Macromolecular assemblies are fundamental to most biological processes and here we attempt to improve the structural characterization of assemblies in the hopes that with new and improved models will produce functional insights on assemblies.

Modeling of macromolecular assemblies begins with an analysis of the computational and experimental data available on the entire assembly, subcomplexes, individual subunits and the interactions between subunits. Having collected the data on the assembly, the next challenge is to integrate the disparate data to produce a structural model. Hybrid approaches, which integrate multiple sources of data, provide a way to increase the coverage and accuracy of structure modeling for macromolecular complexes.

Fitting in with the theme of hybrid methods, Chapters 2 and 3 describe methods for modeling macromolecular assemblies, combining overall shape information (e.g., from cryo-electron microscopy) with interaction data (e.g., tandem affinity purification assays); and protein structures (or models) with NMR spectroscopy, respectively.

Chapter 4 proposes an assessment strategy for structure modeling methods that provides a way to measure how much improvement is left to be made, instead of the traditional approach of measuring how much improvement was already made. This assessment strategy provides more information on the specific limitations of the method and provides specific insight into how to best improve the method. The strategy also presents a more fair method of comparing competing methods that are assessed with different benchmark sets.

Chapter 5 describes the representation of subunits and assemblies by systems of points and restraints, explores the assumptions that underlie using points and restraints to model macromolecular structures, describes the properties of binary and multiple docking, and models the structure modeling framework.

The main contributions of this dissertation are two practical approaches for macromolecular assemblies; an assessment strategy that provides a more explicit description of the accuracy and limitation of assessed methods, improving the confidence with which the resulting models are used; and lastly, a deeper theoretical understanding of modeling macromolecular assemblies, including a path towards a more principled approach for integrating multiple sources of data.

Introduction: Asking family members to leave during invasive procedures has historically been common practice; however, evidence-based recommendations have altered the trend of family presence during pediatric procedures. The aim of this study was to determine factors related to family members’ choice to be present or absent during fracture reductions in a pediatric emergency department (ED), and their satisfaction with that choice.

Methods: We administered role-specific, anonymous surveys to a convenience sample of patients’ family members in the ED of a Level I pediatric trauma center. All family members were given a choice of where to be during the procedure.

Results: Twenty-five family members of 18 patients completed surveys. Seventeen family members chose to stay in the room. Family member satisfaction with their decision to be inside or outside the room during the procedure (median = very satisfied) was almost uniformly high and not associated with any of the following variables: previous presence during a medical procedure; provider-reported procedure difficulty, or anxiety levels. Family member perception of procedure success (median = extremely well) was also high and not associated with other variables. Location during the procedure was associated with a desire to be in the same location in the future (Fisher’s exact test, p=0.001). Common themes found among family members’ reasons for their location decisions and satisfaction levels were a desire to support the patient, high staff competence, and their right as parents to choose their location.

Conclusion: Family members self-select their location during their child’s fracture reduction to high levels of satisfaction, and they considered the ability to choose their location as important.

Introduction

Case presentation

Discussion

Dendrite arborization patterns are critical determinants of neuronal function. To explore the basis of transcriptional regulation in dendrite pattern formation, we used RNA interference (RNAi) to screen 730 transcriptional regulators and identified 78 genes involved in patterning the stereotyped dendritic arbors of class I da neurons in Drosophila. Most of these transcriptional regulators affect dendrite morphology without altering the number of class I dendrite arborization (da) neurons and fall primarily into three groups. Group A genes control both primary dendrite extension and lateral branching, hence the overall dendritic field. Nineteen genes within group A act to increase arborization, whereas 20 other genes restrict dendritic coverage. Group B genes appear to balance dendritic outgrowth and branching. Nineteen group B genes function to promote branching rather than outgrowth, and two others have the opposite effects. Finally, 10 group C genes are critical for the routing of the dendritic arbors of individual class I da neurons. Thus, multiple genetic programs operate to calibrate dendritic coverage, to coordinate the elaboration of primary versus secondary branches, and to lay out these dendritic branches in the proper orientation.