Ex vivo analysis of T-cell responses to Epstein-Barr virus-encoded oncogene latent membrane protein 1 reveals highly conserved epitope sequences in virus isolates from diverse geographic regions

Epstein-Barr virus (EBV)-encoded oncogene latent membrane protein (LMP) 1, which is consistently expressed in multiple EBV-associated malignancies, has been proposed as a potential target antigen for any future vaccine designed to control these malignancies. However, the high degree of genetic variation in the LMP1 sequence has been considered a major impediment for its use as a potential immunotherapeutic target for the treatment of EBV-associated malignancies. In the present study, we have employed a highly efficient strategy, based on ex vivo functional assays, to conduct an extensive sequence-wide analysis of LMP1-specific T-cell responses in a large panel of healthy virus carriers of diverse ethnic origin and nasopharyngeal carcinoma patients. By comparing the frequencies of T cells specific for overlapping peptides spanning LMP1, we mapped a number of novel HLA class I- and class II-restricted LMP1 T-cell epitopes, including an epitope with dual HLA class I restriction. More importantly, extensive sequence analysis of LMP1 revealed that the majority of the T-cell epitopes were highly conserved in EBV isolates from Caucasian, Papua New Guinean, African, and Southeast Asian populations, while unique geographically constrained genetic variation was observed within one HLA A2 supertype-restricted epitope. These findings indicate that conserved LMP1 epitopes should be considered in designing epitope-based immunotherapeutic strategies against EBV-associated malignancies in different ethnic populations.

The value of idiosyncratic markers and changes to conserved tRNA sequences from the mitochondrial genome of hard ticks (Acari: Ixodida: Ixodidae) for phylogenetic inference

Idiosyncratic markers are features of genes and genomes that are so unusual that it is unlikely that they evolved more than once in a lineage of organisms. Here we explore further the potential of idiosyncratic markers and changes to typically conserved tRNA sequences for phylogenetic inference. Hard ticks were chosen as the model group because their phylogeny has been studied extensively. Fifty-eight candidate markers from hard ticks ( family Ixodidae) and 22 markers from the subfamily Rhipicephalinae sensu lato were mapped onto phylogenies of these groups. Two of the most interesting markers, features of the secondary structure of two different tRNAs, gave strong support to the hypothesis that species of the Prostriata ( Ixodes spp.) are monophyletic. Previous analyses of genes and morphology did not strongly support this relationship, instead suggesting that the Prostriata is paraphyletic with respect to the Metastriata ( the rest of the hard ticks). Parallel or convergent evolution was not found in the arrangements of mitochondrial genes in ticks nor were there any reversals to the ancestral arthropod character state. Many of the markers identified were phylogenetically informative, whereas others should be informative with study of additional taxa. Idiosyncratic markers and changes to typically conserved nucleotides in tRNAs that are phylogenetically informative were common in this data set, and thus these types of markers might be found in other organisms.

Effects of additional sequences directly downstream from the AUG on the expression of GFP gene

We have studied the expression of the green fluorescent protein (GFP) gene to gain more understanding of the effects of additional nucleotide triplets (codons) downstream from the initiation codon on the translation of the GFP mRNA in CHO and Cos1 cells. A leader sequence of six consecutive identical codons (GUG, CUC, AGU or UCA) was introduced into a humanized GFP (hm gfp) gene downstream from the AUG to produce four GFP gene variants. Northern blot and RT-PCR analysis indicated that mRNA transcription from the GFP gene was not significantly affected by any of the additional sequences. However, immunoblotting and FACS analysis revealed that AGU and UCA GFP variants produced GFP at a mean level per cell 3.5-fold higher than the other two GFP variants and the hm gfp gene. [35S]-Methionine labeling and immunoprecipitation demonstrate that GFP synthesis was very active in UCA variant transfected-cells, but not in GUG variant and hm gfp transfected-cells. Moreover, proteasome inhibitor MG-132 treatment indicated that the GFPs encoded by each of the GFP variants and the hm gfp were equally stable, and this together with the comparable mRNA levels observed for each construct suggested that the different steady-state GFP concentrations observed reflected different translation efficiencies of the various GFP genes. In addition, the CUC GFP variant, when transiently transfected into CHO or COS-1 cells, did not produce any GFP expressing cells (fully green cells), and the GUG variant produced GFP expressing cells less than 10%, while AGU and UCA GFP variants up to 30–35% in a time course study from 8 to 36 h posttransfection. Analysis of the potential secondary structure of the GFP variant mRNAs especially in the translation initiation region suggested that the secondary structure of the GFP mRNAs was unlikely to explain the different translation efficiencies of the GFP variants. The present findings indicate that a change of the initiation context of the GFP gene by addition of extra coding sequence can alter the translation efficiency of GFP mRNA, providing a means of more efficient expression of GFP in eukaryotic cells.

Phylogeny of the Sporobolus indicus complex, based on internal transcribed spacer (ITS) sequences

The entire internal transcribed spacer ( ITS) region, including the 5.8S subunit of the nuclear ribosomal DNA ( rDNA), was sequenced by direct double-stranded sequencing of polymerase chain reaction (PCR) amplified fragments. The study included 40 Sporobolus ( Family Poaceae, subfamily Chloridoideae) seed collections from 14 putative species ( all 11 species from the S. indicus complex and three Australian native species). These sequences, along with those from two out-group species [ Pennisetum alopecuroides ( L.) Spreng. and Heteropogon contortus ( L.) P. Beauv. ex Roemer & Schultes, Poaceae, subfamily Panicoideae], were analysed by the parsimony method (PAUP; version 4.0b4a) to infer phylogenetic relationships among these species. The length of the ITS1, 5.8S subunit and ITS2 region were 222, 164 and 218 base pairs ( bp), respectively, in all species of the S. indicus complex, except for the ITS2 region of S. diandrus P. Beauv. individuals, which was 217 bp long. Of the 624 characters included in the analysis, 245 ( 39.3%) of the 330 variable sites contained potential phylogenetic information. Differences in sequences among the members of the S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur & Schinz and S. jacquemontii Kunth. collections were 0%, while differences ranged from 0 to 2% between these and other species of the complex. Similarly, differences in sequences among collections of S. laxus B. K. Simon, S. sessilis B. K. Simon, S. elongatus R. Br. and S. creber De Nardi were 0%, compared with differences of 1-2% between these four species and the rest of the complex. When comparing S. fertilis ( Steud.) Clayton and S. africanus (Poir.) Robyns & Tourney, differences between collections ranged from 0 to 1%. Parsimony analysis grouped all 11 species of the S. indicus complex together, indicating a monophyletic origin. For the entire data set, pair-wise distances among members of the S. indicus complex varied from 0.00 to 1.58%, compared with a range of 20.08-21.44% among species in the complex and the Australian native species studied. A strict consensus phylogenetic tree separated 11 species of the S. indicus complex into five major clades. The phylogeny, based on ITS sequences, was found to be congruent with an earlier study on the taxonomic relationship of the weedy Sporobolus grasses revealed from random amplified polymorphic DNA ( RAPD). However, this cladistic analysis of the complex was not in agreement with that created on past morphological analyses and therefore gives a new insight into the phylogeny of the S. indicus complex.

Indicadores e Análise Multidimensional do Processo de Integração do Cone Sul

No trabalho são desenvolvidos indicadores de integração regional com o principal objetivo de apresentar uma analise multidimensional do Mercosul no período de 1991 a 2006. A pesquisa parte da premissa que o Mercosul não é um caso sui generis de integração regional, e sim um exemplo de organização de integração regional assim como, por exemplo, a União Européia ou a Comunidade Andina de Nações. Assim, embora os indicadores sejam desenvolvidos para serem aplicados no Mercosul, eles poderiam potencialmente ser aplicados para outros casos de processos de integração regional.

Robust temporal alignment of multimodal cardiac sequences

Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized crosscorrelation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates di erent temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1:6 1:9% and 4:0 4:2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

Flexibilidade e modelagem de processos de negócio: uma relação multidimensional

A abordagem de gestão de processos de negócio ganhou grande popularidade e ampla disseminação nas últimas décadas. Uma análise dessa abordagem mostra que ela persegue dois objetivos de difícil conciliação: por um lado, visa à formalização dos processos em modelos - a fim de estruturar efetivamente o trabalho - e, por outro lado, visa dar flexibilidade à organização - mantendo a sua capacidade de responder a situações novas e imprevistas. O presente artigo examina a relação entre formalização e flexibilidade na modelagem de processos de negócio, por meio de uma pesquisa empírica em uma companhia de manutenção de aeronaves na Alemanha, adotando um enfoque qualitativo em diálogo com a Teoria Ator-Rede. A análise deste caso oferece duas contribuições principais: (a) evidencia e ilustra a complexidade sociotécnica envolvida na modelagem de processos de negócio e (b) apresenta os contornos de uma compreensão multidimensional sobre a relação entre formalização e flexibilidade na gestão de processos de negócio.

Multilevel and multidimensional scale for online trust

This paper examines the nature of the construct of consumers' trust toward the electronic channel of their financial institution. Through a study of a total of 372 individual users of Internet banking in Spain, we have managed to develop a third-order measuring instrument that integrates a total of seven dimensions. The exploratory and confirmatory factor analyses were used to test the validation and reliability of the proposed scale. Findings provide useful information to professionals who seek to identify how customer's trust is formed in the online channel and in the financial sector.

Os estudos de recepção como modelo multidimensional: A negociação de estereótipos de etnicidade e género

Este artigo pretende analisar a multidimensionalidade do modelo de estudos de recepção, apresentando, para esse efeito, os resultados de dois projectos de investigação. Enquanto o primeiro projecto incide sobre a reacção de imigrantes brasileiras à representação das suas conterrâneas nos media portugueses, o segundo debruça-se sobre a reacção das portuguesas à representação do feminino enquanto sujeito e objecto de notícia na imprensa nacional. Com base num modelo multidimensional dos media que divide a cultura mediática em categorias de fidelidade representativa, espaço público agonístico e funcionalidade dos media, procurase explorar o modo como os estereótipos étnicos e de género são assimilados no quotidiano mediante a adopção de leituras preferenciais, negociadas ou opositivas. Estas interpretações de significados veiculados pelos media indicam que as redefinições de identidades étnica e de género são condicionadas pelo imaginário bem como por imperativos de ordem económica.

Pobreza multidimensional nos municípios da Região Nordeste

Na abordagem das capacitações de Sen (1981, 1985, 2000, 2001), a pobreza significa privação em diferentes aspectos da vida. O objetivo deste estudo é mensurar a pobreza multidimensional nos municípios da Região Nordeste por meio da teoria dos conjuntos fuzzy e dados do Censo Demográfico (IBGE, 2010). São utilizados 19 indicadores (funcionamentos) distribuídos em quatro dimensões: educação, saúde, condições habitacionais e renda. Os resultados indicam pobreza, com destaque nas dimensões da renda e da educação, principalmente nos estados de Maranhão, Alagoas, Piauí e Paraíba. Políticas de redução da pobreza precisam considerar quais são as privações sofridas pelas pessoas e as particularidades do local onde vivem.

Genus and Braid Index Associated to Sequences of Renormalizable Lorenz Maps

We describe the Lorenz links generated by renormalizable Lorenz maps with reducible kneading invariant (K(f)(-), = K(f)(+)) = (X, Y) * (S, W) in terms of the links corresponding to each factor. This gives one new kind of operation that permits us to generate new knots and links from the ones corresponding to the factors of the *-product. Using this result we obtain explicit formulas for the genus and the braid index of this renormalizable Lorenz knots and links. Then we obtain explicit formulas for sequences of these invariants, associated to sequences of renormalizable Lorenz maps with kneading invariant (X, Y) * (S,W)*(n), concluding that both grow exponentially. This is specially relevant, since it is known that topological entropy is constant on the archipelagoes of renormalization.

Spatio-temporal alignment of pedobarographic image sequences

O documento em anexo encontra-se na versão post-print (versão corrigida pelo editor).

Multidimensional aspects related to shiftworkers' health and well-being

The impact of shift and night work on health shows a high inter- and intra-individual variability, both in terms of kind of troubles and temporal occurrence, related to various intervening factors dealing with individual characteristics, lifestyles, work demands, company organisation, family relations and social conditions. The way we define "health" and "well-being" can significantly influence appraisals, outcomes and interventions. As the goal is the optimisation of shiftworkers' health, it is necessary to go beyond the health protection and to act for health promotion. In this perspective, not only people related to medical sciences, but many other actors (ergonomists, psychologists, sociologists, educators, legislators), as well as shiftworkers themselves. Many models have been proposed aimed at describing the intervening variables mediating and/or moderating the effects; they try to define the interactions and the pathways connecting risk factors and outcomes through several human dimensions, which refer to physiology, psychology, pathology, sociology, ergonomics, economics, politics, and ethics. So, different criteria can be used to evaluate shiftworkers' health and well-being, starting from biological rhythms and ending in severe health disorders, passing through psychological strain, job dissatisfaction, family perturbation and social dis-adaptation, both in the short- and long-term. Consequently, it appears rather arbitrary to focus the problem of shiftworkers' health and tolerance only on specific aspects (e.g. individual characteristics), but a systemic approach appears more appropriate, able to match as many variables as possible, and aimed at defining which factors are the most relevant for those specific work and social conditions. This can support a more effective and profitable (for individuals, companies, and society) adoption of preventive and compensative measures, that must refer more to "countervalues" rather than to "counterweights".

A multidimensional scaling analysis of musical sounds based on pseudo phase plane

This paper studies musical opus from the point of view of three mathematical tools: entropy, pseudo phase plane (PPP), and multidimensional scaling (MDS). The experiments analyze ten sets of different musical styles. First, for each musical composition, the PPP is produced using the time series lags captured by the average mutual information. Second, to unravel hidden relationships between the musical styles the MDS technique is used. The MDS is calculated based on two alternative metrics obtained from the PPP, namely, the average mutual information and the fractal dimension. The results reveal significant differences in the musical styles, demonstrating the feasibility of the proposed strategy and motivating further developments towards a dynamical analysis of musical sounds.

Desenvolvimento: um conceito multidimensional

O presente trabalho faz uma reflexão sobre o processo de construção do conceito de desenvolvimento na sociedade capitalista. Para tanto, utiliza-se da análise histórica com ênfase em quatro dimensões: econômica, política, social e ambiental. O estudo demonstra que o conceito surge na biologia, empregado como processo de evolução dos seres vivos para o alcance de suas potencialidades genéticas, porém, incorpora-se nas teorias e práticas sociais, por meio da economia, da sociologia, da antropologia e da ciência política. Ao longo de seu percurso histórico, o termo proporcinou algumas concepções diferentes de sociedade, como sociedade do crescimento, sociedade do bem estar social e sociedade sustentável. Portanto, este ensaio propõe compreender a lógica que fundamenta essas mudanças paradigmáticas do significado de desenvolvimento na sociedade.