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Hybrid CPU-GPU architectures for processing large scale data on limited hardware
No full textIn the ever-evolving domain of data processing, efficiently managing large-scale data in both offline and real-time scenarios has become a significant challenge. This dissertation introduces innovative hybrid CPU-GPU frameworks designed to meet the computational requirements of data-intensive environments in real-time, even with limited hardware. At the heart of these designs is a unique shared-memory-space approach, capable of facilitating data transfers and ensuring synchronization across multiple computations. The dissertation underscores the growing trend towards fast processing of large-scale data. Specifically, in sectors such as distributed sensing, there is a consistent demand for immediate real-time data processing. These designs utilize the strengths of both the CPU and GPU components, effectively navigating fluctuating workloads and overcoming computational challenges. Built to excel in various computing environments, the frameworks offer scalability, adaptability, and increased efficiency. The key components of the framework, including shared memory space utilization, process replication, CPU-GPU synchronization, and real-time visualization capabilities, are thoroughly analyzed to showcase its capacity in real-time data processing.Ph.D.Includes bibliographical reference
Towards in situ membrane protein structural biology using a multimodal integrative approach
No full textMembrane proteins mediate many key physiological functions and are highly acclaimed targets for therapeutic intervention. In fact, more than half of clinically approved drugs target human membrane proteins. The structure and functional dynamics of membrane proteins are intricately coupled to their surrounding membrane environment, making it critical to study them within the cellular context. Within biological membranes, lipid-lipid and lipid-protein interactions play major roles in the molecular organization of the membrane into distinct membrane microdomains featuring unique lipid and protein composition. These membrane microdomains are proposed to be involved in the spatiotemporal coordination of signal transduction and other essential cellular processes. However, the structural characteristics and functional implications of these membrane domains and their associated membrane protein complexes remain poorly understood.
Understanding cellular processes at the molecular and structural level represents the next frontier of biomedical research. In recent years, an integrative spatial and multimodal approach shows great promise in synergizing various experimental and computational techniques to yield significant structural and mechanistic insights into complex biological processes. Cryo-electron tomography (cryo-ET) is gradually becoming a key cornerstone of in situ cell biology research. This imaging modality rapidly emerged as a mainstream structural biology technique due to its unique capability to preserve and directly visualize the structural architecture of subcellular structures and macromolecular assemblies in their native cellular landscape. Cryo-ET provides unique opportunities to bridge the gap between light microscopy of whole cells and in vitro structure determination methods. Recent advances in the field have revolutionized cellular structural biology and have opened new avenues for understanding the structure and functional relationships of biomolecular complexes in their unperturbed state. Despite its potential, structural characterization by cryo-ET suffers from many inherent challenges. To overcome these limitations, cryo-ET is commonly integrated with complementary methods such as mass spectrometry (MS), structure prediction, biochemical and biophysical methods, to obtain a comprehensive glimpse into the subcellular universe at molecular resolution.
In this thesis, a multidisciplinary approach is used to investigate the structural characteristics of membrane microdomains and associated membrane proteins in two distinct biological membrane systems: thylakoid membrane from a marine diatom and plasma membrane from a human fungal pathogen. In Part II, we examine the heterogenous distribution of photosynthetic protein complexes in thylakoid membranes of Phaeodactylum tricornutum. To aid in the identification and localization of photosynthetic protein complexes embedded in isolated thylakoid membranes, we developed an integrative workflow that combines on-grid immunogold labeling and in situ cryo-electron tomography. By applying this methods development to isolated thylakoid membranes, we discovered two subpopulations of Photosystem II (PSII) within native thylakoid membranes, specifically semicrystalline arrays composed of dimeric PSII cores and PSII holocomplexes. This experimental workflow can be further applied to a range of biological specimens and facilitate structural studies of other protein complexes, especially those with no known 3D structures. In Part III, we investigate the structural architecture of plasma membrane microdomains in fungi and their functional relevance in the context of antifungal drug treatment. By combining cryo-ET with MS and biochemical and biophysical analyses, we provide structural and spatial insights into fungal plasma membrane proteins and confirm the existence of membrane compartments. In addition, our data suggest that echinocandin antifungals may interact with the local membrane environment to perturb the spatial distribution of membrane protein complexes.
Future work towards unraveling the structure and dynamics of membrane-embedded protein complexes and their organization into higher-order structures within biological membranes will provide crucial information on their role in regulating various cellular processes.Ph.D.Includes bibliographical reference
The birth of a legend: leitmotif as characterization in The legend of Zelda: skyward sword
No full textWhen the main theme for The Legend of Zelda: Skyward Sword (Wii, 2011) was revealed, dedicated fans were delighted to find it was a clever reversal of “Zelda’s Lullaby,” a theme introduced in A Link to the Past (SNES, 1992) and made famous in Ocarina of Time (N64, 1998). As many scholars have previously addressed (Lind 2016, Walch 2017, Summers 2020, Luo 2021), the Zelda series is well known for this type of musical reworking, in which familiar melodies are transformed across games in the franchise to create thematic continuity. Skyward Sword, however, was the first game in the series to include character themes that evolve within the game itself, similar to the treatment of motives in more narrative-focused series such as Final Fantasy. “Ballad of the Goddess” is one such example, serving both ludic and narrative functions. Ludically, players interact with the music to progress the story in reuniting Link with Zelda. Its most powerful role, however, is its dual narrative function: various iterations of the theme accompany moments in Link and Zelda’s journey, and it shares motivic content with their respective character themes. Most notably, through its link with “Zelda’s Lullaby,” it becomes part of a musical timeline, establishing a transmedial relationship with past Zelda games. Viewing “Ballad of the Goddess” as symbolic of Link’s and Zelda’s shared connection, I trace the musical progression of their relationship through formal, harmonic, and timbral transformations within the theme itself. I then address the theme’s relationship to Link and Zelda’s character themes, “Song of the Hero” and “Zelda’s Lullaby,” demonstrating various transformational procedures that affect the player’s ludic and narrative experiences (Bribitzer-Stull 2015, Anatone 2022). I conclude by addressing the theme’s transmedial implications beyond Skyward Sword through its connection to “Zelda’s Lullaby.” Ultimately, I suggest that the theme’s progression across different games establishes a unique localized timeline within the game’s fictional chronology through its decades-long transformational procedures. Skyward Sword thus serves as a case study for how thematic transformation, both within a single game and across a series, can be intricately connected to the mythology of a game’s fictional universe.M.A.Includes bibliographical reference
Bloom and vegetative bud break phenology of unique eastern filbert blight resistant hazelnut germplasms grown in New Jersey
No full textIn the United States, European hazelnut (Corylus avellana) is cultivated primarily in the Willamette Valley of Oregon; however, there is interest in expanding existing production in the eastern US. The main limiting factors in both regions is the fungal pathogen Anisogramma anomala, which causes the disease eastern filbert blight (EFB). While EFB can be managed with fungicides, the associated costs and challenges of spraying large trees make genetic resistance preferable. In the first study, a seed-based germplasm collection was made in 2009 in the Republic of Georgia and 1,374 of the subsequent seedlings were planted at Rutgers University, New Brunswick, NJ. They were exposed to high EFB pressure, and after 10 years, while most trees succumbed to disease, a small percentage of the trees (n=57) were found to exhibit high levels of resistance and hold significant value for breeding. In the first study, the flowering phenology of 57 trees originating from the Republic of Georgia were documented in the winter seasons of 2021-22 (Year 1) and 2022-23 (Year 2) and compared to a control group of 7 known cultivars with previously documented phenology. Results showed significant variation across the individual trees in the Georgian collection. Overall, the collection of Georgian trees demonstrated a wide range of bloom phenology, with significant overlap between Georgian pollen shed and controls’ pistillate receptivity, and individuals can be separated into early, medium, and late blooming categories. These results are useful to breeders who would integrate these novel sources of EFB resistance into their program, while ensuring that female flower bloom time or pollen release will be similar to that of other selections or cultivars. In addition to novel C. avellana germplasm, hybrids between C. avellana and C. americana are resistant to EFB. In the second study, the flowering phenology of 72 Rutgers University interspecific hybrid breeding selections from 16 different full sibling progenies was documented. The study also included seven hybrid breeding selections from the Upper Midwest Hazelnut Development Initiative and seven C. avellana cultivars as controls. All trees were surveyed twice weekly in the winter seasons of 2021-2022 and 2022-2023, and the phenology of their female flowers, male flowers (catkins), and vegetative buds recorded. The main goal was to document variation in the bloom times of the interspecific hybrid germplasm to identify compatible bloom partners within the trees studied in support of future cultivar releases. Results showed significant variation among the plant material evaluated, with more than 6 weeks in some cases separating the earliest from the latest blooming breeding selections. The European hazelnut controls tended to bloom (pistillate and staminate) earlier than the interspecific hybrids, but there were many that had overlapping bloom times, demonstrating a wide and useful range of bloom dates present in the hybrid germplasm suggesting hybrid selections could be paired with each other as well as with existing commercial cultivars.M.S.Includes bibliographical reference
User segmentation in recommender systems
No full textPersonalized recommendations are key for recommendation systems, which make profits by tailoring marketing strategies and targeting product offerings to distinct user groups. However, current personalized recommendation algorithms do not consider structures in user groups thereby producing non-robust recommendations. Our key insight is to integrate the previously ignored local structure of users into the recommendation algorithm, where we perform a structured user segmentation that considers the hierarchy in user structure. This improves the quality of the recommendations since they enhance their capability to decipher the essence of the user preferences over the noise. Capitalizing on the inherent hierarchical structure of user segments, our method reduces the model size and results in improved accuracy. We conduct experiments using four different approaches for computing user segments and evaluate their performance across various hyperparameter configurations. As far as we know, this is the first comprehensive evaluation on understanding the right user structure to employ for recommendations. Our results demonstrate that our method yields significant improvements in performance metrics across three diverse datasets. The improvement ranges from 9% to 13% across 5 well-known metrics for a large-scale dataset and around 1-2% on two other small datasets. It also gives a significant improvement of around 20% for Relevance to Other Users (ROU) metric that captures the proportion of similar users who have liked an item being recommended to the user.M.S.Includes bibliographical reference
The role of posterior medial thalamic nucleus in the modulation of striatal circuitry and choice behavior
No full textLearned behaviors require the processing and transformation of sensory stimuli intomotor actions, a process known as sensorimotor integration. Disruption of this process is implicated in numerous movement disorders (e.g., Parkinson’s disease) and disproportionately affects the basal ganglia, a collection of subcortical structures vital for decision-making. The striatum, the predominant input of the basal ganglia, receives widespread excitatory input from cortical and thalamic sources, yet their influence over the diverse striatal microcircuitry, and subsequent behavior, is unknown. This thesis strives to elucidate the functional role of the posterior medial (POm) thalamic nucleus in modulating the striatal microcircuitry using a combinatorial approach of mouse genetics, electrophysiology, fiber photometry, optogenetics, and behavioral analysis. Slice electrophysiology revealed robust POm-striatal innervation of three identified striatal cell types (D1-SPN, D2-SPN, and PV interneurons), with similar postsynaptic potential amplitudes, similar degrees of paired-pulse ratio, but cell-type specific differences in short-term synaptic plasticity. In vivo fiber photometry of POm-striatal projections during a Go/NoGo whisker-based discrimination task revealed markedly increased and stereotyped calcium and pupil activity across the learning timespan relating to texture arrival in the whisker field. Strikingly, calcium activity was robustly correlated with pupil activity and became more anticipatory with learning, but not with licking. Further, no differences were observed in the calcium activity related to the two presented textures or to the four potential outcomes, highlighting a potential learning-related arousal role for POm. To interrogate this, POm-striatal axon terminals were inhibited during the same Go/NoGo task, and inhibited mice required a larger number of training sessions to expertly discriminate between the textures. This work posits that POm provides an excitatory priming signal to the striatum in preparation for more processed cortical information to arrive later for action selection.Ph.D.Includes bibliographical reference
Effect of plasma activated mist (PAM) on inactivation of Listeria innocua and Klebsiella michiganensis on selected surfaces
No full textCurrent fresh produce surface treatment methods for food safety include spraying or washing the produce with chemical sanitizers like chlorine, which may not be environmentally friendly. Cold plasma generated by Dielectric Barrier Discharge (DBD) and Plasma-Activated Mist (PAM) have shown the potential as alternatives to these sanitizing treatments. PAM is a mist of micron-sized water droplets that have been exposed to DBD plasma. DBD generates ozone and other excited nitrogen species with antimicrobial properties. PAM contains highly reactive oxygen and nitrogen species (RONS), which act as oxidizing agents and contribute to its antimicrobial properties. The objectives of this study were (1) to enumerate the microbial inactivation caused by DBD and PAM on TSA and glass slides and (2) to determine the efficacy of PAM on grape tomato, lime, and spiny gourd which have different surface topology.
TSA plates separately inoculated with Listeria innocua and Klebsiella michiganensis were exposed to atmospheric pressure DBD plasma from 5 min to 20 min. Listeria innocua is a surrogate of pathogen Listeria monocytogenes and Klebsiella michiganensis is a surrogate of pathogen Salmonella. Bacterial reduction by DBD ranged from 3.4 to 4.8 log CFU/plate for Listeria innocua and from 2.1 to 4.5 log CFU/plate for Klebsiella michiganensis. For glass sides (surface roughness Pq = 0.28 ± 0.02 μm) which were spot inoculated similarly, the resulting log reductions were 2.9 to 4.2 log CFU/slide for Listeria innocua and 3.6 to 5.0 log CFU/slide for Klebsiella michiganensis. Higher values correspond to longer exposure times.
Experiments were conducted on TSA and glass slides which spot inoculated separately by Listeria innocua and Klebsiella michiganensis and exposed to PAM from 5 min to 20 min. TSA plates showed reduction of 2.4 to 5.1 log CFU/plate for Listeria innocua and 2.5 to 4.0 log CFU/plate for Klebsiella michiganensis, depending upon the exposure time. For the glass slides reduction was 1.1 to 3.2 log CFU/slide for Listeria innocua and 3.4 to 4.8 log CFU/slide for Klebsiella michiganensis.
In the experiments involving fresh produce, grape tomato (surface roughness Pq = 5.17 μm ± 0.53 μm), lime (Pq = 18.76 μm ± 3.00 μm) and spiny gourd (Pq = 101.50 μm ± 10.95 μm) were spot inoculated with known concentrations separately by Listeria innocua and Klebsiella michiganensis and treated in PAM for 5 min to 20 min. Bacterial reduction for Listeria innocua on the grape tomato was 2.7 to 3.4 log CFU/surface, on lime it was 2.3 to 2.7 log CFU/surface and for spiny gourd it was 0.7 to 1.0 log CFU/surface. The corresponding reductions for Klebsiella michiganensis were: 2.6 to 4.6 log CFU/surface for grape tomato, 2.2 to 3.7 log CFU/surface for lime, and 0.99 to 1.8 log CFU/surface for spiny gourd.
Thus, both DBD and PAM have antibacterial potential in surface applications. However, between DBD and PAM, PAM is preferred since DBD produces ozone, which may not be environmentally friendly. Further studies can focus on scaling up of PAM for industrial applications.M.S.Includes bibliographical reference
Ökonomien des Untergangs. Krisen und Kreisläufe bei Fritz Lang und Thea von Harbou, Joseph Roth und Franz Kafka
No full textThis dissertation explores how crises in capitalism are depicted in Austrian novels and film of the 1920s. It undertakes an extensive investigation of economic theories that negotiate the prevalence of different economic systems considering socioeconomic factors of Austria and Germany during the interwar period. While the focus of the theoretical framework lies on the Austrian School of Economics, opponent theories are consulted to put the contemporary economic schools of thought into a dialogue. In Fritz Lang’s and Thea von Harbou’s silent film Dr. Mabuse, the Gambler (1922), in Joseph Roth’s novel Hotel Savoy (1924), and in Franz Kafka’s novel fragment The Man Who Disappeared (1927), crises are represented not just in a close relation to the financial instabilities of their characters. Their portrayal and the formal structure of each work are inextricably linked with how the capitalist system of the early twentieth century shaped and changed the European social order. Lang’s and Harbou’s Mabuse illustrates the tension between liberalism and interventionism that was highly debated in politics and economic theory in the context of hyperinflation. While addressing manifold themes of the time, the plot oscillates between critically commenting on neoclassical ideas and elevating liberal ideals. The analysis of Roth’s Hotel Savoy reveals the circular movements of the capitalist system, thus referencing contemporary business cycle theories, through the protagonist’s migration from ascent to descent, from destruction to reinvention, keeping him in a constant loop of unfulfilled dreams. Kafka’s The Man Who Disappeared maps out several stages of the history of capitalism in a series of ironic and nightmarish visions of power dynamics which decipher “free” capitalist societies as systems of radical dependencies. My examination shows how features of today’s form of capitalism have already been observed and reflected in film and literature a century ago: Economic concepts like game theory, animal spirits, creative destruction, hegemony, and surveillance capitalism are discussed in Mabuse, Hotel Savoy, and The Man Who Disappeared. While approaching these issues very differently, the fate of the protagonists and the narrative structures of all three works allow one common conclusion: It is easier to imagine no end than the end of capitalism.Ph.D.Includes bibliographical reference
Injustice and the criminal law: defending radical solutions
No full textOur present criminal legal institutions are deeply flawed and require radical change. This dissertation presents, evaluates, and defends a series of proposals about how we should restructure our criminal-legal institutional landscape. Each chapter addresses a different proposal, including calls to (i) abolish incarceration, (ii) reallocate institutional responsibilities and powers from police to other institutions, and (iii) institute non-carceral, transformative justice strategies in response to gender-based and sexual violence. These proposals have precipitated divisive and at times murky debates. One goal of the project is to add philosophical clarity to these debates and to help refine the most normatively attractive versions of these proposals. A second goal is to offer arguments in favor of them. Proposals in this vicinity have too often been dismissed and not given due attention in ethics, political philosophy, and philosophy of criminal law.
In “Defending Incarceration Abolition,” I analyze and ultimately defend the abolitionist claims (1) that jails and prisons are flawed beyond repair and that we should gradually do away with them (the abolitionist negative proposal), and (2) that we should install an alternative set of institutions and measures, including a more robust system of social support to prevent crime upstream and transformative justice systems to respond to it without incarceration when it inevitably occurs (the abolitionist positive proposal) (Davis 2011; Mathiesen 1974; McLeod 2015). I begin by providing a detailed account of this abolitionist institutional design proposal. I then canvas a series of objections to the practice of punishment by incarceration, ranging from skepticism about moral responsibility to the concern that incarceration perpetuates endemic injustice. I show how we can use these objections to ground the conclusion that we should abolish incarceration, discussing how, among other issues, abolitionists must respond to the “appeal to necessity,” or the charge that though objectionable, incarceration may be justified if alternatives are worse still (Boonin 2008). In responding to the appeal to necessity and a variety of other objections, the paper offers a novel defense of abolitionism in light of criticisms, especially that advanced in Tommie Shelby’s The Idea of Prison Abolition (Shelby 2022).
I focus on a second radical proposal in “Why We Should Unbundle the Police,” arguing that we ought to reallocate powers and resources away from police towards other public institutions that are not tied to the criminal-legal system— what I call the unbundling proposal (Kaba and Ritchie 2022; Vitale 2021). Unbundling requires reimagining the present distribution of responsibilities among institutions, and in the chapter, I draw on and engage with several extant reform proposals. I first present one version of the unbundling proposal, distinguishing the various components of policing that ought to be reallocated to other institutions. Some of these components include traffic patrol, intervening in non-serious interpersonal conflicts, and responding to people dealing with addiction, homelessness, and mental health crises. I then offer three arguments in support of the proposal which reflect rationales that emerge in policing-critical social movements. The first, the argument from minimally violent capacities, claims that we should redistribute police responsibilities because public institutions ought to have violent capacities only as a last resort. The expertise argument claims that we should assign more narrow roles to police because requiring police to respond to a motley array of social problems is epistemically over-demanding. The third argument, the argument from injustice, focuses on non-ideal considerations about the effects of policing in inegalitarian societies. These non-ideal considerations include the fact that policing is disproportionately burdensome to marginalized people and racial minorities (especially Black people in the case of the United States). Drawing on broad principles of what we should do when institutions are infected with injustice, I argue that significant structural changes, like unbundling, offer an appealing ameliorative solution.
The final chapter is entitled “Beyond Carceral Feminism.” Over the past several decades, feminist movement organizing has come up against a dilemma in determining appropriate responses to gender-based and sexual violence. On one hand, taking gendered violence seriously and working to eradicate it are central and urgent feminist projects. On the other hand, as many critics have noted, employing the criminal law towards these feminist ends not only fails to achieve them, but also expands the web of mass incarceration and perpetuates structural injustice (Davis et al. 2022; Goodmark 2020; Gruber 2020; Richie 2012). In this chapter, I clarify what this tension amounts to and argue for the anti-carceral, abolitionist feminist ideas that incarceration is an inappropriate response to gender-based and sexual violence and that we should look towards transformative justice and community accountability (TJCA) solutions instead. My negative argument appeals to how carceral responses to gendered violence undercut the functions at which they aim in the context of racialized mass incarceration. The positive argument for transformative justice solutions claims that they foster a more robust form of corrective justice because they enable morally valuable forms of interpersonal engagement, empower victim survivors, and effectively express condemnation of wrongful behavior. I conclude by responding to some of the objections raised against transformative justice and community accountability approaches, particularly in the context of responses to gender-based and sexual violence.
Together, the three chapters explore largely uncharted territory at the intersection of philosophy of criminal law, political philosophy, and social movement theory. Throughout, I engage with analytic philosophers in moral, legal, and political philosophy, such as Tommie Shelby, John Rawls, Anthony Duff, Charles Mills, and David Boonin, but I also draw on and engage with activism-oriented scholars including Angela J. Davis, Mariame Kaba, Beth Richie, Dorothy Roberts, and Alex Vitale.Ph.D.Includes bibliographical reference
Exploring students' sense of agency over course performance in an extended general chemistry course
No full textGeneral chemistry is often considered a “weed out” course by students due to its perceived difficulty and high failure rates. Here we explored how students’ perspectives of their agency over their performance relate to their success in general chemistry and their chemistry self-concept using a mixed methods research design. We also explored factors that impacted students’ sense of agency. Logistic regression analysis of survey results indicated that a general positive relationship exists between sense of agency and final course outcomes but not with chemistry self-concept. Frequent knowledge of performance and attitudes towards chemistry were positively correlated with sense of agency, while self-reported attendance at lectures, recitations, and office hours or study groups was not significantly correlated with agency. Qualitative survey results supported these findings and suggested that student agency influences course outcomes through its impact on motivation and self-regulated study behaviors. Frequent feedback, resource use, and effort beliefs contributed to high sense of agency. The results presented herein form the basis for future exploration of the impact of course structure on student agency and achievement in chemistry courses.M.S.Includes bibliographical reference