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The Complete Interactome with 5-D GPU Accelerated Analysis, Visualization, and UI for Biological Microscopy Applications
No full textMicroscopes now have the ability to collect highly complex data. This thesis presents new algorithms and software packages for analyzing, visualizing, and interacting with biological microscopy image datasets. These new software packages provide functionality not available with existing methods. Along with new functionality, the methods described here are of higher accuracy compared to existing methods. These new software packages provide significant improvements in computational efficiency and usability. Contributions described within this thesis are biologically motivated with examples given throughout. The analysis presented has enabled new biological discoveries along with new mathematical analytic techniques. This thesis is broken into three distinct areas: analysis of interactions between organelles describing the complete interactome, a hardware accelerated image processing library, and software packages providing visualization, validation and analysis. First the complete interactome describes a new method of quantifying the interactions of all of the organelles within a single cell. Where prior methods focus on pairwise interactions, methods described here include a robust quantification method for these high order interactions. Secondly, a hardware accelerated image processing library and framework called Hydra Image Processor (HIP). HIP is capable of swiftly processing arbitrarily large datasets. The HIP framework automatically (without user intervention) distributes data and schedules processing across all available graphic processing units. In addition, HIP processes the edges of images with higher precision than currently available methods. Lastly, visualization, validation, and analysis tools are presented. Visualization of high dimensional datasets captured by modern microscopes is non-trivial. Integrating processing, segmentation, and tracking results embedded is also a challenge. Software packages presented here perform all three of these task within the scripting environment of MATLAB for fast prototyping and swift user interface generation. Validation tools are also described that incorporate user input to inform unsupervised algorithms and reduce underlying segmentation and tracking results significantly. All methods and contributions of this thesis are biologically motivated. Within the three areas described above are biological examples where these methods contributed significantly. They range from describing the high-order interactions within a single cell, to lineaging stem cells in 5D, to the reconstruction of large montage images of the Subventricular Zone. The adoption of these methods will enable future biological findings within highly complex datasets captured by modern and future microscopes.Ph.D., Computer Engineering -- Drexel University, 201
Neighborhood Business Improvement District Planning: Representative Collaboration in Philadelphia
No full textBusiness Improvement Districts (BIDs) are an increasingly popular format for sustainably providing supplemental services and enhancements to neighborhood-scale commercial corridors and their surrounds. Some have argued that they are a neoliberal mechanism for privatization of community production that ought to be commonly held, an antidemocratic institution that favors an elite marginal class of property owners. In contrast, others view BIDs as instruments for effective and representative commons management, devices that create opportunities for participative citizenship and collectively pool resources for the benefit of many. This thesis describes the processes of planning and establishing BIDs in the Philadelphia neighborhoods of Northern Liberties and Fishtown. It sites them in the context of Pennsylvania’s unique BID legislation and employs theories of the commons to evaluate the collaborative community definition that they underwent. Their cases qualitatively demonstrate that neighborhood BID planning can produce truly representative BIDs. Part I contains an introductory statement of purpose and methodology. In Part II, I situate this project in the literature on BIDs and their controversies, and cover the particular history of Pennsylvania’s legislative basis and how it impacts BIDs in Philadelphia. I also suggest that the urban implications of certain theories of the commons can form a basis for optimal neighborhood BID planning. Part III contains my case studies, fronted by a contextualization of the two neighborhoods. Lastly, in Part IV I present my analysis, evaluating these neighborhood planning processes as considerations of unique community contexts and the particular BID scales and forms that followed.M.S., Urban Strategy -- Drexel University, 201
Visual Feedback within Virtual Reality with the use of Exaggeration
No full textVirtual Reality environments provide a novel setting for studying the interaction between a player and virtual objects. In particular, this setting allows an exploration of the use of visual feedback to improve qualities of this interaction. With a lack of suitable visual feedback within VR games, we believe that the use of the Animation Principle of Exaggeration within interactions can improve immersion within VR games. We constructed a corresponding prototype in which participants interacted with two types of objects (materials) five times, each object reacted differently than one another during these interactions. While these interactions were taking place we asked a number of questions referring to how the materials felt physically, how real they felt, and how fun or enjoyable they were to interact with. During the project, most testers expressed that materials with higher levels of exaggeration in their visual feedback were more physical and fun. But it was split between materials with less exaggeration and more exaggerated feedback when it came to the materials feeling real. Overall, we present a promising approach on how to further investigate this topic.M.S., Arts Administration -- Drexel University, 201
Characterization of Testosterone-Loaded Polydimethylsiloxane Pellets for a Mouse Model of Metastatic Prostate Cancer
No full textApproximately one in six men are affected by prostate cancer, making it the most common cancer among men in the United States. For localized disease, the five-year survival rates are around 99%, however two out of every three patients that progress to metastatic disease will succumb to prostate cancer within five years. Androgens play a significant role in prostate cancer progression and biology and are a therapeutic target to slow metastatic progression. Most mouse models that are used to study prostate cancer do not incorporate changes in androgen level into the system. Here, we produce and characterize a silicone-based pellet loaded with testosterone optimized for use in a mouse model. The pellet provides slow release of bioactive testosterone in vitro and induces no cytotoxicity. Subcutaneously implanted in mice, the pellet provides elevated testosterone levels for two weeks, and surgical removal of the pellet causes serum testosterone levels to drop to castrate levels within two days. Importantly, the pellet induces minimal inflammation as observed histologically, meaning that the pellet can be implemented in a mouse model of metastatic prostate cancer without inducing the release of cytokines and other factors that may alter disease biology.M.S., Biomedical Engineering -- Drexel University, 201
Division I Athletic Directors' Leadership Influence on Athletic Departments: A Multi-Site Case Study
No full textThe purpose of this multi-site case study was to explore the leadership practices of NCAA Division I athletic directors to better understand how their leadership approaches influence goal attainment at the institutions that they serve. This research sought to provide insights that may inform those responsible for the selection of effective athletic directors at Division I institutions. The findings of this research may also offer information for professionals seeking to become athletic directors in Division I institutions that will allow them to hone their leadership skills. The goal of this multi-site study was to create a holistic view of athletic director leadership by replicating data collection within the three different sites (Yin, 2014). The overarching research question that guided this study was, "What influence does a Division I athletic director's leadership have on the athletic department?" Subquestions that supported this research included: (a) How do Division I athletic directors describe their leadership practices? (b) How do Division I athletic department staff describe the athletic director's leadership approach and its effect on the work environment? (c) What are the best leadership practices of Division I athletic directors and how are they perceived to influence the outcomes of athletic programs? The conceptual framework that informed the current study consisted of three streams of theory, research, and practice: background of college athletics; development of the athletic director's role; and athletic director leadership. Findings that emerged from thick descriptions included that: (a) Successful Division I athletic directors have strong interpersonal skills and relate well with others. (b) Strong athletic director leadership requires the ability to identify, cultivate, develop and delegate to staff. (c) The athletic director's ability to create a vision in alignment with the university is significant. (d) The student athlete's experience is central to operational practices. (e) Athletic director abilities are aided through background and training experiences in management, as well as through working with and relating to others. All three sites within this study offered clear evidence that athletic director leadership is linked directly with the effectiveness of their athletic departments, and the skills cited in the study influence outcomes within their departments.Ed.D., Educational Leadership and Management -- Drexel University, 201
Metaphor in Motion: Using Dance/Movement Therapy with Women Living with Eating Disorders
No full textThe purpose of this project was to develop a method to engage women living with eating disorders in an exploration of metaphor through movement in order to deepen their capacity for working with abstract metaphor while using it to explore therapeutic themes. Relevant literature and research are reviewed in order to provide a strong theoretical rationale for the method. The literature review includes a selection of articles addressing eating disorders, the use of metaphor in therapy, metaphor in the context of eating disorder treatment, metaphors used by women living with eating disorders, concretized metaphor and eating disorders, dance/movement therapy approaches for eating disorders, dance/movement therapy and metaphor, Space, Weight, and Time Factors, and metaphor and body memory. The method, Metaphor in Motion, is intended to provide a framework for engaging patients in a movement exploration of three therapeutic themes: the self, the function of the eating disorder, and the recovery/change process. Metaphor in Motion utilizes Space, Weight, and Time Effort factors to encourage exploration of movement metaphors in a group setting. Additionally, I discuss the sources of method development, how the method fit into the site’s existing treatment model, my own reflections on the development process, and my insights about myself as the person of the therapist.M.A., Dance/Movement Therapy and Counseling -- Drexel University, 201
Improving Team Behaviors Utilizing Simulation
No full textA team of healthcare professionals responds immediately when a call for help occurs during cardiac arrest in a hospital setting. Patients who suffer from a cardiac arrest in the hospital rely on a high level of team performance for improved survival. The inability to have a consistent team available seven days a week, day and night, creates challenges to produce a high functioning team for success. Simulation has been identified as an education methodology that allows teams to practice clinical events in a safe environment. Incorporating team behaviors in this training can improve team functions even when the team changes from shift to shift. The purpose of this Doctor of Nursing Practice project is to demonstrate the effectiveness of a one-hour simulation training exercise on team behaviors of ad hoc resuscitation teams. The structure of the team includes registered nurses (RN), physicians, physician assistants (PA), respiratory therapists (RT) and pharmacists, who respond to rapid response/code alerts. Participants will take part in a simulated cardiac emergency. A team attitudes survey was presented both pre and post simulation. There was no statistical difference in team attitudes, however post survey comments denoted positive learning experience. The Team Emergency Assessment and Measurement (TEAM) tool measured the simulation pre and post debriefing after repeating the same scenario. The overall TEAM score noted a statistical significant change in the team behaviors (p=.000). Results noted an improvement of the score for the TEAM tool.D.N.P., Nursing Practice -- Drexel University, 201
A Knitting Group for Survivors of Intimate Partner Violence: Untangling the Unraveling
No full textThe following capstone describes a knitting group which takes place in a safe haven for survivors of intimate partner violence. This method was developed based on the potential benefits of using fiber arts, the capability of knitting to fulfill a neurodevelopmental approach to art therapy, and the ability for the group to be informed by an intersectional approach. Implementation of this method highlighted knitting as building social support, experiences of mastery, aspects of growth, development of coping skills, relaxation, increased self-worth, opportunities for gift giving, inspiration of humor, and reflection from the staff. Recommendations for future research include pre and post group assessments, greater diversity within the group, distinction between children and adult groups, observations of stages of change, and incorporating knitting into mindfulness groups.M.A., Art Therapy and Counseling -- Drexel University, 201
High Performance Polymer Membranes for CO2 Removal and Water Treatment
No full textTo decrease the current level of CO2 emissions appreciably, more efficient CO2-capture technologies are needed. Absorption is currently used widely to lower CO2 level in gases. However, it is relatively expensive (in terms of both operating and capital costs), bulky, and challenging to operate (foaming, entrainment and flooding of the absorber). Compared to absorption, the membrane technology is more energy-efficient, has lower operating costs, is compact and modular, and has a simple process. Among membranes, polymer of intrinsic microporosity (PIM) membranes with high free-volume created by rigid moieties have superior gas-transport properties. However, presently these membranes suffer from two fundamental and industrially‐important problems of low-to-modest selectivity and fast physical aging. Among PIMs, pentiptycene-based membranes exhibit satisfactory selectivity, and excellent resistance against plasticization and physical aging. However, the presence of two ethereal oxygens in the backbone of these membranes causes efficient chain packing, resulting in a decrease in free volume and consequently gas permeability. Pentiptycene is a highly rigid moiety from iptycene family consisting of five benzene rings forming an H-shaped core block. A fractional free volume (FFV) of less than 0.2 has been reported for existing pentiptycene-based membranes. To enhance the FFV of pentiptycene-based membranes, in this work: for the first time a pentiptycene-based dianhydride containing two etheric oxygens was synthesized and characterized; and a high molecular-weight pentiptycene-based polyimide was synthesized and characterized. The polyimide showed remarkable thermal stability, excellent solubility in common organic solvents, and the highest CO2 permeability (812 barrer) among all reported pentiptycene-containing polymers (about 6 times higher than the most permeable one) without sacrificing the selectivity. Currently polymer membranes suffer from the trade-off relationship between the permeability and selectivity. The fabrication of membranes made from polymers embedded with nanomaterials can lead to mixed matrix membranes (MMMs) with high gas permeability and excellent sieving ability. However, the agglomeration of nanomaterials, the formation of interfacial defects, and the incompatibility between the polymer and nanomaterials are still challenges in the fabrication of MMMs. In this research, these fundamental problems were studied through engineering the dispersion of the nanoparticles in polymer matrices via nanoparticles functionalization and considering polymer chemistry. TiO2 nanoparticles were grafted using 3-aminopropyl-diethoxymethylsilane [a silane coupling agent (AS)], their surface was then modified using carboxymethyl chitosan (CMC), and, the modified TiO2 nanoparticles were incorporated into the Pebax as the polymer matrix. The Pebax-modified-TiO2 nanocomposite membranes showed improved CO2 permeability and CO2/N2 selectivity, compared to the pristine Pebax. Characterization techniques showed good compatibility of the nanoparticles and the polymer and satisfactory dispersion of the nanofillers into the polymer. The influence of cyanuric chloride (CC) nanoparticles and its derivatives, melamine (M) and 2, 4, 6-trihydazino-1, 3, 5-triazine (THDT), on the performance and characteristics of a polyurethane (PU)-based nanocomposite membranes was investigated. Characterization results showed that the CC nanoparticles were mostly distributed in the PU hard segments. Also, M and THDT nanoparticles were scattered in the PU soft segments. Incorporating organic nanoparticles with many amine groups (i.e., M and THDT) showed to be an appealing strategy to fabricate highly selective membranes. This work indicated how robust interfacial interactions between nanoparticles and a polymer improve the polymer/nanoparticles compatibility and lower the level of defects in CO2-separating membranes. Increasing daily demand for clean water and limited fresh water resources has motivated studies on sustainable water furification. The membrane technology is suitable for water and wastewater treatment owning to its compactness, simplicity, small footprints, and sustainability. Among membrane-based processes, forward osmosis (FO) is one of the most promising methods having high water recovery, hydraulic pressure independency, and low-cost. However, fouling and biofouling of thin-film composite (TFC) FO membranes are still major challenges. An attractive strategy to improve fouling-resistance of FO membranes is the addition of antibacterial nanomaterials to the active layer of a TFC membrane. We studied the primary antibacterial mode-of-action (MoA) of Ti3C2Tx MXene nanosheets against both Gram-negative and Gram-positive bacteria. To characterize the antibacterial properties of Ti3C2Tx MXene in a well-quantitative manner, we used the flow cytometry (FC) and fluorescence imaging (FI) techniques. Our results indicated that the antibacterial activity of the MXene nanosheets are both size- and time-dependent; that is, smaller sizes of the nanosheets result in the release of bacteria cytoplasmic DNA and eventually dispersion of the bacteria envelope. In another work, we synthesized and characterized a silver-based metal-organic framework (Ag-MOF) embellished with graphene oxide (GO) [GO-Ag-MOF] with potent antibacterial activity. A thin-film nanocomposite (TFN) membrane with superior anti-biofouling and good antifouling properties was fabricated the GO-Ag-MOF nanocomposite to the selective layer of a TFC membrane. In addition to membrane characterization, fouling and antifouling resistance of the membrane was assessed through FO experiments in the presence of sodium alginate and E.coli and in the feed solution, respectively.Ph.D., Chemical Engineering -- Drexel University, 201
Data-driven Whole Building Fault Detection and Diagnosis
No full textResidential and commercial buildings are responsible for more than 40% of the primary energy consumption in the United States. Energy wastes are estimated to reach 15% to 30% of total energy consumption due to malfunctioning sensors, components, and control systems, as well as degrading components in Heating, Ventilation, Air-conditioning (HVAC) systems and lighting systems in commercial buildings in the U.S. Studies have demonstrated that a large energy saving can be achieved by automated fault detection and diagnosis (AFDD) followed by corrections. Field studies have shown that, AFDD tools can help to reach energy savings by 5-30% from different systems such as HVAC systems, lighting systems, and refrigeration systems. At the same time, the deployment of AFDD tools can also significantly improve indoor air quality, reduce peak demand, and lower pollution. In buildings, many components or equipment are closely coupled in a HVAC system. Because of the coupling, a fault happening in one component might propagate and affect other components or subsystems. In this study, a whole building fault (WBF) is defined as a fault that occurs in one component or equipment but causes fault impacts (abnormalities) on other components and subsystems, or causes significant impacts on energy consumption and/or indoor air quality. Over the past decades, extensive research have been conducted on the development of component AFDD methods and tools. However, whole building AFDD methods, which can detect and diagnose a WBF, have not been well studied. Existing component level AFDD solutions often fail to detect a WBF or generate a high false alarm rate. Isolating a WBF is also very challenging by using component level AFDD solutions. Even with the extensive research, cost-effectiveness and scalability of existing AFDD methods are still not satisfactory. Therefore, the focus of this research is to develop cost-effective and scalable solutions for WBF AFDD. This research attempts to integrate data-driven methods with expert knowledge/rules to overcome the above-mentioned challenges. A suite of WBF AFDD methods have hence been developed, which include: 1) a weather and schedule based pattern matching method and feature based Principal Component Analysis (WPM-FPCA) method for whole building fault detection. The developed WPM-FPCA method successfully overcome the challenges such as the generation of accurate and dynamic baseline and data dimensionality reduction. And 2) a data-driven and expert knowledge/rule based method using both Bayesian Network (BN) and WPM for WBF diagnosis. The developed WPM-BN method includes a two-layer BN structure model and BN parameter model which are either learned from baseline data or developed from expert knowledge. Various WBFs have been artificially implemented in a real demo building. Building operation data which include baseline data, data that contain naturally-occurred faults and artificially implemented faults are collected and analyzed. Using the collected real building data, the developed methods are evaluated. The evaluation demonstrates the efficacy of the developed methods to detect and diagnose a WBF, as well as their implementation cost-effectiveness.Ph.D., Architectural Engineering -- Drexel University, 201