Thesis: Ph. D., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / Cataloged from the official PDF of thesis. / Includes bibliographical references (pages 62-65). / Numerous protein variants have been made to expand the repertoire of CRISPR-Cas nucleases that can recognize protospacer-adjacent motifs (PAMs) other than the canonical NGG discovered in wild-type Streptococcus pyogenes. While Cas nuclease engineering has largely yielded proteins with enhanced specificity for NGG and variations on G-containing PAMs, we were able to construct a chimeric Cas protein with consistent specificity for a 5'-NAA-3' PAM by rationally combining the PAM-interacting domain of Streptococcus macacae with the S. pyogenes Cas9 scaffold. We have been able to demonstrate during in vitro incubations that our chimeric protein is capable of cleaving dsDNA with an NAA PAM, but a deeper biochemical understanding of the nature of these new chimeric proteins' binding and cleavage activities is of paramount importance for their practical use. Here, we use of the principles of enzyme kinetics to investigate our chimeric protein's comparative efficiency to Cas12a and the biophysical mechanism by which our grafted S. macacae segment works synergistically with the S. pyogenes Cas9 scaffold to cleave target DNA with an NAA PAM. We show that SpySmacCas9 does not bind or cleave at rates comparable to Casl2a, but its overall performance rivals that of wild-type SpyCas9 with a new PAM preference. / Lisa Nip / Ph. D. / Ph. D. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2019 / Cataloged from the official PDF version of thesis. / Includes bibliographical references (pages 38-40). / To circumvent the limitations of spectrally multiplexing sensors, fluorescent sensors are clustered by type and spatially separated in the cytoplasm to avoid cross-talk. Each sensor is fused to an orthogonal viral capsid protein that binds to a long, repetitive strand of its corresponding RNA sequence. All sensors fluoresce green and are indistinguishable during recording but are identified with post-hoc antibody or FISH staining for each sensor-specific puncta. This spatial multiplexing strategy will allow for easier scaling of the number of fluorescent reporters of physiological activity. / by Shannon L. Johnson. / S.M. / S.M. Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2003. / Includes bibliographical references (p. 146-150). / Woodstein is a software agent that works with a user's web browser to explain and help diagnose problems in web processes, such as purchases. It enables the user to inspect data items in ordinary web pages, revealing the processes that created them. It provides an integrated view of the processes and data associated with a user's actions at a web site, and retrieves related information on the same web site, or even on different web sites. When the user inspects data that looks incorrect, Woodstein helps manage hypotheses about causally related data and processes that look incorrect and provides guidance in the process of elimination to isolate the unsuccessful process or wrong data. / by Earl Joseph Wagner. / S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2008. / Includes bibliographical references (v. 2, leaves 248-253). / In this work, a system for recognizing activities in the home setting that uses a set of small and simple state-change sensors, machine learning algorithms, and electronic experience sampling is introduced. The sensors are designed to be "tape on and forget" devices that can be quickly and ubiquitously installed in home environments. The proposed sensing system presents an alternative to sensors that are sometimes perceived as invasive, such as cameras and microphones. Since temporal information is an important component of activities, a new algorithm for recognizing activities that extends the naive Bayes classifier to incorporate low-order temporal relationships was created. Unlike prior work, the system was deployed in multiple residential environments with non-researcher occupants. Preliminary results show that it is possible to recognize activities of interest to medical professionals such as toileting, bathing, and grooming with detection accuracies ranging from 25% to 89% depending on the evaluation criteria used. Although these preliminary results were based on small datasets collected over a two-week period of time, techniques have been developed that could be applied in future studies and at special facilities to study human behavior such as the MIT Placelab. The system can be easily retrofitted in existing home environments with no major modifications or damage and can be used to enable IT and health researchers to study behavior in the home. Activity recognition is increasingly applied not only in home-based proactive and preventive healthcare applications, but also in learning environments, security systems, and a variety of human-computer interfaces. / by Randy Joseph Rockinson. / S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2003. / Pages 98 and 99 blank. / Includes bibliographical references (p. 75-81). / This work builds an infrastructure called Location Linked Information that offers a means to associate digital information with public, physical places. This connection creates a hybrid virtual/physical space, called glean space, that is owned, managed, and rated by the public, for the benefit of the populace. Initially embodied by an interactive, dynamic map viewed on a handheld computer, the system provides two functions for its urban users: 1) the retrieval of information about their surroundings, and 2) the optional annotation of location for communal benefit. Having the ability to link physical location with arbitrary information is an essential function to building immersive information environments and the smart city. Public computing systems such as Location Linked Information will enhance the urban experience, just as access to transportation dramatically altered the sensation and form of the city. / by Matthew William David Mankins. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 131-135). / Robotic vehicles walk on legs, roll on wheels, are pulled by tracks, pushed by propellers, lifted by wings, and steered by rudders. All of these systems share the common character of momentum transport across their surfaces. These existing approaches rely on bulk response among the fluids and solids. They are often not finely controllable and complex approaches suffer from manufacturing and practical operational challenges. In contrast I present a study of a dynamic, programmable interface between the surface and its surrounding fluids. This research explores a synthetic hydrodynamic regime, using a programmable surface to dynamically alter the flow around an object. Recent advances in distributed computing and communications, actuator integration and batch fabrication, make it feasible to create intelligent active surfaces, with significant implications for improving energy efficiency, recovering energy, introducing novel form factors and control laws, and reducing noise signatures. My approach applies ideas from programmable matter to surfaces rather than volumes. The project is based on covering surfaces with large arrays of small cells that can each compute, communicate, and generate shear or normal forces. The basic element is a cell that can be joined in arrays to tile a surface, each containing a processor, connections for power and communications, and means to control the local wall velocity The cell size is determined by the characteristic length scale of the flow field ranging from millimeters to centimeters to match the desired motion and fluidic system. Because boundary layer effects are significant across fluid states from aerodynamics to hydrodynamics to rheology, the possible implications of active control of the boundary layer are correspondingly far reaching, with applications from transportation to energy generation to building air handling. This thesis presents a feasibility study, evaluating current manufacturing, processing, materials, and technologies capabilities to realize programmable surfaces. / by Amy Sun. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 79-81). / The purpose of this thesis is to present the design and evaluation of a new type of socially assistive robot, one that can interact with people and collect various types of sensory input while being small enough to hold in one's arms. This project is a completely new revision of the Huggable project created by Dan Stiehl and Cynthia Breazeal, which features a new mechanical design, a revamped electronics structure, and a polished control system based off of its sister project, DragonBot (developed by Adam Setapen). This thesis describes the process of how this new design came to be, and provides extensive content on how it was designed, along with all major components that were included. An evaluation is also presented as a test run for the new Huggable, in the form of an online survey. The results, along with much of the work done with the initial prototype, showed that there is still much work to be done to be convincing as a robust research robot. Improvements are listed, as well as its future work with Boston Children's Hospital. This new design hopes to finally bring the Huggable project out into the field for actual use with people. / by Kristopher B. Dos Santos. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Program in Media Arts & Sciences, 1996. / Includes bibliographical references (p. [223]-238). / Kristinn Rúnar Thórisson. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2004. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 115-120) and index. / The eRadio project proposes to be an effective aid to increase interaction and reduce alienation among the members of dispersed communities by using a holistic approach to participatory and interactive web radio-production, with ad hoc methodology and ad hoc electronic tools. Through eRadio individuals can contribute to a participatory process of community self-discovery, identification, and assimilation by voicing their concerns and views as well as by expressing aesthetic and cultural ways of rejoicing. eRadio participators can trigger processes that may lead to the sustainability and empowerment of different segments of the dispersed community, and of the whole, by airing issues of collective importance and thus moving individuals, groups, and institutions to reflection and cooperation. Volunteers become communicators that get others to tell anecdotes or discuss issues as they audio-record them. Then they creatively edit and transmit the finished audio pieces via the web and, if local conditions permit it, they radio broadcast it. Interactive transmission from different sites is done by two or more segments of the dispersed community. The project includes development of a hardware and software package that supports simple task-based production of digital audio files. The hardware is a simple computer called "VoxPopBox" which can be connected to a portable digital recorder in order to download audio clips that have been recorded in the field. The software is divided into four task areas which guide the user through gathering audio, producing a piece, publishing their work, and listening to other audio publications. Each box is connected to other boxes via the Internet. This thesis describes the pilot implementation of the eRadio project with the Tulcingo community, which is a dispersed transnational community with a hometown in Mexico and about half of its population in New York City. After two nine-day workshops, we produced and transmitted two radio programs, one from the town of Tulcingo and the other from the city of New York. As a result the Tulcingo community is interested in a long-term eRadio implementation. If done, Tulcingo would be an eRadio seed community from which other communities can bloom. / by Carla Gomez-Monroy. / S.M.

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2006. / Includes bibliographical references (p. 58-60). / Graphs are often used in artificial intelligence as means for symbolic knowledge representation. A graph is nothing more than a collection of symbols connected to each other in some fashion. For example, in computer vision a graph with five nodes and some edges can represent a table - where nodes correspond to particular shape descriptors for legs and a top, and edges to particular spatial relations. As a framework for representation, graphs invite us to simplify and view the world as objects of pure structure whose properties are fixed in time, while the phenomena they are supposed to model are actually often changing. A node alone cannot represent a table leg, for example, because a table leg is not one structure (it can have many different shapes, colors, or it can be seen in many different settings, lighting conditions, etc.) Theories of knowledge representation have in general concentrated on the stability of symbols - on the fact that people often use properties that remain unchanged across different contexts to represent an object (in vision, these properties are called invariants). However, on closer inspection, objects are variable as well as stable. How are we to understand such problems? How is that assembling a large collection of changing components into a system results in something that is an altogether stable collection of parts? / (cont.) The work here presents one approach that we came to encompass by the phrase "graph dynamics". Roughly speaking, dynamical systems are systems with states that evolve over time according to some lawful "motion". In graph dynamics, states are graphical structures, corresponding to different hypothesis for representation, and motion is the correction or repair of an antecedent structure. The adapted structure is an end product on a path of test and repair. In this way, a graph is not an exact record of the environment but a malleable construct that is gradually tightened to fit the form it is to reproduce. In particular, we explore the concept of attractors for the graph dynamical system. In dynamical systems theory, attractor states are states into which the system settles with the passage of time, and in graph dynamics they correspond to graphical states with many repairs (states that can cope with many different contingencies). In parallel with introducing the basic mathematical framework for graph dynamics, we define a game for its control, its attractor states and a method to find the attractors. From these insights, we work out two new algorithms, one for Bayesian network discovery and one for active learning, which in combination we use to undertake the object recognition problem in computer vision. To conclude, we report competitive results in standard and custom-made object recognition datasets. / by Andre Figueiredo Ribeiro. / S.M.