The role of visual analogy in information visualisation

This thesis is inspired by the growing domain of information visualisation, and the potentially open-ended choice of visual representations which can be used to represent any given abstract concept. Such a potentially unlimited choice means that the question of choosing an appropriate visual form is not insubstantial. This thesis therefore attempts to explore how to usefully inform such a choice through the concept of visual analogy. To this end a series of multidimensional icons are developed which differ in terms of level of analogy for a given concept. The practical studies outlined then set out first to confirm this difference in practical terms and then explore the implications of using different levels of explicit visual analogy in tasks appropriate to the use of multidimensional icons. The results reveal that a continuum of 'degree' of analogy can be practically established which increasingly constrains the interpretation users assign to representations as the level of analogy increases. [Continues.

Chla

chlorophyll a concentrations in initial lake water and in experimental replicates. column definitions are provided in ReadMe.tx

park_lakes_db

675 dissolved inorganic nitrogen (NO3-N and NH3-N) observations from lakes above 1,200 m sampled between 1988 and 2014 across Mount Rainier, North Cascades, and Olympic National Parks. The database was compiled by Jason Williams. Column definitions and information about data origins and compilation are provided in ReadMe.tx

Current (grey) and future (blue) data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) (percent responding affirmatively, 387 ≤ <i>n</i> ≤ 551).

<p>Current (grey) and future (blue) data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) (percent responding affirmatively, 387 ≤ <i>n</i> ≤ 551).</p

experiments_phyto_12_26_15

cell densities of phytoplankton taxa in initial lake water and in each experimental replicate. column definitions are provided in ReadMe.txt

Current and future data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) by the NSF BIO division.

<p>Current and future data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) by the NSF BIO division.</p

Unmet data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) (percent responding negatively, 318 ≤ <i>n</i> ≤ 510).

<p>Unmet data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs) (percent responding negatively, 318 ≤ <i>n</i> ≤ 510).</p

Current and future data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs): Bioinformaticians versus others, large versus small research groups.

<p>Current and future data analysis needs of National Science Foundation (NSF) Biological Sciences Directorate (BIO) principal investigators (PIs): Bioinformaticians versus others, large versus small research groups.</p

Effect of PARP-1 on the steady-state rate of AP-site incision catalyzed by APE1.

<p>The DNA substrate with THF (100 nM) was preincubated with 25–500 nM PARP-1. After adding 0.5 nM APE1, the reaction mixture was incubated for 10 s to 5 min at 37°C. The reaction conditions and data analysis are described in Materials and Methods. The data representing the reaction products were fitted to an exponential equation to determine the steady-state rate of the APE1 incision reaction in the absence and presence of PARP-1. The average from three repeats is represented.</p

Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair

<div><p>The apurinic/apyrimidinic- (AP-) site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER) pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol) β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1), however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1’s AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.</p></div