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Machine Learning for Anatomical Structures Segmentation of Contrast-Enhanced Cardiac Computed Tomography Images
No full textContrast enhanced cardiac computed tomography angiography (CTA) is an important imaging modality for assessing the morphology of the heart and coronary arteries for diagnosing cardiovascular disease. Accurate heart segmentation in cardiac CTA images is an important task for quantitative assessment of aorta, myocardium, and different cardiac chambers. However, manual segmentation is time-consuming, prone to errors and variations between observers while automatic segmentation is very challenging due to large shape variations in the cardiac anatomy among different subjects, indistinct boundaries between substructures of the heart (e.g. right ventricle and right atrium) or between the heart and surrounding tissues (e.g. liver, ribs, sternum) and long processing time may not be efficient in clinical practice. This dissertation provides a new method that uses machine learning based approach to improve the accuracy and efficiency of the commonly used multi-atlas and deep neural network based approaches for 17 different cardiac and non-cardiac structures segmentation in cardiac CTA images. Specifically, an automatic framework combining multi-atlas and corrective segmentation to identify several cardiovascular and intrathoracic structures from cardiac CTA images is proposed. The proposed multi-atlas based framework significantly improves the segmentation accuracy without suffering from high computational burden existed in conventional multi-atlas based approach. In addition, large amounts of annotated data are required for deep neural networks to produce reliable results. This is a common limitation in deep learning-based approach, especially in medical field as the annotated data required efforts by domain experts and it can be very challenging and time consuming when multiple labels are desired in 3D volumetric data. To tackle this limitation, the proposed multi-atlas based framework can be used to generate reliable segmentations with less annotated samples to serve as training data for deep learning methods.This work would allow much less expert supervision while providing comparable high-quality automatic segmentation results which is also more suitable for 3D CTA volume data and large-scale studies. Furthermore, the automated methods should be more consistent and faster than manual labeling methods.Computer scienceArtificial intelligenceMedical imagingcardiac computed tomography angiography, deep learning, image segmentation, machine learning, multi-atlas segmentationElectrical Engineering and Computer ScienceDegree Awarded: Ph.D. Electrical Engineering and Computer Science. The Catholic University of Americ
Identifing the Amino Acid Residues Responsible for Molecular Diode Function in Pdr5, a Major Multidrug Efflux Pump
No full textAntimicrobial resistance (AMR) occurs when a microorganism gains resistance to antimicrobial agents that were originally designed to cure infections caused by these microorganisms. Overexpression of ATP-binding cassette (ABC) multidrug transporters is a mechanism of AMR, which acts by pumping the drugs out of the cell. ABC transporters are a superfamily of polytopic proteins that uses the energy of ATP hydrolysis to transport the substrates across the membrane against a concentration gradient. The typical ABC transporters consist of two transmembrane domains (TMDs), composed of six transmembrane helices (TMHs) that are connected by extracellular loops (ECLs) and intracellular loops (ICLs), and two nucleotide-binding domains (NBDs). ABC transporters export substrates through a series of conformational changes. Many ABC transporters shift between an inward-facing, drug-binding (high-affinity) conformation to an outward-facing, drug-releasing (loose-binding) conformation using ATP binding and hydrolysis. When the drug is released from the drug-binding pocket, it must be prevented from reentering through the transporter. The outward-facing or drug-releasing conformation results in only a 10-to-30-fold reduction in binding affinity, which is not sufficient to prevent some rebinding of the drugs if the extracellular concentration is high (Sauna and Ambudkar, 2000). For this reason, it was proposed that ABC transporters have a molecular gate or diode that prevents reflux (Gupta, et al., 2011). The first evidence for a molecular diode mechanism was the observation that a Ser 1368 Ala (S1368A) mutation in the yeast multidrug transporter Pdr5 exhibited significant drug reflux during transport (Mehla, et al., 2014). More recently, multiple cryo-electron microscopy structures of the ABCG2 mammalian multidrug transporter clearly showed the presence of a molecular gate between an inner and outer drug-binding pocket. Two prominent residues—Leu-554 and Leu-555—were identified as constituents of this gate (Manolaridis, et al., 2018). When the sequences of Pdr5 and ABCG2 are aligned, Ser-1368 is quite close to Leu-554 and Leu-555. The corresponding residues in Pdr5 are Val-1372 and Met-1373. Bioinformatics analysis of the Pdr subfamily (Lamping, et al., 2010) revealed highly conserved residues adjacent to Ser-1368, including Phe-1369, Gly-1371, Val-1372, and Met-1373. The corresponding residues to this S1368 adjacent motif in the amino-terminus of Pdr5, extending from Tyr-680 to Ilv-685, also exhibit conservation. The first goal of this study is to determine whether the conserved set of amino acids spanning residues (1369–1373) in the carboxyl-terminus motif of Pdr5 make up a molecular diode motif. The second goal is to investigate whether the molecular diode is composed of residues from both halves of this large, polytopic protein. Our results suggest that this conserved motif plays a variety of roles including signal transmission, protein folding, and molecular gating. Our results also suggest that Ile-685, Val-1372, and Met-1373 are the actual gate, where Ser-687, Ser-1368, and Phe-1369 provide structural support. Alanine substitutions in these residues exhibit a unique gating-defect phenotype. Characterization of mutants in these two motifs might lead to specific chemical inhibitors of these transporters during disease treatment.BiologyBiologyDegree Awarded: Ph.D. Biology. The Catholic University of Americ
The Image of the Church as the Family of God: A Systematic Study in the Igbo Catholic Church of Nigeria
No full textABSTRACTThe Catholic Church in Africa is in need of renewal. The 1994 Special Assembly of the Synod of Bishops for Africa endorsed the image of the Church as the family of God as the most appropriate image for Africans. The present study examines the image within the context of the Igbo Catholic Church of Nigeria. Successive chapters contain: first, a discussion of Igbo people and the Igbo family; second, an examination of the advent and influence of Christianity in Igboland; third, a consideration of some essential aspects of the Catholic Church, the wider context of the present study; fourth, a critical assessment of Igbo traditional religion and culture in light of the image; fifth, a critical analysis of the image; and sixth, an examination of the prospects and challenges the image holds for the Igbo Church in the 21st century. Scholarly research, and the life and experience of the present writer as an Igbo Catholic priest, were both valuable resources for the writing of this dissertation. The main conclusions of the research are as follows: First, the Igbo understanding of the family is under threat today from the forces of contemporary culture. Second, plural belonging is an unfortunate feature of present-day Igbo Catholicism. Third, Igbo traditional religion and Igbo culture have semina veritatis (seeds of truth) that could potentially contribute to an understanding of the Church as the family of God for Igbo people, though significant corrections to the Igbo understanding of the family must also be made if that image is to be a satisfactory one for the Church. Fourth, the image complements, and needs to be complemented by, other scriptural and theological images of the Church. The present study concludes that a proper understanding of the Church as the family of God can be crucial for addressing the needs of the Igbo Church in the twenty-first century, with particular reference to evangelization, aggiornamento (the bringing-up-to-date of the Church), and the construction of an authentic and indigenous Catholic Church in Igboland.TheologySystematic TheologyDegree Awarded: Ph.D. Systematic Theology. The Catholic University of Americ
“Of Thine Own Have We Given Thee:” A Liturgical Theology of the Offertory as Practiced by the Churches of the Anglican Communion
No full textOne of the most controversial theological issues of the liturgy during the English reformations of the sixteenth century was oblation. While the Eucharistic Prayer proper has often been the site of this theological controversy, the offertory rite has also received great attention. The 1552 English Book of Common Prayer excised all references to oblation in the offertory rite, but oblationary language and actions, such as the offertory procession, returned in full force by the twentieth century. The movement from the near elimination of oblation in the offertory rite to its widespread usage in the churches of the Anglican Communion is a remarkable liturgical and theological development. The purpose of this dissertation is to develop a liturgical theology of the offertory rites as practiced among churches in the Anglican Communion to elucidate not only the development of oblation but also other theological themes which contributed to its progression. This dissertation utilizes a modified application of Kevin Irwin’s liturgical theological methodology as found in Context and Text. This dissertation takes a primarily historical approach proceeding from the sixteenth century to the present providing a comparative analysis that involves historical and textual analyses of relevant liturgical books and contextual analysis of sources such as architecture, music, published ceremonials, and other contextual materials.This dissertation provides three contributions. First, it significantly expands on the work of previous treatments of the offertory rite in Anglicanism. Second, it utilizes both textual and contextual analyses of the offertory rite in Anglicanism. Finally, it proposes a theory for the development of oblation in the offertory rite from its near elimination to its widespread use in the churches of the Anglican Communion. This dissertation concludes with a liturgical theology reflecting the comparative analysis of all the historical periods. It shows that the historical, liturgical, and theological development of the offertory rite as practiced in the churches of the Anglican Communion elucidates five theological themes: almsgiving, propitiation, preparation, participation, and oblation. Furthermore, the development of oblation in the offertory rite from its near elimination in the sixteenth century to its widespread use in the present results from the development of the four other theological themes. They interweave to produce a reformed understanding of oblation in the offertory rite as practiced by the churches of the Anglican Communion.TheologyHistoryAnglicanism, liturgical history, liturgical theology, liturgy, offertory, theologyLiturgical Studies/Sacramental TheologyDegree Awarded: Ph.D. Liturgical Studies/Sacramental Theology. The Catholic University of Americ
Development of optical indices of articular cartilage damage and microstructure
No full textArticular cartilage is a microstructurally and biochemically complex tissue with distinct zonal architecture. The primary interactions of articular cartilage with polarized light are depolarization, diattenuation, and retardance. Damage to this tissue leads to osteoarthritis (OA), the most common chronic disease affecting 30 million adults in the United States. There is currently no cure for OA. Thus, methods to detect early or pre-OA, focusing on detection of cartilage surface damage and microstructural alterations, are of great interest to clinical orthopedics. Collagen fibers in articular cartilage possess strong birefringence. Birefringence signals and other polarization sensitive optical parameters can probe both surface and subsurface feature of pre-OA cartilage. The goal of this dissertation was to develop polarized reflectance microscopy as an imaging technique to detect OA-related alterations to articular cartilage. Three separate but related studies were conducted to investigate the sensitivity of polarized reflectance parameters. The first study found that polarized reflectance signal is associated with microscale damage to the articular surface and sub-surface collagen structure, similar to alterations that occur in early OA. The second study analyzed the origins of polarized reflectance image textural patterns and related them to underlying collagen network microstructure in the superficial zone. The third study separated polarized reflectance signal into major linear retardance and depolarization components by polar decomposition of experimentally-acquired Mueller matrix images, using a custom-built reflectance polarimeter. Together, these findings support the relevance of polarized reflectance signals from articular cartilage to orthopedic research and suggest clinical utility. Polarized reflectance imaging provides a noninvasive, label-free and fast way to assess superficial articular cartilage microstructure and may contribute to the development of novel optical biomarkers for prediction of early OA. Quantitative optical indices and image textural parameters derived from polarized reflectance imaging hold promise for clinical translation in arthroscopic modalities, or ex vivo tissue analysis.Biomedical engineeringBioengineeringarticular cartilage, birefringence, microscopy, polarization, reflectanceBiomedical EngineeringDegree Awarded: D.Engr. Biomedical Engineering. The Catholic University of Americ
Obstacles to Innovation in Rentier Economies: States, Elites, and the Squandering of the Demographic Dividend
No full textAfter the Arab Spring shook governments throughout the Middle East in the early 2010s, youth activism has increased with simmering tensions over corruption, obstacles to economic empowerment, and the deteriorating welfare state as states across the Gulf region witness their youth majorities evolve into a working-age population. This opportunity to capitalize on this age structure and increase economic productivity is an exigent matter of both political and economic stability in the Gulf rentier states along with the broader Middle East. With the wealth of the Gulf States based largely on hydrocarbon resources, these states share a unique economic situation, and often are termed “rentier economies.” The resulting institutional ecosystem is often extractive by design and undermines innovation at its core. Thus, the capacity of the state to attain a demographic dividend― a sweet spot in the age structure that can be the highest opportunity for economic productivity―will be limited for decades to come if not framed by the appropriate institutional design and policies that allow for innovation-led development. Theoretically, the dependency on hydrocarbons creates distinct interaction between the institutional environment of the economy and the political logic of stakeholders such as the business elite and the labor force. In this context, this dissertation’s question is: How does the institutional environment of state-business relations affect the necessary economic reform that fosters innovation needed for rentier economies to convert youth bulges into demographic dividends? This dissertation has three primary arguments. First, that rentier economies’ institutional characteristics and market dominance by elites can stifle innovation, which consequently undermines prospects of achieving the demographic dividend. Through a cross-national quantitative analysis, the results indicate that rentier economies generally have a negative relationship with innovation, but that institutional quality and design can drive successful innovation in these economies. Second, by applying a historical institutional approach, this study explains how rentier economies originated from particular socio-political antecedents and were influenced by various power brokers in the pre-oil era economies, impacting the institutional structure that undergirds the politics of economic reform. This historical arrangement spurred differing levels of business elite dominance in the economy and therefore caused variance in the level of state-led capitalism across the three states— Qatar, Kuwait, and Bahrain. In evaluating the histories of these three case studies, one main variable emerges that influenced different institutional development pathways—economic diversification. Diversification was a driving force behind the trajectory and influence of merchants on the private sector’s institutional development, and that elite roles have affected contemporary political obstacles for innovation-led economic development. Third, in the current context, the institutional arrangements of rentier states, the state with the highest level of centralized state-led capitalism and lowest level of business elite dominance is more empowered to realize the innovation-led economic development necessary to successfully attain the demographic dividend.Existing currents of thinking on the literature on the resource curse, rentier economies, and the demographic dividend have failed to highlight the connection between political forces and the economic policies that affect societies with youth bulges. A central goal of mixed-methods research is to illuminate this gap and to point to alternative strategies to make the most of an extraordinary moment of opportunity that may only arise once for decades to come.Political scienceEconomicsdemographic dividend, economic development, Gulf Cooperation Council (GCC), innovation, rentier state theory, resource curseGovernmentDegree Awarded: Ph.D. Government. American Universit
Forming God’s Family: Building and Mentoring the Domestic Church Using the Six Tasks of Catechesis in the General Directory for Catechesis
No full textThe family is a domestic church. Since Vatican II, this term has returned to magisterial and theological discussion; however, its pastoral application is still wanting. Parents, the first, best, and primary educators of the faith are not able to delegate this role totally to others. Parents who lack understanding of how to form their family, will struggle to teach the faith to their children. Families not fully living their faith, often fall away from the practice of their faith. Parents must assume their God-given responsibility to teach their children and form their family as a domestic church.The Catholic Church teaches six integrated tasks to her children: To know the revelation of God, to worship him in the liturgy, to live the Christian life, to seek God in prayer, all within the context of a family community, while never failing to share this good news with others. The parent formation in this project is structured upon these areas, summarized in the General Directory for Catechesis. These six tasks, abbreviated as: creed, cult, code, contemplation, community, and call, are the six dimensions of formation of the domestic church, which give parents a structure and enable them to apply a particular approach in the formation of their family. Secondarily, the project seeks to identify parents who feel capable and willing to mentor other parents to do the same. Parents learned about forming their family as a domestic church during six, two-hour in length sessions, followed by four months of follow-up newsletters. The methodology employed was directed at conversion to Jesus Christ, helping parents to understand the faith as revealed by God, and leading to transformation in their lives as they responded to God’s grace. Parents who are better evangelized, catechized, and living as disciples, are best suited to apply the faith in the formation of their family as a domestic church. For young parents, or those attempting this familial formation, mentor parents are greatly needed to support them. Marriage and family, as revealed in God’s plan, are attacked in today’s culture. Well-formed families will overcome this attack and strengthen the Catholic Church.Religious educationTheologyAdult educationCatholic family, Domestic church, Domestic church formation, Family, Family formation, Parents teaching childrenReligious Education/CatecheticsDegree Awarded: D.Min. Religious Education/Catechetics. The Catholic University of Americ
Passions, Virtue, and Moral Growth in John of Apamea’s Dialogues on the Soul
No full textVirtue cultivation is an under-researched topic in theological virtue ethics. Moreover, little attention is given in virtue ethics to vice and its impact on virtue cultivation. In this dissertation, I respond to this lacuna by examining the role of the removal of evil passions in moral growth in the Dialogues on the Soul, whose author, John of Apamea, is a fifth-century ascetic who has introduced the discussion of passions in Syriac Christianity. For John, moral growth occurs in three stages: somaticity, psychicality, and pneumaticity. I argue that, for John, the gradual healing from evil passions facilitates one’s moral progress from one stage to another. After examining John’s theological anthropology, in the first chapter, I explore his views on the relationship of the body and the soul with the passions in chapters two and three. In chapter four, I focus on the morality of the passions, that is, whether the passions in themselves are good or evil, and to what degree one is morally responsible for them. I, then, reconstruct, in chapter five, a list of the passions and their variations in the Dialogues on the Soul, as well as the structure of the passions as stirrings that are intimately connected to thoughts. In chapter six, I synthesize the different techniques of the ascetic therapy of the passions, and, finally, in chapter seven, I show how the ascetic therapy of the passions helps one to progress morally from somaticity to psychicality. The state one must reach on earth is the purity of the soul, which is characterized by the absence of evil passions. This paves the way for the manifestation of true virtue at the pneumatic level. The full manifestation of the natural virtue of the soul, however, is an eschatological gift of the Divine Grace.Finally, through this dissertation, I aim to draw attention to the central role of removing vice in moral growth and, more broadly, to the significance of Syriac asceticism for virtue ethics.EthicsSpiritualityClassical literatureJohn of Apamea, Moral Growth, Passions, Patristics, Syriac, VirtueMoral Theology/EthicsDegree Awarded: Ph.D. Moral Theology/Ethics. The Catholic University of Americ
Access to Justice at the Asylum Office
No full textThis dissertation focuses on legal representation and interpretation, which are arguably two of the most salient factors in guaranteeing an asylum seeker’s due process rights. Nevertheless, current United States law dictates that the burden is upon asylum seekers to find and pay for their own attorneys and interpreters at the Asylum Office. This dissertation’s first article uses mixed methods to assess the relationship between legal representation and case outcomes at the Asylum Office, and whether this relationship is consistent across all eight asylum offices. This dissertation’s second article analyzes 28 in-depth, semi-structured interviews with immigration attorneys to better understand their case acceptance policies, how they conceptualize high-quality legal representation, best practices for the preparation of asylum cases, and their views of the quality-level of the private immigration bar. This dissertation’s third article analyzes the same 28 in-depth, semi-structured interviews, but focuses on a subset of interview questions that query how asylum officers exercise their discretion to provide asylum applicants with interpreters, whether this discretion is exercised in a uniform manner, and how interpreters affect the dynamics of asylum interviews. These three dissertation articles have normative as well as theoretical implications. From a normative perspective, this dissertation informs current initiatives to provide indigent immigrants with legal representation by analyzing the relationship between legal counsel and asylum outcomes. This dissertation also discusses the qualities and best practices that immigration attorneys view as indispensable to providing high-quality representation, as well as the challenges of interpretation at the Asylum Office. From a theoretical perspective, this dissertation argues that more rigorous quantitative analyses need to be conducted before academics and advocates can conclusively infer the relationship between legal representation and asylum outcomes at the Asylum Office. This dissertation also emphasizes the need for additional dialogue around how to conceptualize the quality of legal representation in order to ensure equitable asylum case outcomes. Finally, this dissertation highlights the importance of securing competent interpretation services at the Asylum Office.LawLanguageAccess to Justice, Asylum, Immigration, Interpretation, Language Access, Legal RepresentationJustice, Law and SocietyDegree Awarded: Ph.D. Justice, Law and Society. American Universit
To Feed and Follow: Peter, Bishops, and the Church in St. Augustine's Exegesis
No full textAugustine’s view of the episcopacy is often derived from a consideration of his actions as bishop. That Augustine assumed a role does not however corroborate its inclusion in the essential roles of the episcopacy as instituted by Christ and exemplified in the apostles. In each ecclesial epoch, the bishops have borrowed from the dominant model of temporal leadership: Roman governor, feudal prince, corporate bureaucrat, etc. To discern what is essential rather than circumstantial to the episcopacy as taught by Augustine it is apposite to consult his figural exegesis during his years as bishop of Hippo Regius. In c. Faust., Augustine primarily utilizes abstract episcopal figurae under two aspects: the paternal and the prophetic. The apostle Peter emerges as episcopal exemplar and prophet of the definitive Pentecost. He broadly represents the New Covenant in Christ. In Io. eu. tr. 55-124 and festal sermons on John 21, the Petrine figural mosaic expands. In contrast to the abstract figurae of c. Faust., the Petrine figura of the Johannine sermons spans the entire ark of the apostle’s life, accreting scriptural allusions. As the representative of the apostolic-episcopal office and the figure of the Bridal Church wedded to and built upon the Christic rock, Peter as exegeted illustrates Augustine’s ecclesiology and theology of the episcopacy. The most important pericope in Augustine’s Petrine mosaic is John 21 and the double dominical command to “feed my sheep” and “follow me.” The commands correspond to the two episcopal aspects which predominate in the Johannine sermons: the pastoral and the martyrial. The pastoral absorbs the paternal and prophetic from c. Faust. The project concludes with a treatment of the neglected ciu. XV-XVIII. Augustine evokes the biblical theology of c. Faust. in ciu., indicating the consistency of his figural exegesis across his episcopacy. An explanation of the significance of the apostle Peter at the conclusion of ciu. XVIII permits a defense of Book XVIII’s coherence and its role in ciu. XV-XVIII and in ciu. as a whole. It also exhibits the relevance of Augustine’s preached exegesis to understanding his lengthier treatises, even when the connections seem brief or tangential.TheologyHistoryBiblical studiesApostle Peter, Augustine, Bishop, Church, Episcopacy, ExegesisHistorical TheologyDegree Awarded: Ph.D. Historical Theology. The Catholic University of Americ