Kaposi’ sarcoma-associated herpesvirus (KSHV) causes primary effusion lymphoma (PEL). PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival, although KSHV encodes a viral homolog of this protein (vFLIP). Cellular and viral FLIP proteins have several functions, including, most importantly, the inhibition of pro-apoptotic caspase 8...
Dental enamel is a complex bio-composite with compositional and structural features across a wide range of length scales. Defects in these features can compromise enamel’s ability to protect the tooth, resulting in adverse health outcomes. Acquired defects like tooth decay are familiar to most people and are the subject of...
Caves are accessible windows into the shallow subsurface, serving as transitional ecosystems between the photosynthesis-dependent surface and the deeper subsurface. Without a source of solar energy to ultimately power carbon (C) fixation (photolithoautotrophy), cave ecosystems are either reliant on surface-derived nutrients, recovering reducing power from the microbial oxidation of redox-sensitive...
Cancer is a complex and heterogeneous disease characterized by aberrant gene regulation. Gene regulation is fundamentally orchestrated by the 3D genome organization which involves chromatin looping, compartmentalization, and the formation of topologically associating domains (TADs). Structural variations (SVs), such as genomic rearrangements, deletions, inversions, and duplications, are commonly observed in...
In shared workspaces users have real-time access to others’ actions, allowing greater access to potentially informative cues. However, there has been little exploration about what impact the ability to view each other’s work in real time has on group members’ perception of both each other and their understanding of the...
Directional freeze-casting is a porous materials fabrication technique that is used to create materials with complex, three-dimensional pore structures. Particle suspensions are solidified under a thermal gradient, promoting anisotropic growth of dendrites and incorporation of particles within interdendritic space. A fully-solidified directional freeze-cast structure is composed of dendrites that are...
This dissertation uses the case of Colombia to examine the causes and reproductive mechanisms of civil wars that last more than fifty years, which I call perpetual civil wars. It draws on network analysis of violent events and political claims, content analysis of official archival documents and historical records of...
Swallowing impairment or dysphagia has many possible causes with severe sequelae. One major mediator of the relationship between causes and sequelae is the physiologic impairment of the swallowing mechanism. Assessing the physiology of swallowing impairment is of great importance so that treatment can target physiology to mitigate sequelae. The assessment...
Recent experiments in participatory democracy, such as Iceland’s 2013 Constitutional Reform process to Chicago’s annual participatory budgeting process, have empowered members of the public to directly make policy decisions. These new participatory democratic institutions depend on citizens having capacity to organize new institutions and the capacity to participate in them....
Derivative-free optimization (DFO) has received growing attention due to important problems arising in practice. Various research communities, ranging from machine learning to engineering design, have adopted distinct DFO methods. In this thesis, we present extensive studies as a meaningful step towards a comprehensive understanding of DFO methods. We study the...