Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure-function relationships in sequence families and superfamilies.     

Netgram: Visualizing Communities in Evolving Networks

Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems.     

Combined Review: Architectural Anthropology and Minaret Building and Apprenticeship in Yemen

Architectural Anthropology. Mari-José Amerlinck, ed. Westport, CT: Bergin and Garvey, 2001. 232 pp.
Minaret Building and Apprenticeship in Yemen. Trevor H. J. Marchand. Richmond, Surrey: Curzon Press, 2001. 304 pp.     

Visualizing themselves: Tongan videography in Utah 1

This paper examines the process and product of video visualizations made by and for Tongan immigrants in Salt Lake City, Utah. Videographers and other members of the Tongan community collaborate on videos of events such as birthdays, weddings, funerals, and fund‐raising dances. Through video recording, editing, and viewing processes, they have many opportunities to create images of themselves within American society. The videos, prized among Utah Tongans and often sent to relatives in the islands, reflect their values and ideals. Here, I offer my examination of Tongan videography as a new approach to understanding others through their own visualizations.     

Sayl andghayl: The ecology of water allocation in Yemen

In this article, comparison is made between the two major types of water allocation systems in Yemen: seasonal flood (sayl)and highland spring flow (ghayl).Constraints in the nature of water as a flowing resource are defined for each system. The major distinctions between the two types of systems are variability in water flow (which influences the determination of access rights), techniques of water control, measurement of water turns, the need for supervision of irrigation activities, and the potential for economic expansion of the production system. It is argued that tribal political organization is an adaptive response to highland spring flow allocation in Yemen, but undergoes stress in coastal flood systems where competition for the same water source extends across tribal boundaries in upstream-downstream conflict.     

GeneViTo: Visualizing gene-product functional and structural features in genomic datasets

Background  

The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies.     

Visualizing chromatin and chromosomes in living cells

The dynamic organization of eukaryotic genomes in cell nuclei recently came into the focus of research interest. The kinetics of genome dynamics can be addressed only by approaches involving live cell microscopy. Different methods are available to visualize chromatin, specific chromatin fractions, or individual chromosome territories within nuclei of living mammalian cells. Appropriate labeling procedures as well as cell chamber systems and important controls for live cell microscopy are described.     

Gc subtyping in south Indian tribal and caste populations

Seven tribal (Konda Kammara - 2 samples; Koya Dora - 3 samples; Lambadi) and caste (Madiga) populations from Andhra Pradesh (South India) have been analyzed for the distribution of Gc subtypes. The observed heterogeneity in the distribution of Gc1F, Gc1S and Gc2 alleles was found to be statistically significant. Comparisons are made with North Indian populations as well as with those of other racial affiliation. The anthropological impact of the Gc subtype polymorphism is discussed.     

Circulating Cults in Highland New Guinea: Pointers for Research

Trance and dreams become emphasized in inverse proportion to the emphasis on achieved leadership by means of exchange. That is, trance and dream are less emphasized as a means of establishing political leadership when they are replaced by leadership based on competitive exchange activities. The hypothesis is intended to apply regionally in the first instance.     

Dance Education Matters: Rebuilding Postsecondary Dance Education for Twenty-First Century Relevance and Resonance

Postsecondary dance education is at a crucial juncture in its history in academe. Emerging from women's physical education programs in the 1930s, the profession's realignment with the arts broadly and arts-based education specifically has been characterized by ambitious goals and steady growth through the 1990s. However, a number of critical developments over the past decade have displaced many previous gains and undermined the overall stability and integrity of the field. Four primary challenges are investigated in this article: curricular equity, expansive dance education programs, graduate study opportunities, and national leadership. I urge dance educators and administrators to re-envision and expand P–12 dance education in the liberal arts tradition to include private studio, commercial-sector dance in community and related teaching professions. This article provides recommendations and strategies for developing relevant and resonant twenty-first-century dance education programs beyond current confines.