The Nordin group at Brigham Young University has been focused on developing 3D printing technology for fabrication of lab-on-a-chip (microfluidic) devices since 2013. As we showed in 2015, commercial 3D printers and resins have not been developed to meet the highly specialized needs of microfluidic device fabrication. We have therefore created custom 3D printers and resins specifically designed to meet these needs. As part of this development process, ad hoc 3D printer control software has been developed. However, the software is difficult to modify and maintain to support the numerous experimental iterations of hardware used in our custom 3D printers. This highlights the need for modular yet reliable system software that is easy to use, learn, and work with to adapt to the unique challenges of a student workforce. This thesis details the design and implementation of new 3D printer system software that meets these needs. In particular, a software engineering principle-based design approach is taken that lends itself to several specific development patterns that permit easy incorporation of new hardware into a 3D printer to enable rapid evaluation of and development with such new hardware.

La voie Wnt/β-caténine est impliquée dans la prolifération et le contrôle du destin cellulaire de nombreux tissus à la fois au cours du développement et pour le maintien de l’homéostasie chez l’adulte. L’équipe a montré qu’une activation aberrante de la β-caténine conduisait au développement de carcinomes hépatocellulaires (CHC), alors que son activation physiologique dans une souspopulation d'hépatocytes du foie adulte (les hépatocytes éricentraux) permet la mise en place et le maintien du zonage métabolique. Ce zonage hépatique peut être considéré comme une différenciation terminale des hépatocytes, et permet au foie d'être pleinement fonctionnel. L’objet de ma thèse a été d’identifier les déterminants moléculaires expliquant la diversité d’action de la β-caténine dans le foie. J'ai tiré profit de modèles génétiques développés au laboratoire d'activation ou d'inactivation inductibles de la voie β-caténine dans le foie. A partir d'hépatocytes isolés de ces modèles, j'ai recherché par ChIp-seq (immunoprécipitation de chromatine couplée à un séquençage haut-débit) les sites de fixation sur l’ADN de la β-caténine et de Tcf4, que j'ai identifié comme principal médiateur de l’activité nucléaire de la β-caténine dans le foie. Ces données, couplées à des études d’accessibilité de la chromatine et de transcriptome ont permis d’identifier la structure de la chromatine et Hnf4a comme déterminants majeurs permettant à la beta-caténine de contrôlerpositivement et négativement des programmes génétiques spécifiquement hépatiques, qui luipermettent d'assurer le zonage métabolique du foie. En effet, Hnf4a a un rôle antagoniste de la β-caténine, contrôlant positivement la transcription des gènes réprimés par la β-caténine. Ce contrôles'exerce grâce à un dialogue d'Hnf4a avec Tcf4 et la β-caténine, qui s'opère majoritairement via des interactions entre ces protéines. Nous proposons ainsi que la β-caténine coopère avec le facteur de transcription Hnf4a, connu pour contrôler les gènes du métabolisme hépatocytaire, pour assurer la différenciation terminale hépatique. J'ai également recherché les partenaires protéiques nucléaires de la β-caténine par coimmunoprécipiatation couplée à de la spectrométrie de masse. Plusieurs protéines jouant un rôle dans l'épissage des ARN ont pu être identifiées de cette manière. La quantification exon par exon des transcrits séquencés par RNA-Seq m'ont également permis d'identifier une possible régulation directede l’épissage des gènes SLC39A14 et NDRG2 par la β-caténine. Enfin, nous nous sommes attachés à comprendre comment la β-caténine jouait un rôle prolifératif suite à son activation aberrante dans le foie d'une part (par l'utilisation d'un modèle transgénique prénéoplasique) et lors de la régénération hépatique d'autre part. Nous avons pu démontré que ce rôle prolifératif était complexe, seulement partiellement autocrine, mettant en jeu la Cycline D1 et le facteur de croissance Tgfa, que nous avons définis comme étant des cibles directes de la β-caténine dans le foie. Ces derniers résultats évoquent également un dialogue fonctionnel entre la voie β-caténine et la cascade de signalisation Tgfa-Egf/Egfr/Erk pour assurer la prolifération hépatocytaire. / The Wnt/β-catenin pathway is involved in proliferation and cell fate control and regulatesdevelopmental stages as well as adult tissue homeostasis. Our team has previously shown that aberrantB-catenin signaling induced Hepatocellular Carcinoma (HCC) development, whereas physiologicalactivation in a subpopulation of adult liver hepatocytes (pericentral hepatocytes) patterns liverzonation. This hepatic zonation can be considered as hepatocytes terminal differenciation.My thesis aimed to identify key molecular determinants allowing diversity upon β-catenin activation.I took advantage of genetically engineered mice models of activation or inactivation of β-catenin,developped in the laboratory. Using hepatocytes obtained from these models I identified β-catenin andTcf4, that I previously identifed as the main effector of nuclear β-catenin in liver, binding sites byChIp-seq (Chromatin Immunoprecipitation followed by high-throughput sequencing). Couplingbinding site localization to transcriptomic and chromatin accessibility studies allowed to identifychromatin structure and tissue specific transcription factor HNF4A as key modulators of β-cateninsignaling in the liver and therefore modulators of metabolic zonation. Indeed, β-catenin negativelyregulates Hnf4a target genes. This negative control exerts essentially via protein interactions. Wepropose that β-catenin and Hnf4a cooperates to ensure terminal hepatic differenciation.I also searched for nuclear β-catenin partners by co-immunoprecipitation followed by massspectrometry. This approach revealed many splicing factors as beta-catenin partners. RNA seqanalysis revealed a possible direct regulation of splicing of SL39A14 and NDRG2 genes.Finally we tried to understand the proliferative role of β-catenin during liver regeneration. Wedemonstrated a complex and partially autocrine role of B-catenin. We defined CyclinD1 and thegrowth factor Tgfa as β-catenin direct targets in the liver. These latest results also imply a functionnaldialog between the β-catenin pathway and Tgfa-Egf/Egfr/Erk signalisation cascade to allowhepatocytes proliferation.

Recent increases in hard fault rates in modern chip multi-processors have led to a variety of approaches to try and save manufacturing yield. Among these are: fine-grain fault tolerance (such as error correction coding, redundant cache lines, and redundant functional units), and large-grain fault tolerance (such as disabling of faulty cores, adding extra cores, and core salvaging techniques). This paper considers the case of core salvaging techniques and the heterogeneous per- formance introduced when these techniques have some salvaged and some non-faulty cores. It proposes a hypervisor-based hardware thread scheduler, triggered by detection of spin locks and thread imbalance, that mitigates the loss of throughput resulting from this het- erogeneity. Specifically, a new algorithm, called Most ProgressMade algorithm, reduces the number of synchronization locks held on a salvaged core and balances the time each thread in an application spends running on that core. For some benchmarks, the results show as much as a 2.68x increase in performance over a salvaged chip multi-processor without this technique.

Chips with high computational power are the crux of today’s pervasive complex digital systems. Microprocessor circuits are evolving towards many core designs with the integration of hundreds of processing cores, memory elements and other devices on a single chip to sustain high performance computing while maintaining low design costs. Two decisive paradigm shifts in the semiconductor industry have made this evolution possible: (a) architectural and (b) organizational. At the heart of the architectural innovation is a scalable high speed data communication structure, the network-on-chip (NoC). NoC is an interconnect network for the glueless integration of on-chip components in the modern complex communication centric designs. In the recent days, NoC has replaced the traditional bus based architecture owing to its structured and modular design, scalability and low design cost. The organizational revolution has resulted in a globalized and collaborative supply chain with pervasive use of third party intellectual properties to reduce the time-to-market and overall design costs. Despite the advantages of these paradigm shifts, modern system-on-chips pose a plethora of security vulnerabilities. This work explores a threat model arising from a malicious NoC IP embedded with a hardware trojan affecting the resource availability of on-chip components. A rigorous simulation infrastructure is established to evaluate the feasibility and potency of such an attack. Further, a non-invasive runtime monitoring technique is proposed and thoroughly investigated to ensure the trustworthiness of a third party NoC IP with low overheads.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19300号 / 工博第4097号 / 新制||工||1631(附属図書館) / 32302 / 京都大学大学院工学研究科建築学専攻 / (主査)教授 金子 佳生, 教授 田中 仁史, 教授 竹脇 出 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19935号 / 工博第4218号 / 新制||工||1652(附属図書館) / 33021 / 京都大学大学院工学研究科マイクロエンジニアリング専攻 / (主査)教授 小寺 秀俊, 教授 中部 主敬, 准教授 横川 隆司 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Many drugs and environmental chemicals, such as antibiotics and chemotherapeutic agents, are nephrotoxic (toxic to the kidney) and are a common cause of acute kidney injury and chronic kidney disease. Conventional tissue models for assessment of drug-induced nephrotoxicity rely on animals or simple cell culture models, which lack tissue characteristics of the human kidney required to accurately predict a drug’s effect in clinical trials. Microfluidic kidney-on-chips can generate tissue with improved human relevance compared to traditional models, however, generally lack high-throughput and multiparametric data collection capabilities for evaluation of nephrotoxic drug exposures. Standard data collection techniques remain limited to fluorescent imaging or colorimetric assays that often focus on single endpoints, are invasive due to the addition of labels, and fail to capture dynamic changes in tissue function. Additionally, conventional toxicological readouts rely on bulk measures of injury, such as cell death, which are less sensitive than sub-lethal changes in cell function and morphology that occur prior to cell death. Due to the challenges above, there is a need for new measurement approaches that enable collection of kinetic, multi-parametric, and sub-lethal readouts of injury in kidney-on-chip systems. In this work, we developed and characterized several measurement approaches for evaluation of tissue function in kidney-on-chip systems and assessment of drug-induced nephrotoxicity. In chapter 2, we developed a novel optical-based oxygen sensing technique for measurement of sub-lethal mitochondrial dysfunction in an array of kidney-on-chips. In chapter 3, we investigated an approach for simultaneous transepithelial electrical resistance (TEER) sensing and flow control to enable near-continuous monitoring of tissue barrier function under different flow conditions. In chapter 4, we demonstrated the use of different data collection modalities, including multiple sensors, fluorescent imaging, and colorimetric-based assays, to generate multi-parametric readouts for evaluation of drug-induced nephrotoxicity in kidney-on-chips. / 2024-05-24T00:00:00Z

The technology and telecommunication industries have made significant progress in the past few decades leading to several inventions and designs that have significantly improved efficiency in all aspects of human life. These innovations in science and technology improve our quality of life. Modern technology enables us to access vast amounts of information and services through a network of interconnected computers and machines. Recently, various technologies have been proposed to incorporate the human body into this incorporated network. One of these proposed technologies are chip implants meant to be inserted into the human body at various suitable body parts, such as the human brain or wrist. As they are a relatively recent technological innovation, chip implants are neither popular nor common yet (Caldera, 2020; Michael et al., 2017). Previous research on chip implants has produced limited information regarding the motivation aspects of using this technology. So, this study uses a self-determination theory to see which motivational factors lead to the use and trust of chip implants. This thesis discusses how implantable technology works, to explore which factors affect an individual's willingness to get a chip implant, personality traits associated with implant adoption, motivational factors affecting adoptions, and other user-centered perspectives of the technology.

Two-dimensional cell culture and animal models inadequately represent human pharmacokinetics and diseases like inflammatory bowel disease and colorectal cancer. This means missed diagnostic and therapeutic opportunities, high drug attrition rates, and a portfolio of approved drugs that underdeliver the desired benefits to patient outcomes. This encourages the development of a more physiologically relevant intestine model. The objective of this work was to develop a 384-well plate organ-on-a-chip platform, IFlowPlateTM, that can accommodate up to 128 human intestine models with accessible lumens and perfusable branched vasculature in an ECM environment. Fibrin-Matrigel® was used a structurally supportive and biologically instructive substrate that enabled: (1) prolonged cell culture (at least 15 days) with routine refreshment of aprotinin-supplemented medium, (2) formation of a confluent Caco-2 monolayer with barrier function, and (3) de novo assembly of a vascular network with barrier function. A fluorescent dextran permeability assay was used for in situ real-time measurements of epithelial barrier function in a high-throughput manner. Mixed co-culture of endothelial cells and fibroblasts in fibrin-Matrigel® resulted in the formation of an interconnected network of patent vessels that retained an albumin surrogate tracer within the luminal space indicating endothelial barrier function. To improve the success rate of anastomoses between living vessels and fluidic channels, the modification of inherently hydrophobic PDMS and polystyrene culture surfaces with ECM protein was explored. To address the limitations of a cancer cell line-derived intestine model, the replacement of Caco-2 cells with biopsied-derived colon organoid cells was investigated. Different gel formulations were assessed for their ability to induce colon organoid fragments to form monolayers. Finally, the incorporation of multiscale intestinal topography and luminal flow was considered through a modified approach to plate fabrication, whereby moulded alginate is embedded in ECM and sacrificed to generate a scaffold. Work to make the moulded alginate more robust is presented. / Thesis / Master of Applied Science (MASc) / Two-dimensional cell culture and animal models inadequately represent human drug metabolism and diseases like inflammatory bowel disease and colorectal cancer. The objective of this work is to develop a more physiologically relevant human intestine model. Using fabrication techniques pioneered by the semiconductor industry, a custom organ-on- a-chip platform in the format of a 384-well plate was developed. This platform is compatible with standard laboratory equipment and practices and can accommodate up to 128 human intestine models comprised of the intestinal epithelium and associated network of blood vessels. In this platform, the cells of the intestinal epithelium and vasculature are supported by a network of natural proteins. This allows processes like vessel growth to be modelled in this platform. Vessel growth plays a key role in the progression of inflammatory bowel disease and cancer, and this model could help scientists better understand these diseases.

G-quadruplexes (G4s) are four-stranded, non-canonical secondary DNA structures which have been shown to readily form in G-rich sequences in vitro. G4 formation can affect chromatin architecture and has been implicated in promoting genomic instability, and linked to biological processes such as transcription, replication and telomere maintenance. In this project, ChIP-seq data derived with G4-specific antibodies from mouse embryonic stem cells (mESC) are analysed and integrated with different histone 3 (H3) modification data sets.The analysis method follows a standard ChIP-seq data analysis workflow, which includes steps such as calculation of quality metrics, peak calling and downstream analyses. The results show enrichment of G-rich motifs and prevalence of G4s in functional regions such as promoter-TSSs and 5'UTRs. In addition, there is some evidence of a potential association with oncogene promoter regions and location of G4s, which would support previous findings. Furthermore, the results indicate a possible correlation between loss of histone modifications H3 lysine 4 trimethylation (H3K4me3) and H3 lysine 27 acetylation (H3K27ac), and G4 occurence. G4s have become increasingly popular to study in recent times and may harbour potential to be targeted for cancer therapy.