VictorJuiz/thesis huggingface dataset:
Empowering deep learning with graphs

Deep learning has reshaped the research and applications in artificial intelligence. Modern deep learning models are primarily designed for regular-structured data, such as sequences and images. These models are built for tasks that take these regular-structured data as the input (e.g., classification, regression), as the output (e.g., generation), or as the structural prior (e.g., neural architecture design). However, not all forms of data are regular-structured. One notable example is graph-structured data, a general and powerful data structure that represents entities and their relationships in a succinct form. While graph-structured data is ubiquitous throughout the natural and social sciences, its discrete and non-i.i.d. nature brings unique challenges to modern deep learning models. In this thesis, we aim to empower deep learning with graph-structured data, by facilitating deep learning models to take graphs as the input, the output, and the prior. My research in these three directions has opened new frontiers for deep learning research: (1) Learning from graphs with deep learning. We develop expressive and effective deep learning methods that can take graphs as the input, which promotes the learning and understanding of graphs. (2) Generation of graphs with deep learning. We formulate the generation process of graphs using deep learning models, which advances the discovery and design of graphs. (3) Graph as the prior for deep learning. We discover that graph structure can serve as a powerful prior for neural architectures and machine learning tasks, which opens a new direction for the design and understanding of deep learning. Finally, we discuss the wide applications of the above-mentioned techniques, including recommender systems, drug discovery, neural architecture design, and missing data imputation

Advisor: Leskovec Jurij
Ermon Stefano
Ma Tengyu
Empowering disease diagnostics and deriving biological insight with publicly available gene expression data

Public data repositories and other data sharing platforms have been a massive boon to researchers in the biomedical sciences. Data sharing can reduce costs, save valuable time, and helps ensure the transparency of public research. In our lab, these public data have become the foundation of most of our analyses -- many projects would not be possible without access to a wide array of datasets comprising many different diseases, regions, ethnicities, medical histories, and so on. Furthermore, as we have repeatedly demonstrated, the robustness that we can achieve from integrating large amount of heterogeneous data has allowed us to make findings that are both significant and durable. However, designing projects around public data can be a double-edged sword. When relevant data is available, it can allow for more efficient and more powerful analyses. But when the data is not present or lacking in quality, it can impose severe limitations on the types of analyses that can be done and on the types of questions that can be asked. Here, we designed a novel multi-cohort analysis framework called Multicohort ANalysis of AggregaTed gEne Expression (MANATEE) to integrate large numbers of gene expression datasets for use in generating signatures of disease. MANATEE utilizes a conormalization method to pool samples across many datasets, as long as each dataset contains healthy control samples. This framework lets us utilize far more datasets than was previously possible, which not only allows for existing analyses to be made substantially more robust, but it also opens new avenues of exploration that were previously impossible to analyze using publicly available data. By utilizing MANATEE with publicly available gene expression datasets, we developed multiple host-response-based signatures of disease, all of which were derived from gene expression in human blood. These include a diagnostic for differentiating between bacterial and viral infection in febrile individuals, a prognostic for assessing whether a patient with viral infection will have a severe or mild outcome, and a signature for both distinguishing tuberculosis from other conditions and for predicting when patients with latent tuberculosis infection will progress to active tuberculosis. We validated each of these signatures in prospective cohorts, demonstrating their ability to generalize to new data. These results highlight MANATEE's ability to leverage public data in creating signatures that maintain performance across the heterogeneity present in real-world patient populations. Furthermore, the signatures we have developed are in the process of being translated into point-of-care, non-invasive diagnostic and prognostic tests which have the potential to significantly improve clinical practice

Keywords: Immunology.
Advisor: Khatri Purvesh
Andrews Jason Randolph 
Jagannathan Prasanna
Utz Paul
Engineered biosynthesis of high-value therapeutics in a plant chassis

Plants are known to produce a wide array of chemicals, and many plant natural products display medicinal properties beneficial to human health. These compounds have served as an inspiration to modern medicine, and recent technological advances have accelerated discovery and engineering of plant biosynthetic pathways. With the improved understanding of plant chemistry, we engineered biosynthesis of natural products and their analogs for therapeutic development. To demonstrate the value of engineered biosynthesis, we sought to improve production of etoposide aglycone, the complete biosynthetic pathway of which has been fully elucidated and reconstituted in a plant chassis, Nicotiana benthamiana. We first demonstrate milligram-scale production of a late-stage intermediate to etoposide aglycone and its desmethoxy analog through overexpression of primary metabolic enzymes and engineering of secondary metabolism. We then aimed to exploit the native transcriptional regulation for metabolic engineering and show that a single transcription factor can not only improve the pathway flux for etoposide aglycone biosynthesis but also suppress the competing metabolism. Additionally, we proposed to improve etoposide through development of its analogs with an altered activity profile. Previously, a hepatic metabolite of the chemotherapeutic etoposide has been implicated with treatment-related leukemogenesis. To address this issue, we hypothesized that etoposide analogs resistant to hepatic metabolism could be biosynthetically prepared. The first step of the pathway, coupling of coniferyl alcohol, is stereoselectivity-guided by a plant dirigent protein. We show that the plant dirigent protein demonstrates expanded substrate versatility, promoting asymmetric heterocoupling of coniferyl alcohol and its analog. Furthermore, we show that the heterocoupled (+)-pinoresinol analogs can be further processed by the rest of the pathway enzymes and display reduced propensity for oxidation. Taken together, we showcase flexibility of heterologous biosynthetic pathways in a plant chassis for improved biosynthetic yields of high-value therapeutic compounds and expanded chemical space of therapeutic analogs previously inaccessible by traditional synthetic approaches

Keywords: Chemical Engineering.
Advisor: Sattely Elizabeth
Khosla Chaitan
Swartz James R.
Engineered methods for studying and manipulating in vitro culture systems

The development of new cell culture techniques allows in vitro cell cultures to replicate in vivo biology more faithfully. In this thesis, I will discuss two projects that broadly seek to expand the modalities for manipulating cell cultures and interrogating cell behavior. Magnetogenetics is a new field that leverages genetically encoded proteins and protein assemblies that are sensitive to magnetic fields to study and manipulate cell behavior. Theoretical studies show that many proposed magnetogenetic proteins do not contain enough iron to generate substantial magnetic forces. Here, we have engineered a genetically encoded ferritin-containing protein crystal that grows inside mammalian cells. Each of these crystals contains more than 10 million ferritin subunits and is capable of mineralizing substantial amounts of iron. When isolated from cells and loaded with iron in vitro, these crystals generate magnetic forces that are 9 orders of magnitude larger than the forces from the single ferritin cages used in previous studies. These protein crystals are attracted to an applied magnetic field and move toward magnets even when internalized into cells. While additional studies are needed to realize the full potential of magnetogenetics, these results demonstrate the feasibility of engineering protein assemblies for magnetic sensing. Brain organoids are an emerging three-dimensional cell culture system that models human brain development. Derived from clusters of induced pluripotent stem cells, brain organoids develop over many months and recapitulate key aspects of brain organization, such as cell identity and diversity, gene expression, and functional characteristics such as electrical activity. As a result, they have been employed to model various neurodevelopmental disorders. To date, electrophysiology in brain organoids has employed traditional techniques, such as multi-elecrode recordings and patch clamp. Here, we have developed a flexible mesh electrode for the long-term chronic integration of electrodes into the growing organoid. Over two generations of meshes, one made from SEBS and PEDOT:PSS and one made from SU-8 and gold, we have demonstrated that such electrodes have good biocompatibility, and are able to electrically stimulate organoids. Work is currently ongoing to establish consistent extracellular recordings of action potentials using the mesh

Keywords: Chemistry.
Advisor: Cui Bianxiao
Pasca Sergiu
Boxer Steven G. (Steven George)
Engineering ammonia production in free-living diazotrophs for plant fertilization

In this dissertation we engineer ammonia production in the plant-symbiotic associative diazotroph Azospirillum brasilense towards addressing the engineering grand challenge of nitrogen fixation. Our approach leverages synthetically controllable post-translational deactivation of glutamine synthetase by unidirectional adenylyltransferases (uATs) causing nitrogen over-fixation and release. We demonstrate that uAT strains can promote the growth of the model grass Setaria viridis in mono-association and prove using isotope labeling that 15N2 is transferred from the air into the plant specific chlorophyll derivative pheophytin. To improve our strains, we study the evolutionary pressure on ammonia production and show that multicopy genetic redundancy extends their ammonia production lifetime in culture. By finetuning multicopy uAT expression strength, we then demonstrate that an optimal expression strength maximizes ammonia production rate. These expression optimized multicopy strains further increase the growth promotion of Setaria viridis, as well as promote the growth of Zea mays in nitrogen-poor, non-sterile soil compared to wild-type and mock inoculation. Finally, we show throughout our work that uAT strains can be used as tools to probe questions in fundamental biology, such as what metabolism is regulated by ammonia versus glutamine

Keywords: Bioengineering.
Advisor: Sattely Elizabeth
Endy Andrew D.
Huang Kerwyn Casey
Long Sharon
Engineering and Characterizing D5_AR, a Monoclonal Antibody that Targets the gp41 N-Heptad Repeat of HIV-1 with Broad Tier-2 Neutralizing Activity

HIV-1 infection is initiated by the viral glycoprotein Env, which, after interaction with cellular coreceptors, adopts a transient conformation known as the pre-hairpin intermediate (PHI). The N-heptad repeat (NHR) is a highly conserved region of gp41 exposed in the PHI; it is the target of the FDA-approved drug enfuvirtide and of neutralizing monoclonal antibodies (mAbs). However, to date these mAbs have only been weakly effective against tier-1 HIV-1 strains, which are most sensitive to neutralizing antibodies. Here, we engineered and tested 11 IgG variants of D5, an anti-NHR mAb, by recombining previously described mutations in four of D5’s six antibody complementarity-determining regions. One variant, D5_AR, demonstrated 6-fold enhancement in ID50 against lentivirus pseudotyped with HXB2 Env. D5_AR exhibited weak cross-clade neutralizing activity against a diverse set of tier-2 HIV-1 viruses, which are less sensitive to neutralizing antibodies than tier-1 viruses and are the target of current antibody-based vaccine efforts. In addition, the neutralization potency of D5_AR IgG was greatly enhanced in target cells expressing FcγRI, with ID50 values below 0.1 μg/mL; this immunoglobulin receptor is expressed on macrophages and dendritic cells, which are implicated in the early stages of HIV-1 infection of mucosal surfaces. D5 and D5_AR have equivalent neutralization potency in IgG, Fab, and scFv formats, indicating that neutralization is not impacted by steric hindrance. Taken together, these results provide support for vaccine strategies that target the PHI by eliciting antibodies against the gp41 NHR and support investigation of anti-NHR mAbs in non-human primate passive immunization studies.

Keywords:  Department of Biology
Biology
Virology
Immunology
HIV-1
Antibodies
Vaccines
Thesis
Advisor: Kim Peter S
Jones Patricia P
Engineering better treatments for diabetes : from next-gen insulin drugs to autonomous insulin delivery

Insulin was first isolated a century ago, yet commercial formulations of insulin and its analogues for hormone replacement therapy falls short of mimicking the endogenous glycemic control that occurs in non-diabetic individuals. Moreover, diabetes management is increasingly relying automated insulin delivery using closed-loop systems to improve glucose management and reduce patient burden. However improvements in insulin formulations, sensors, and algorithms are required to shift from hybrid systems to fully autonomous delivery. Insulin formulations that better mimic secretion from the beta-cells, by enabling more rapid insulin absorption kinetics and/or co-delivering complementary hormones (i.e. amylin), would improve diabetes management. However, formulation innovation is complicated by the poor stability of insulin monomers and amylin. During my time in the Appel lab, I have developed two polymeric excipient platforms (non-covalent PEGylation and amphiphilic copolymer excipients) that can be used to increase the stability of insulin in formulation. Using these designer excipients, I have developed three enhanced insulin formulations: (i) an ultrafast monomeric insulin lispro (ii) an insulin-amylin co-formulation and (iii) an ultra-stable insulin for improved global access. These three enhanced insulin formulations are promising candidates for improving glucose control and reducing burden for patients with diabetes. Beyond formulation engineering, through collaborations I have investigated the use of open-source algorithms in a full closed-loop setting as well as helped to develop a continuous real-time ELISA microfluidic device for continuous monitoring of insulin and glucose. Together, this collection of work describes the development of new technologies towards insulin delivery with the goal of improving glucose management in patients with diabetes

Keywords: Bioengineering.
Advisor: Appel Eric (Eric Andrew)
Cochran Jennifer R.
Maahs David M.
Engineering contact layers in metal halide perovskite solar cells using atomic layer deposition

Solar energy is an attractive, renewable energy source because of its massive abundance and its capacity for distributed generation. Photovoltaics (PV) allow us to convert this solar energy directly into usable electricity. Metal halide perovskite solar cells are a new, thin film PV technology on the cusp of commercialization; however, more research is needed to improve their power conversion efficiency and long-term stability, as well as to scale-up their manufacturing. Contact layers and their interfaces with the perovskite absorber are an important component in each of these facets of research. Engineering these contact layers to improve the collection of photogenerated charge carriers often requires precise control over their film properties, such as thickness, composition, and crystallinity. Atomic layer deposition is a versatile, nanoscale synthesis tool that is well-suited for these applications. In this dissertation, we develop low temperature (< 100 C) ALD processes to grow metal oxide contact layers above the perovskite absorber. We focus primarily on vanadium oxide and tin oxide, which are hole- and electron-selective contact materials, respectively. Conformal ALD vanadium oxide contacts enable the fabrication of semi-transparent devices which have potential applications as the wide band gap subcell in tandem solar cells. Tuning the organic hole contact in these devices also leads to improvements in device photocurrent. We show that the ALD vanadium oxide is morphologically stable at temperatures (70 C) relevant to solar cell operation in the field, resulting in devices with good long-term stability. The growth behavior of ALD contacts also has important implications for overall solar cell performance and stability. We find that functionalizing the ALD growth surface to help initiate film growth leads to more compact ALD tin oxide contacts that extend the lifespan of perovskite solar cells. Lastly, we investigate strategies to limit adverse reactions between ALD metal-organic precursor molecules and the perovskite that lead to a poor interface for charge extraction from the solar cell

Keywords: Chemical Engineering.
Advisor: Bent Stacey
Bao Zhenan
Tarpeh William
Engineering designer biomaterials from topologically diverse polyacrylamide derivatives

The translational pharmaceutical landscape is rapidly changing and demands new polymers for both drug stability and delivery. Polyacrylamide derivatives have demonstrated a lack of immunogenicity, water solubility, chemical stability, and are both commercially available and inexpensive, making them attractive candidates for translational use. Moreover, polyacrylamides with the chemical, size, and topological control needed for translation can be synthesized via reverse addition fragmentation transfer (RAFT) polymerization, a scalable, robust, and coming-off-patent polymerization technique. This research in this dissertation highlights the promise of polyacrylamide derivatives, synthesized via RAFT, as translational biomaterials. The first portion of this dissertation will describe new developments in insulin formulation technology. I propose the use of polyacrylamide amphiphilic carrier/dopant copolymers (AC/DC) as novel excipients to occupy the air-water interface I will cover the synthesis of a library of AC/DC excipients, the proposed mechanism of action, and formulation work to generate both the (1) fastest acting, stable, injectable insulin formulation and (2) a commercial cold chain resilient insulin formulation. The second portion of the dissertation will describe a new adjuvant platform for subunit vaccines enabled by a hyperbranched polyacrylamide derivative. I will (1) highlight a universal scaling behavior uncovered during the synthesis of these materials, (2) a processing step to generate low-dispersity hyperbranched polymers, and (3) the implementation of adjuvant-conjugated hyperbranched polymers as adjuvants for vaccines. In summary, in this dissertation I will explain how novel polyacrylamide derivative biomaterials can be used to address the need of rapidly changing pharmaceutical landscape

Keywords: Materials Science and Engineering.
Advisor: Appel Eric (Eric Andrew)
Heilshorn Sarah
Waymouth Robert M.
Engineering reagents to target the sialic acid glyco-immune checkpoint

Sugar molecules decorate the human cell surface, creating a dense network of glycoproteins, glycolipids, and proteoglycans known as the glycocalyx. One "hallmark" of cancer cells is an overrepresentation of sialic acid-containing sugar structures (sialoglycans) in the glycocalyx. These sialoglycans bind to the "Sialic acid binding Ig-like Lectin" (Siglec) inhibitory receptor family expressed on both innate and adaptive immune cells. Immune inhibitory signaling of sialoglycans is therefore exploited by cancer cells to prevent an antitumor immune response and promote cancer cell survival. Because of this, sialic acids can be considered glyco-immune checkpoint ligands and represent promising therapeutic targets. Blocking sialoglycan interactions with typical antibody reagents is challenging, however, due to their vast chemical diversity; sialic acids are a family of ~50 sugar molecules in humans that can be chemically linked in multiple ways to numerous glycoproteins and glycolipids. In addition, there is a relative scarcity of high-affinity, glycoform-specific antibodies, and the precise structures of the most potent Siglec ligands remain unclear. To address this, this work describes the development of unique biological reagents to block the sialoglycan-Siglec inhibitory checkpoint interaction for cancer therapy

Keywords: Chemistry.
Advisor: Bertozzi Carolyn R.
Boxer Steven G. (Steven George)
Cegelski Lynette
Engineering reduced precious metal catalysts for proton exchange membrane water electrolyzers

As a renewable chemical and fuel, hydrogen produced from water electrolyzers is playing an increasingly important role across many sectors of the economy. However, proton exchange membrane (PEM) water electrolyzers are still at an economic disadvantage relative to the competing methane-derived hydrogen production process, in part due to the expensive precious metal catalysts, Pt and IrOx. The aim of this dissertation is to design and develop hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) catalysts with reduced precious metal content, while maintaining or improving efficiency and stability. In the first section, we rationalize the need to diversify catalysts beyond Pt and IrOx using market-based analysis and we use technoeconomic analysis to develop a cost-based framework for establishing novel catalyst performance targets. We then demonstrate the feasibility to utilize non-precious metal HER catalysts in a commercial PEM electrolyzer, highlighting its remarkable stability. We then investigate the fundamental properties of reduced precious metal OER catalysts. We combine lab-scale aqueous electrolyte experiments, computational material methods, and advanced characterization techniques to explain the high OER activity of Ru- and Ir-based pyrochlores. While these materials did not demonstrate greater stability than commercially-used IrOx, this wholistic approach to studying catalysts is important for determining new design principles for OER catalyst stability. We further show that these OER catalysts can be integrated into a PEM electrolyzer configuration and maintain high activity and stability at moderate current densities

Keywords: Chemical Engineering.
Advisor: Jaramillo Thomas Francisco
Cargnello Matteo
Tarpeh William