The phylogeny of Ureaplasma urealyticum based on the mba gene fragment

Sequencing of mba gene fragments of reference strains of Ureaplasma urealyticum serovars 1, 3, 6, 14, in addition to 33 clinical U. urealyticum isolates is reported. A phylogenetic tree deduced from an alignment of these sequences clearly demonstrates two major clusters (confidence limit 100%), which equate to the parvo and T960 biovars, and five types which we have designated mba 1, 3, 6, 8 and X. These relationships are supported by bootstrap analysis. Polymorphisms within the mba fragment of types mba 1, 3, and 6 were used to define nine subtypes (mba 1a, 1b, 3a, 3b, 3c, 3d, 3e, 6a, and 6b) thus facilitating high resolution typing of U. urealyticum. Inclusion of the reference strains for serovars 1, 3, 6, and 8 in the mba typing scheme showed that the results of this analysis are broadly consistent with currently accepted serotyping. In addition a ure gene fragment from nine of the clinical isolates was amplified and sequenced. Comparisons of the sequences clearly distinguished the two biovars of U. urealyticum; however this fragment was invariant within the parvo biovar. This study has shown that the sequence of the mba can reveal the fine details of the relationships between U. urealyticum isolates and also supports the significant evolutionary gap between the two biovars.

Interior spaces in other places [Introduction]

To comprehend other places through the lens of the ‘shifting’ interior – examining interior histories and theories, and by association, the constructed and performed practices of a range of interior conditions – is to enable speculation on the production and occupation of interior space in other territories and societies. Forms of inspiration are, as both keynote papers acknowledge, often overlooked; whether this is a result of western-centric approaches to aesthetics, or their methods of enquiry. Evidently as the Symposium papers demonstrate, the discussion is more complicated than it might at first appear and the observation of interior decoration/design as critical practice offers one way to engage.

Seed-based biclustering of gene expression data

Background Accumulated biological research outcomes show that biological functions do not depend on individual genes, but on complex gene networks. Microarray data are widely used to cluster genes according to their expression levels across experimental conditions. However, functionally related genes generally do not show coherent expression across all conditions since any given cellular process is active only under a subset of conditions. Biclustering finds gene clusters that have similar expression levels across a subset of conditions. This paper proposes a seed-based algorithm that identifies coherent genes in an exhaustive, but efficient manner. Methods In order to find the biclusters in a gene expression dataset, we exhaustively select combinations of genes and conditions as seeds to create candidate bicluster tables. The tables have two columns: (a) a gene set, and (b) the conditions on which the gene set have dissimilar expression levels to the seed. First, the genes with less than the maximum number of dissimilar conditions are identified and a table of these genes is created. Second, the rows that have the same dissimilar conditions are grouped together. Third, the table is sorted in ascending order based on the number of dissimilar conditions. Finally, beginning with the first row of the table, a test is run repeatedly to determine whether the cardinality of the gene set in the row is greater than the minimum threshold number of genes in a bicluster. If so, a bicluster is outputted and the corresponding row is removed from the table. Repeating this process, all biclusters in the table are systematically identified until the table becomes empty. Conclusions This paper presents a novel biclustering algorithm for the identification of additive biclusters. Since it involves exhaustively testing combinations of genes and conditions, the additive biclusters can be found more readily.

Introduction to grounded theory

Grounded theory, first developed by Glaser and Strauss in the 1960s, was introduced into nursing education as a distinct research methodology in the 1970s. The theory is grounded in a critique of the dominant contemporary approach to social inquiry, which imposed "enduring" theoretical propositions onto study data. Rather than starting from a set theoretical framework, grounded theory relies on researchers distinguishing meaningful constructs from generated data and then identifying an appropriate theory. Grounded theory is thus particularly useful in investigating complex issues and behaviours not previously addressed and concepts and relationships in particular populations or places that are still undeveloped or weakly connected. Grounded theory data analysis processes include open, axial and selective coding levels. The purpose of this article was to explore the grounded theory research process and provide an initial understanding of this methodology.

Business process management : an introduction to the special focus issue

The management and improvement of business processes are a core topic of the information systems discipline. The persistent demand in corporations within all industry sectors for increased operational efficiency and innovation, an emerging set of established and evaluated methods, tools, and techniques as well as the quickly growing body of academic and professional knowledge are indicative for the standing that Business Process Management (BPM) has nowadays. During the last decades, intensive research has been conducted with respect to the design, implementation, execution, and monitoring of business processes. Comparatively low attention, however, has been paid to questions related to organizational issues such as the adoption, usage, implications, and overall success of BPM approaches, technologies, and initiatives. This research gap motivated us to edit a corresponding special focus issue for the journal BISE/WIRTSCHAFTSINFORMATIK. We are happy that we are able to present a selection of three research papers and a state-of-the-art paper in the scientific section of the issue at hand. As these papers differ in the topics they investigate, the research method they apply, and the theoretical foundations they build on, the diversity within the BPM field becomes evident. The academic papers are complemented by an interview with Phil Gilbert, IBM’s Vice President for Business Process and Decision Management, who reflects on the relationship between business processes and the data flowing through them, the need to establish a process context for decision making, and the calibration of BPM efforts toward executives who see processes as a means to an end, rather than a first-order concept in its own right.

Introduction: Cuba's Capacity to Share

The Capacity to Share is the first book to document how Cubans share their highly developed educational services with other low-income states, especially those in Africa, Latin America, and the Caribbean. A variety of international and Cuban authors break new ground in presenting this research. They investigate the experiences of people who have studied in Cuba on scholarships from the Cuban government, the implications for their home countries, and the work of Cuban teachers and administrators to support education in other countries. The authors discuss how the Cuban "solidarity" approach prioritizes global educational cooperation for mutual support, rather than imposing conditional aid. The book offers original and unusual insights into issues of culture, education, aid, development, and change as they relate to low-income states.

Google Android : a comprehensive introduction

Google Android, Google's new product and its first attempt to enter the mobile market, might have an equal impact on mobile users like Apple's hyped product, the iPhone. In this Technical report we are going to present the Google Android platform, what Android is, describe why it might be considered as a worthy rival to Apple's iPhone. We will describe parts of its internals, take a look "under the hood" while explaining components of the underlying operating system. We will show how to develop applications for this platform, which difficulties a developer might have to face, and how developers can possibly use other programming languages to develop for Android than the propagated language Java.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Candidate gene analysis for quantitative traits using the transmission disequilibrium test : the example of the melanocortin 4-receptor in pigs

Population-wide associations between loci due to linkage disequilibrium can be used to map quantitative trait loci (QTL) with high resolution. However, spurious associations between markers and QTL can also arise as a consequence of population stratification. Statistical methods that cannot differentiate between loci associations due to linkage disequilibria from those caused in other ways can render false-positive results. The transmission-disequilibrium test (TDT) is a robust test for detecting QTL. The TDT exploits within-family associations that are not affected by population stratification. However, some TDTs are formulated in a rigid-form, with reduced potential applications. In this study we generalize TDT using mixed linear models to allow greater statistical flexibility. Allelic effects are estimated with two independent parameters: one exploiting the robust within-family information and the other the potentially biased between-family information. A significant difference between these two parameters can be used as evidence for spurious association. This methodology was then used to test the effects of the fourth melanocortin receptor (MC4R) on production traits in the pig. The new analyses supported the previously reported results; i.e., the studied polymorphism is either causal of in very strong linkage disequilibrium with the causal mutation, and provided no evidence for spurious association.

Basic graphics : an introduction to rudimentary graphic design

These notes were compiled from several authorities to be used for teaching and learning purposes here at QUT, with the focus on first and second year landscape architecture design studio units.