Characterizations of diverse residue clusters in protein three-dimensional structures.

We present new methods for identifying and analyzing statistically significant residue clusters that occur in three-dimensional (3D) protein structures. Residue clusters of different kinds occur in many contexts. They often feature the active site (e.g., in substrate binding), the interface between polypeptide units of protein complexes, regions of protein-protein and protein-nucleic acid interactions, or regions of metal ion coordination. The methods are illustrated with 3D clusters centering on four themes. (i) Acidic or histidine-acidic clusters associated with metal ions. (ii) Cysteine clusters including coordination of metals such as zinc or iron-sulfur structures, cysteine knots prominent in growth factors, multiple sets of buried disulfide pairings that putatively nucleate the hydrophobic core, or cysteine clusters of mostly exposed disulfide bridges. (iii) Iron-sulfur proteins and charge clusters. (iv) 3D environments of multiple histidine residues. Study of diverse 3D residue clusters offers a new perspective on protein structure and function. The algorithms can aid in rapid identification of distinctive sites, suggest correlations among protein structures, and serve as a tool in the analysis of new structures.

Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.

A computer analysis of 2328 protein sequences comprising about 60% of the Escherichia coli gene products was performed using methods for database screening with individual sequences and alignment blocks. A high fraction of E. coli proteins--86%--shows significant sequence similarity to other proteins in current databases; about 70% show conservation at least at the level of distantly related bacteria, and about 40% contain ancient conserved regions (ACRs) shared with eukaryotic or Archaeal proteins. For > 90% of the E. coli proteins, either functional information or sequence similarity, or both, are available. Forty-six percent of the E. coli proteins belong to 299 clusters of paralogs (intraspecies homologs) defined on the basis of pairwise similarity. Another 10% could be included in 70 superclusters using motif detection methods. The majority of the clusters contain only two to four members. In contrast, nearly 25% of all E. coli proteins belong to the four largest superclusters--namely, permeases, ATPases and GTPases with the conserved "Walker-type" motif, helix-turn-helix regulatory proteins, and NAD(FAD)-binding proteins. We conclude that bacterial protein sequences generally are highly conserved in evolution, with about 50% of all ACR-containing protein families represented among the E. coli gene products. With the current sequence databases and methods of their screening, computer analysis yields useful information on the functions and evolutionary relationships of the vast majority of genes in a bacterial genome. Sequence similarity with E. coli proteins allows the prediction of functions for a number of important eukaryotic genes, including several whose products are implicated in human diseases.

HLA-Cw allele analysis by PCR-restriction fragment length polymorphism: study of known and additional alleles.

We describe a technique for HLA-Cw genotyping by digestion of PCR-amplified genes with restriction endonucleases. Locus-specific primers selectively amplified HLA-Cw sequences from exon 2 in a single PCR that avoided coamplification of other classical and nonclassical class I genes. Amplified DNAs were digested with selected enzymes. Sixty-three homozygous cell lines from International Histocompatibility Workshop X and 113 unrelated individual cells were genotypes for HLA-Cw and compared with serology. The present protocol can distinguish 23 alleles corresponding to the known HLA-Cw sequences. Genotyping of serologically undetectable alleles (HLA-Cw Blank) and of heterozygous cells was made possible by using this method. Six additional HLA-Cw alleles were identified by unusual restriction patterns and confirmed by sequencing; this observation suggests the presence of another family of allele-sharing clusters in the HLA-B locus. This PCR-restriction endonuclease method provides a simple and convenient approach for HLA-Cw DNA typing, allowing the definition of serologically undetectable alleles, and will contribute to the evaluation of the biological role of the HLA-C locus.

Competitividade em clusters de alta tecnologia: estudo comparativo de clusters de ciências da saúde no Brasil e na Inglaterra

Este trabalho teve como objetivo desenvolver um modelo específico para analisar a competitividade de clusters de alta tecnologia. Foi realizado um estudo de casos múltiplos em que foram analisados os clusters de ciências da saúde de Ribeirão Preto, no Brasil, e de Oxfordshire, na Inglaterra. Coletaram-se dados primários e secundários. Os dados primários foram coletados por meio de entrevistas em ambos os clusters e os dados secundários por meio de relatórios, papers, websites, além de coleta realizada nos bancos de dados Fame e Orbis. O modelo Zaccarelli et al. (2008), utilizado como ponto de partida para o desenvolvimento do modelo, foi aprimorado de três maneiras: i. Por meio do ajustamento das métricas utilizadas para avaliar cada fundamento, o que incluiu, dentre outras coisas, uma adaptação do modelo para mapeamento de clusters desenvolvido por Todeva (2008); ii. Pela verificação da aderência de seus fundamentos aos clusters de alta tecnologia analisados; e iii. Pela identificação de fatores emergentes, importantes para competitividade de clusters de alta tecnologia. Os resultados mostram evidências de que entre os onze fundamentos do modelo original, nove se mostraram relevantes aos clusters de alta tecnologia, ratificando sua importância para a análise da competitividade de clusters. Além dos fundamentos originais, os resultados sugerem a inclusão de dois fundamentos emergentes: \"Inserção em cadeias globais\" e \"Disponibilidade de investimentos financeiros\", até então ignorados pelo modelo Zaccarelli et al. (2008). A pesquisa traz como contribuição teórica o desenvolvimento de um modelo específico para clusters de alta tecnologia; como contribuição metodológica as novas métricas, incluindo a incorporação da adaptação da metodologia de Todeva (2008); como contribuição empírica traz a comparação entre clusters de ciências da saúde reconhecidamente competitivos, mas pertencentes a países de realidades culturais e econômicas distintas; e como contribuição gerencial um modelo que pode ser utilizado por empresários e instituições pertencentes a clusters e que desejam analisar fatores que influenciam a sua competitividade.

NGC 7419 as a template for red supergiant clusters

Context. The open cluster NGC 7419 is known to contain five red supergiants and a very high number of Be stars. However, there are conflicting reports about its age and distance that prevent a useful comparison with other clusters. Aims. We intend to obtain more accurate parameters for NGC 7419, using techniques different from those of previous authors, so that it may be used as a calibrator for more obscured clusters. Methods. We obtained Strömgren photometry of the open cluster NGC 7419, as well as classification spectroscopy of ~20 stars in the area. We then applied standard analysis and classification techniques. Results. We find a distance of 4 ± 0.4 kpc and an age of 14 ± 2 Myr for NGC 7419. The main-sequence turn-off is found at spectral type B1, in excellent agreement. We identify 179 B-type members, implying that there are more than 1200 M⊙ in B stars at present. Extrapolating this to lower masses indicates an initial cluster mass of between 7000 and 10 000 M⊙, depending on the shape of the initial mass function. We find a very high fraction (≈40%) of Be stars around the turn-off, but very few Be stars at lower masses. We also report for the first time a strong variability in the emission characteristics of Be stars. We verified that the parameters of the red supergiant members can be used to obtain accurate cluster parameters. Conclusions. NGC 7419 is sufficiently massive to serve as a testbed for theoretical predictions and as a template to compare more obscured clusters. The distribution of stars above the main-sequence turn-off is difficult to accommodate with current evolutionary tracks. Though the presence of five red supergiants is marginally consistent with theoretical expectations, the high number of Be stars and very low number of luminous evolved B stars hint at some unknown physical factor that is not considered in current synthesis models.

Massive open star clusters using the VVV survey III. A young massive cluster at the far edge of the Galactic bar

Context. Young massive clusters are key to map the Milky Way’s structure, and near-infrared large area sky surveys have contributed strongly to the discovery of new obscured massive stellar clusters. Aims. We present the third article in a series of papers focused on young and massive clusters discovered in the VVV survey. This article is dedicated to the physical characterization of VVV CL086, using part of its OB-stellar population. Methods. We physically characterized the cluster using JHKS near-infrared photometry from ESO public survey VVV images, using the VVV-SkZ pipeline, and near-infrared K-band spectroscopy, following the methodology presented in the first article of the series. Results. Individual distances for two observed stars indicate that the cluster is located at the far edge of the Galactic bar. These stars, which are probable cluster members from the statistically field-star decontaminated CMD, have spectral types between O9 and B0 V. According to our analysis, this young cluster (1.0 Myr < age < 5.0 Myr) is located at a distance of 11+5-6 kpc, and we estimate a lower limit for the cluster total mass of (2.8+1.6-1.4) · 103 M⊙. It is likely that the cluster contains even earlier and more massive stars.

Políticas de innovación en turismo y desarrollo de clusters: la percepción gerencial en el programa Agrupaciones Empresariales Innovadoras (AEIs)

Este trabajo se enmarca en el análisis de las políticas de innovación en turismo. Estudia la aplicación de políticas cluster y la configuración de clusters como iniciativas planificadas, centrándose en el análisis del Programa de AEIs turísticas en España. Se emplea una metodología cualitativa para investigar la percepción de las gerencias como actores fundamentales del Programa. Los resultados de la investigación están relacionados con el proceso de configuración de clusters, los factores favorables y limitantes de su actividad, la valoración general del programa y la identificación de propuestas de mejora.

Discontinuity spacing analysis in rock masses using 3D point clouds

The complete characterization of rock masses implies the acquisition of information of both, the materials which compose the rock mass and the discontinuities which divide the outcrop. Recent advances in the use of remote sensing techniques – such as Light Detection and Ranging (LiDAR) – allow the accurate and dense acquisition of 3D information that can be used for the characterization of discontinuities. This work presents a novel methodology which allows the calculation of the normal spacing of persistent and non-persistent discontinuity sets using 3D point cloud datasets considering the three dimensional relationships between clusters. This approach requires that the 3D dataset has been previously classified. This implies that discontinuity sets are previously extracted, every single point is labeled with its corresponding discontinuity set and every exposed planar surface is analytically calculated. Then, for each discontinuity set the method calculates the normal spacing between an exposed plane and its nearest one considering 3D space relationship. This link between planes is obtained calculating for every point its nearest point member of the same discontinuity set, which provides its nearest plane. This allows calculating the normal spacing for every plane. Finally, the normal spacing is calculated as the mean value of all the normal spacings for each discontinuity set. The methodology is validated through three cases of study using synthetic data and 3D laser scanning datasets. The first case illustrates the fundamentals and the performance of the proposed methodology. The second and the third cases of study correspond to two rock slopes for which datasets were acquired using a 3D laser scanner. The second case study has shown that results obtained from the traditional and the proposed approaches are reasonably similar. Nevertheless, a discrepancy between both approaches has been found when the exposed planes members of a discontinuity set were hard to identify and when the planes pairing was difficult to establish during the fieldwork campaign. The third case study also has evidenced that when the number of identified exposed planes is high, the calculated normal spacing using the proposed approach is minor than those using the traditional approach.

Gaia-ESO Survey: Analysis of pre-main sequence stellar spectra

Context. The Gaia-ESO Public Spectroscopic Survey is obtaining high-quality spectroscopy of some 100 000 Milky Way stars using the FLAMES spectrograph at the VLT, down to V = 19 mag, systematically covering all the main components of the Milky Way and providing the first homogeneous overview of the distributions of kinematics and chemical element abundances in the Galaxy. Observations of young open clusters, in particular, are giving new insights into their initial structure, kinematics, and their subsequent evolution. Aims. This paper describes the analysis of UVES and GIRAFFE spectra acquired in the fields of young clusters whose population includes pre-main sequence (PMS) stars. The analysis is applied to all stars in such fields, regardless of any prior information on membership, and provides fundamental stellar atmospheric parameters, elemental abundances, and PMS-specific parameters such as veiling, accretion, and chromospheric activity. Methods. When feasible, different methods were used to derive raw parameters (e.g. line equivalent widths) fundamental atmospheric parameters and derived parameters (e.g. abundances). To derive some of these parameters, we used methods that have been extensively used in the past and new ones developed in the context of the Gaia-ESO survey enterprise. The internal precision of these quantities was estimated by inter-comparing the results obtained by these different methods, while the accuracy was estimated by comparison with independent external data, such as effective temperature and surface gravity derived from angular diameter measurements, on a sample of benchmarks stars. A validation procedure based on these comparisons was applied to discard spurious or doubtful results and produce recommended parameters. Specific strategies were implemented to resolve problems of fast rotation, accretion signatures, chromospheric activity, and veiling. Results. The analysis carried out on spectra acquired in young cluster fields during the first 18 months of observations, up to June 2013, is presented in preparation of the first release of advanced data products. These include targets in the fields of the ρ Oph, Cha I, NGC 2264, γ Vel, and NGC 2547 clusters. Stellar parameters obtained with the higher resolution and larger wavelength coverage from UVES are reproduced with comparable accuracy and precision using the smaller wavelength range and lower resolution of the GIRAFFE setup adopted for young stars, which allows us to provide stellar parameters with confidence for the much larger GIRAFFE sample. Precisions are estimated to be ≈120 K rms in Teff, ≈0.3 dex rms in log g, and ≈0.15 dex rms in [Fe/H] for the UVES and GIRAFFE setups.

The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars

Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 105 stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected Teff-log  g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55 K for Teff, 0.13 dex for log  g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50−100 K for Teff, 0.10−0.25 dex for log  g and 0.05−0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.

Desenvolvimento económico baseado na teoria dos Clusters: o exemplo do calçado em Portugal

Este trabalho aborda o tema dos clusters industriais - concentrações geográficas de empresas interligadas, fornecedores de produtos e serviços, empresas em setores afins e entidades que lhes estão associadas, como as universidades, entidades públicas, associações empresariais. A competitividade resulta da ação das empresas, e estas devem competir e cooperar para criar lucro económico, mas também gerar benefícios para a região e o país. O objetivo deste trabalho é demonstrar que a aplicação da teoria dos clusters no nosso país, - introduzida na sequência de um estudo pedido em 1994 ao criador desta teoria, o Dr. Michael Porter – teve efeitos muito positivos no desenvolvimento dos últimos 20 anos e que maiores poderiam ter sido esses efeitos, se tivesse sido feita a sua aplicação em todos os setores em que se identificavam vantagens competitivas da nossa economia. Foi realizada uma análise da evolução do mais reconhecido cluster, o da indústria do calçado, cujos resultados apontam para as estratégias a adotar em muitos outros setores da nossa economia. Numa extrapolação, fica claro que as regiões nacionais e os países que contam com clusters industriais são aqueles que apresentam desempenho superior, em termos de intensidade exportadora e valor acrescentado. Estas zonas apresentam ainda níveis elevados de riqueza e longevidade dos seus cidadãos. Em termos europeus, a Alemanha, que tem como grandes clusters os setores automóvel, da automação, da eletrónica e da pesquisa laboratorial, é o melhor exemplo deste facto.

Changing cultural clusters: A research note. ACES Working Papers, August 2009

The purpose of this research note is to investigate the changing cultural clusters that emerged between the studies of Hofstede (1970s) and GLOBE (1990s) using similar measures and overlapping countries. Our study analyzes the world's cultural clusters using two seminal and comparable cultural classifications: Hofstede and GLOBE. Four common cultural dimensions are empirically examined: individualism, power distance, uncertainty avoidance, and masculinity. We use two leading methods from cluster analysis and display data in both dandrograms and pie chart forms showing the grouping of countries. Our results suggest diverging cultural typologies that transcend geography, language, and religion. Countries are engaged in selective cultural borrowing that leads to new and changing global cultural structures.

Illinois as a leader in the international economy : an analysis of the challenges of the 1990s /

Executive summary -- Overview of findings -- Some summary conclusions -- Purpose -- A changing national and international marketplace -- Cluster dynamics in the Illinois economy: defining key industry clusters -- The cost of doing business in Illinois -- Occupational structure: the key to success in the 1990s is retaining and attracting high value-added jobs in Illinois -- Regional differences: while northeastern Illinois dominates the economy, many of the state's key clusters are widely dispersed around the state -- Summary and conclusions -- appendix 1. Illinois' industry cluster performance: detailed analysis -- appendix 2. Illinois' occupational challenges in the 1990s by industry cluster.

Analytical analysis of consumption in Brazil

This thesis is an analytical analysis of consumption in Brazil, based on data from the Consumer Expenditure Survey, years 2008 to 2009, collected by the Brazilian Institute of Geography and Statistics. The main aim of the thesis was to identify differences and similarities in consumption among Brazilian households, and estimate the importance of demographic and geographic characteristics. Initially, households belonging to different social classes and geographical regions were compared based on their consumption. For further insights, two cluster analyses were conducted. Firstly, households were grouped according to the absolute values of expenditures. Five clusters were discovered; cluster membership showed larger spending in all of the expense categories for households having higher income, and a substantial association with particular demographic variables, including as region, neighborhood, race and education. Secondly, cluster analysis was performed on proportionate distribution of total spending by every household. Five groups of households were revealed: Basic Consumers, the largest group that spends only on fundamental goods, Limited Spenders, which additionally purchase alcohol, tobacco, literature and telecommunication technologies, Mainstream Buyers, characterized by spending on clothing, personal care, entertainment and transport, Advanced Consumers, which have high relative expenses on financial and legal services, healthcare and education, and Exclusive Spenders, households distinguished by spending on vehicles, real estate and travelling.

Molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16S rDNA sequence analysis

Aim: The aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. Methods and Results: Pinch samples of the terminal ileum, proximal and distal colon were taken from a healthy 35-year-old, and a 68-year-old subject with mild diverticulosis. The 16S rDNA genes were amplified using a low number of PCR cycles, cloned, and sequenced. In total, 361 sequences were obtained comprising 70 operational taxonomic units (OTU), with a calculated coverage of 82.6%. Twenty-three per cent of OTU were common to the terminal ileum, proximal colon and distal colon, but 14% OTU were only found in the terminal ileum, and 43% were only associated with the proximal or distal colon. The most frequently represented clones were from the Clostridium group XIVa (24.7%), and the Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides ) cluster (27.7%). Conclusion: Comparison of 16S rDNA clone libraries of the hindgut across mammalian species confirms that the distribution of phylogenetic groups is similar irrespective of the host species. Lesser site-related differences within groups or clusters of organisms, are probable. Significance and Impact: This study provides further evidence of the distribution of the bacteria on the mucosal surfaces of the human hindgut. Data contribute to the benchmarking of the microbial composition of the human digestive tract.