Whole-genome sequencing revealed different demographic histories among the Korean endemic hill pigeon (Columba rupestris), rock pigeon (Columba livia var. domestica) and oriental turtle dove (Streptopelia orientalis).

BACKGROUND: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. OBJECTIVES: Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. RESULTS: The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. CONCLUSION: The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5-1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes.

Biosensors-Publication Trends and Knowledge Domain Visualization.

The number of scholarly publications on the topic of biosensors has increased rapidly; as a result, it is no longer easy to build an informed overview of the developments solely by manual means. Furthermore, with many new research results being continually published, it is useful to form an up-to-date understanding of the recent trends or emergent directions in the field. This paper utilizes bibliometric methods to provide an overview of the developments in the topic based on scholarly publications. The results indicate an increasing interest in the topic of biosensor(s) with newly emerging sub-topics. The US is identified as the country with highest total contribution to this area, but as a collective, EU countries top the list of total contributions. An examination of trends over the years indicates that in recent years, China-based authors have been more productive in this area. If research contribution per capita is considered, Singapore takes the top position, followed by Sweden, Switzerland and Denmark. While the number of publications on biosensors seems to have declined in recent years in the PubMed database, this is not the case in the Web of Science database. However, there remains an indication that the rate of growth in the more recent years is slowing. This paper also presents a comparison of the developments in publications on biosensors with the full set of publications in two of the main journals in the field. In more recent publications, synthetic biology, smartphone, fluorescent biosensor, and point-of-care testing are among the terms that have received more attention. The study also identifies the top authors and journals in the field, and concludes with a summary and suggestions for follow up research.

Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

Developing and evaluating Quilts for the depiction of large layered graphs.

Traditional layered graph depictions such as flow charts are in wide use. Yet as graphs grow more complex, these depictions can become difficult to understand. Quilts are matrix-based depictions for layered graphs designed to address this problem. In this research, we first improve Quilts by developing three design alternatives, and then compare the best of these alternatives to better-known node-link and matrix depictions. A primary weakness in Quilts is their depiction of skip links, links that do not simply connect to a succeeding layer. Therefore in our first study, we compare Quilts using color-only, text-only, and mixed (color and text) skip link depictions, finding that path finding with the color-only depiction is significantly slower and less accurate, and that in certain cases, the mixed depiction offers an advantage over the text-only depiction. In our second study, we compare Quilts using the mixed depiction to node-link diagrams and centered matrices. Overall results show that users can find paths through graphs significantly faster with Quilts (46.6 secs) than with node-link (58.3 secs) or matrix (71.2 secs) diagrams. This speed advantage is still greater in large graphs (e.g. in 200 node graphs, 55.4 secs vs. 71.1 secs for node-link and 84.2 secs for matrix depictions).

GeneaQuilts: a system for exploring large genealogies.

GeneaQuilts is a new visualization technique for representing large genealogies of up to several thousand individuals. The visualization takes the form of a diagonally-filled matrix, where rows are individuals and columns are nuclear families. After identifying the major tasks performed in genealogical research and the limits of current software, we present an interactive genealogy exploration system based on GeneaQuilts. The system includes an overview, a timeline, search and filtering components, and a new interaction technique called Bring & Slide that allows fluid navigation in very large genealogies. We report on preliminary feedback from domain experts and show how our system supports a number of their tasks.