniculatus) is socially and genetically promiscuous; consistent with these differences in mating behavior, the diversity of bacteria present within the reproductive tracts of females is significantly greater for P. maniculatus. To test the prediction that more reproductive partners and exposure to a greater range of sexually transmitted pathogens are associated with enhanced diversifying selection on genes responsible for immune function, we compared patterns and levels of diversity at the Class II MHC-DQα locus in sympatric populations of P. maniculatus and P. californicus. Using likelihood based analyses, we show that selection is enhanced in the promiscuous P. maniculatus. This study is the first to compare the strength of selection in wild sympatric rodents with known differences in pathogen milieu

Comparative genomics reveals insights into avian genome evolution and adaptation

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits