Quarternary structure amplification of protein folding differences observed in ‘native’ platelet factor-4

AbstractPlatelet factor 4 (PF4), a protein of 70 residues, exists in solution as a distribution of monomer, dimer and tetramer (M-D-T) states in slow exchange on a 600 MHz 1H-NMR chemical shift time scale. Well-resolved Y60 ring proton resonances in each aggregate state allow derivation of M-D-T populations. Under the same set of solution conditions, M-D-T aggregate state distributions vary from prep to prep or with repeated freeze-drying or raising/lowering the solution pH. These variations are not the result of chemical modifications and reflect differences in the strength of subunit associations and therefore folding. Variations are greatest at pH values at or below the pKas of carboxylate groups, supporting the idea that electrostatic interactions modulate PF4 subunit interactions. Treating these distributions as true equilibria results in free energy differences of about 0.5 kcal/mol subunit. Quarternary structure amplifies free energy differences among various folded states of monomer PF4

Synthesis-Oriented Situational Analysis in User Interface Design

Analytic evaluation is a term describing a class of techniques for examining a representation of a user interface design, discovering design flaws and/or predicting user task performance. In our work with analytic evaluation, we have observed limitations on the effectiveness and efficiency of analytic techniques for formative evaluation supporting the iterative design and re-design cycle. Here we support those observations with arguments based on theoretical limitations of the models underlying these techniques. By way of comparison we discuss desirable characteristics for an alternative approach. In our search for such an alternative, we have developed the Task Mapping Model, a substantively different approach to analysis for supporting the user interface design. We briefly describe the Task Mapping Model and give some examples illustrating its desirable characteristics

Studying the Robustness of the Triadic Trust Design with Mechanical Turk Subjects

This paper uses subjects recruited from an online employment exchange to study the robustness of the triadic trust design with a different subject pool. In running our experiments we tried to take advantage of the cost reducing features of the micro-employment culture found on Amazon’s Mechanical Turk. We find that first mover trust is robust to the change in subject pool, but second mover reciprocity was not

The Computational Philosophy: Simulation as a Core Philosophical Method

Modeling and computer simulations, we claim, should be considered core philosophical methods. More precisely, we will defend two theses. First, philosophers should use simulations for many of the same reasons we currently use thought experiments. In fact, simulations are superior to thought experiments in achieving some philosophical goals. Second, devising and coding computational models instill good philosophical habits of mind. Throughout the paper, we respond to the often implicit objection that computer modeling is "not philosophical.

Studying the Robustness of the Triadic Trust Design with Mechanical Turk Subjects

This paper uses subjects recruited from an online employment exchange to study the robustness of the triadic trust design with a different subject pool. In running our experiments we tried to take advantage of the cost reducing features of the micro-employment culture found on Amazon’s Mechanical Turk. We find that first mover trust is robust to the change in subject pool, but second mover reciprocity was not

Task Mapping Model (TMM) Analysis Manual

This guide presents the task mapping model (TMM), a snythesis/analysis methodology for aiding the interface specialist in designing interfaces with better usability. Briefly, TMM describes necessary knowledge for user task completion, and analyzes if this knowledge is supported by the user or interface. This framework consists of various abstract levels of task decomposition and description. TMM focuses on the mappings users make among domains (during task performance) to provide designers with specific information about task structure and user knowledge requirements. This model allows descriptions of tasks using hierarchical decomposition coupled with abstraction of user knowledge requirements

First Experiences with TMM

The Task Mapping Model (TMM) is a human-computer interaction technique that supports situational analyses to derive new design requirements from formative evaluation findings. While the TMM methodologies and formalisms are currently being developed and validated, this paper reports some informal first experiences and findings. Two developers who are presently working on independent non-trivial interfaces were asked to use TMM and comment on it. The developers found benefit in TM analyses, albeit in different ways, and their views were captured with an informal subjective post-analysis survey and reported here

Static and Dynamic Software Quality Metric Tools

The ability to detect and predict poor software quality is of major importance to software engineers, managers, and quality assurance organizations. Poor software quality leads to increased development costs and expensive maintenance. With so much attention on exacerbated budgetary constraints, a viable alternative is necessary. Software quality metrics are designed for this purpose. Metrics measure aspects of code or PDL representations, and can be collected and used throughout the life cycle [RAMC85]