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Unmasking The Language Of Science Through Textual Analyses On Biomedical Preprints And Published Papers
Get PDFScientific communication is essential for science as it enables the field to grow. This task is often accomplished through a written form such as preprints and published papers. We can obtain a high-level understanding of science and how scientific trends adapt over time by analyzing these resources. This thesis focuses on conducting multiple analyses using biomedical preprints and published papers. In Chapter 2, we explore the language contained within preprints and examine how this language changes due to the peer-review process. We find that token differences between published papers and preprints are stylistically based, suggesting that peer-review results in modest textual changes. We also discovered that preprints are eventually published and adopted quickly within the life science community. Chapter 3 investigates how biomedical terms and tokens change their meaning and usage through time. We show that multiple machine learning models can correct for the latent variation contained within the biomedical text. Also, we provide the scientific community with a listing of over 43,000 potential change points. Tokens with notable changepoints such as “sars” and “cas9” appear within our listing, providing some validation for our approach. In Chapter 4, we use the weak supervision paradigm to examine the possibility of speeding up the labeling function generation process for multiple biomedical relationship types. We found that the language used to describe a biomedical relationship is often distinct, leading to a modest performance in terms of transferability. An exception to this trend is Compound-binds-Gene and Gene-interacts-Gene relationship types
Cellular And Mechano-Active Material Approaches To Improve Disc Repair After Herniation
No full textThe intervertebral disc (IVD) relies on its complex microarchitecture and composition to transmit forces throughout the spine. A nucleus pulposus (NP) core is surrounded circumferentially by the annulus fibrosus (AF), which together transmit loads to adjacent vertebra. Although this specialized structure evolved over millennia, the disc failed to develop mechanisms for self-repair. Instead, cell apoptosis and inflammation after injury lead to the loss of extracellular matrix and further compromise disc function. Furthermore, adult disc cells are sparse and have decreased biosynthetic abilities. Disc herniations, resulting from annular tears, enable the extrusion of NP tissue which can result in spinal nerve compression and consequent pain. The gold standard for the surgical management of symptomatic disc herniation is microdiscectomy, in which the herniated tissue is removed. This alleviates pain yet fails to repair the injured disc, leaving an uninhibited track for recurrent herniation. This highlights the need for the development of disc repair strategies that improve healing and prevent recurrent herniation. To that end, the main objectives of this work were to develop cellular, molecular, and structural augmentation strategies for the repair of disc herniations. For cellular augmentation, an AF-like cell population was developed through differentiation of human induced pluripotent stem cells (iPSCs). Factors present during disc development were screened and their inductive effects were assessed through transcriptional signature comparisons between iPSC-derived AF-like cells and mature AF cells. To enable molecular augmentation of the injury, a drug delivery system termed mechanically-activated microcapsules (MAMCs) was developed. MAMC properties, including mechano-activation and degradation, were investigated to characterize the tunability of the system. Finally, structural augmentation of the injured disc was achieved through the development of tension-activated repair patches (TARPs), which deliver factors through the activation of encapsulated MAMCs. TARP-mediated disc repair and provision of anti-inflammatory factors was analyzed in a large animal model. The provision of structural support and anti-inflammatory molecules improved the retention of disc composition and improved repair. These annular augmentation strategies hold promise for continued preclinical development and future translation into humans
Experimental Study Of The Electronic-Phonon Coupling In Low-Dimensional Materials
No full textIn this thesis, we investigate the effects of electron-phonon coupling as manifested in exciton-polarons and Cooper pairs. The electron-phonon coupling imparts a level of protection on the electronic states in both cases, though in qualitatively different ways. This result is surprising considering the traditional scattering role of the electron-phonon interaction.We start with a theoretical description of excitons, polarons, and exciton-phonon coupling, all of which play a primary role in the subsequently introduced and focused on hybrid organic-inorganic perovskite materials class. Here we distinguish between bulk 3D and layered 2D hybrid perovskites, and highlight how polarons in these systems have been hypothesized to protect charge carriers from scattering. Next, we discuss time-resolved absorption and photoluminescence techniques that we employed to explore the exciton dynamics in 2D hybrid perovskites. These materials presented unique challenges for conventional time-resolved absorption methods, and we detail the development of a novel experimental scheme that permitted high-quality data collection and helped provide new insights into the exciton-phonon behavior. We follow up with an account of the excitonic fine structure in 2D hybrid perovskites, chronicling recent work suggesting a vibronic sideband origin, and then illustrating how the dynamical perspective provided by our measurements give strong evidence for the vibronic hypothesis. We close our discussion on 2D hybrid perovskites by presenting evidence for the formation dynamics of large exciton-polarons. Finally, we turn our attention to measurements of the superconducting proximity effect in low dimensional heterostructures of superconductors and antiferromagnets. Superconductivity is an example of the electron-phonon coupling mediating an electron-electron attraction, which leads to a scattering-protected Cooper pair. Here, we present results suggesting a singlet to triplet transformation in the Cooper pair, indicating the possibility for the protection of spin polarization via Cooper pairs. The appendix describes one of several experiments constructed in support of the Property Measurement Facility and the NSF funded MRSEC center at Penn. The work in this thesis has been supported by the Penn NSF MRSEC DMR-1120901 and DMR-1720530
Role Of Structure In Mechanics: Glassy Polymer Nanocomposites Under Active Deformation
No full textPolymer Nanocomposites (PNCs) have become an emerging class of materials due to their advanced thermal, transport, electrical, and mechanical properties. It has been shown in many experiments and simulations that nanoparticles in the polymer matrix can induce a \u27bound layer\u27 of polymers, where the density is higher and the dynamics are much slower than the bulk. This bound layer is widely believed to be responsible for many of the desirable properties of PNCs. Intuitively, the slow dynamics should originate from the compacted structure, however, many studies have shown that the dynamics are usually modified over a wider range than the structure. Thus, there should be at least a second process affecting polymer dynamics in addition to the structure itself. An explicit relationship between the structure and dynamics in the PNCs, especially in the bound layer, is still missing. Moreover, most applications of PNCs require the system to be in a glassy state and under external loads, making this question even more challenging because: (i) the relationship between glassy structure and dynamics is still an open question; (ii) glassy dynamics can be accelerated by external loads and the material can exhibit either brittle or ductile responses before the failure. In this dissertation, we use Molecular Dynamics simulation combined with machine learning analysis and study five different polymer systems. We propose three physical models: the Structure-dependent Eyring Model (StEM), the Interfacial Dynamical Decomposition (IDD) Model, and the Structuro-elasto-plasticity (StEP) Model to describe how the dynamics of PNCs are affected by a variety of processing conditions. These models incorporate a machine-learned structural field, softness, and connect the microscopic structure to dynamics and mechanical responses for both neat polymers and PNCs under active deformation. In addition to these models, we also study the formation process and the exchange dynamics of the bound layer in PNCs, which is critical for tuning the PNCs\u27 properties but where many outstanding questions remain
Early Childhood Development Implementation Research In Humanitarian Settings
No full textChildren living in situations affected by conflict experience multiple adversities including exposure to violence, displacement, and family separation and can experience high levels of stress and insecurity. In order to bolster the case for interventions focused on young children in conflict-affected settings, this dissertation focuses on implementation research for early childhood development programming in humanitarian settings. With a clear focus on this overarching theme, this dissertation includes three connected, yet distinct papers in Chapters 2, 3, and 4. Chapter 2 presents a literature review of empirical research of early childhood development programs in humanitarian settings and draws from existing theories to present a framework for early childhood development implementation research in humanitarian settings. Chapters 3 and 4 focus on a specific example of the implementation of an ECD program in a humanitarian setting: Lebanon’s Preschool Healing Classroom (PHC) program. Chapter 3 includes an analysis of children’s developmental growth over the course of the PHC program using the International Development and Early Learning Assessment (IDELA); an exploration of the associations between demographic characteristics and IDELA scores; a psychometric analysis of an adaptation of the Monitoring Early Learning Environments (MELE) through exploratory factor analysis; and a multi-level analysis of the associations between the empirically obtained factors of classroom quality and children’s development. Using a concurrent mixed-methods approach, chapter 4 extends the findings reported in Chapter 3 and focuses on the factors affecting access and quality implementation that may influence children’s learning outcomes through the analysis of the perspectives of parents, Lebanese teachers, Syrian facilitators and Lebanese staff. The emergent themes are then integrated with a quantitative analysis of performance scores for each of the locations included in the qualitative study to shed light on potential influences of children’s developmental outcomes that were not previously captured in quantitative analysis presented in Chapter 3. In sum, this dissertation provides important insights for practitioners, researchers, and donor institutions looking to change the trajectory and enhance the lives of young children and families living in situations of conflict and crisis
Immigrant Volunteering And Integration
Get PDFThis three-paper dissertation aims to evaluate whether, how, and the extent to which immigrants\u27 volunteering affects their integration into the host country. I approach the thesis with a conceptual examination built on social theories (Paper 1), a quantitative analysis conducted with Canadian data (Paper 2), and a qualitative exploration based on 24 interviews conducted in Philadelphia (U.S.) (Paper 3). For Paper 1, I find that while existing social theories may explain ways volunteer activities positively influence the relationship between immigrants and nonimmigrants, they do not account for additional barriers newcomers experience during resettlement. Using an intersectional approach, I expand existing knowledge on immigrant-nonimmigrant relations by exploring volunteering as support that improves immigrant integration. In Paper 2, I use Canadian national survey data to examine three dimensions of immigrant integration: professional, psychosocial, and political. General volunteering is not significantly related to integration; however, there is a relationship between dimensions of integration and where immigrants choose to volunteer. Thus, the relationship between immigrant integration and volunteering is nuanced; it matters where immigrants decide to volunteer. I expand on this in Paper 3 by analyzing 24 semi-structured interviews to explore differences in social-integration experiences and perceptions of social integration between immigrant volunteers and nonvolunteers in Philadelphia. While past studies assert that volunteering increases feelings of social integration, this empirical study offers a comparative perspective between immigrants who volunteer and those who do not. The findings suggest that immigrant volunteers build a stronger sense of agency in their social integration journeys through contributions to society. Most nonvolunteering participants achieve similar yet minor benefits by engaging in informal volunteering outside of organizational auspices. This dissertation inspires recommendations for researchers, policymakers, and practitioners working towards improved immigrant integration. Voluntary venues are unique for positive relational dynamics between immigrants and nonimmigrants. More research on the integrative qualities of voluntary work may lead to discovering best practices on how immigrants achieve high levels of integration within communities and beyond
Reinventing Poetry: Popular Audiences And Polyphonic Space During The Song-Jin-Yuan Transition (1050–1300)
No full textThis dissertation studies poetry as a linguistic topos that traveled across cultural and class boundaries during the Song-Jin-Yuan transition (1050–1300). Literary scholars often examine poetry in light of leading literati’s cultural practices and political experience. Moving away from canonical authors and works, this project focuses instead on how poetry was used when the transformation of social institutions, the democratization of entertainment, the advent of print, and the urbanizing spaces afforded it new avenues of production and circulation. By tracing the movement of poetic messages in diverse cultural circuits, my inquiry offers a revisionist understanding of poetry as a malleable artifact integrated into urban life, which also reshaped contemporary political dynamics. Drawing evidence from historical miscellanies, excavated artifacts, local literary collections, and court documents, this project maps out an expanding poetry market and the emergence of professional poets who wrote for profit. Potential consumers of poetry consisted of both educated readers, whose demands revolutionized conventional writing ideals, and commoners, who purchased household ware inscribed with performed verses to create a space reminiscent of the theatergoing experience. The percolation of poetry in quotidian life brought about an unexpected political consequence. When entertainers updated their repertoire with contemporary events and urbanites drew knowledge from popular performance to engage with politics, poets straddled the elite and popular spheres to make a profit. Connected to publishers and performers, they commodified political struggles by spreading satires in various linguistic registers. Many further sold their public influence to powerful officials, making the dissemination of defamatory verses into service in demand
Infrared Spectroscopic Signature And Unimolecular Dissociation Dynamics Of A Hydroperoxyalkyl Radical (•qooh)
No full textDirect detection of the carbon centered hydroperoxyalkyl radicals (•QOOH) transiently formed in the oxidation of volatile organic hydrocarbons in atmospheric and combustion environments has long been elusive. This thesis demonstrates the jet-cooled stabilization, infrared spectral signature, and energy-dependent unimolecular decay dynamics of a prototypical •QOOH, •CH2(CH3)2COOH, which would result from isobutane oxidation. •QOOH is generated in the laboratory by H atom abstraction from a methyl group of tert-butyl hydroperoxide ((CH3)3COOH, TBHP) using photolytically generated •Cl atoms. The infrared (IR) fingerprint of •QOOH is obtained by IR action spectroscopy utilizing OH laser induced fluorescence (LIF) detection. •QOOD (•CH2(CH3)2COOD), a partially deuterated analog, is also studied using partially deuterated TBHP, (CH3)3COOD, with OD LIF detection. Spectral features characterizing •QOOH/D are observed in the 2950-7050 cm-1 range at energies that lie below and above the transition state barrier leading to OH/D and cyclic ether products. The observed features include fundamental OH and CH stretch transitions, combination bands involving OH/D or CH stretch and a low frequency mode, and overtone OH/D and CH stretch transitions. Most of the observed •QOOH/D IR transitions are readily distinguished from TBHP, including the overtone OH stretch of TBHP characterized in this work. Energy-resolved rates for the unimolecular decay of •QOOH/D to OH/D, recorded by IR pump-UV probe time-delay measurements, are determined ranging from 3.2 ± 1.0 × 106 s-1 to ≥2.6 ± 0.5 × 108 s-1. The observed rates prompted state-of-the-art electronic structure calculations to characterize the transition state (TS) barrier region and bring computed Rice-Ramsperger-Kassel-Marcus rates in accord with experiment. A TS barrier of 10.3 kcal mol-1 is established for •QOOH with heavy atom tunneling along the reaction pathway enhancing the unimolecular dissociation rates. Partial deuteration in •QOOD results in a small increase in the TS barrier to 10.5 kcal mol-1 due to changes in zero-point energies. Comparison of experimental and theoretically predicted rates confirm that unimolecular decay is enhanced by heavy-atom tunneling along the reaction pathway for both •QOOH and •QOOD
Peripheral Neuronal Encoding Of Pleasurable Social Touch
Get PDFPleasurable touch during social behavior is key to building familial bonds and meaningful connections. As revealed by a global pandemic, isolation from these social contacts can have devastating effects on mental health. Yet, the identity and role of sensory neurons that transduce social touch remain unknown, limiting our understanding of what makes social touch beneficial and pleasurable, and therefore what goes wrong when it is missing or perturbed. A population of sensory neurons labeled by the G-protein coupled receptor Mrgprb4 detect stroking touch in mice, however, these neurons have never been implicated in any natural social behaviors. Here, we study the social relevance of Mrgprb4-lineage neurons by genetically engineering mice to allow activation or ablation of this population and reveal that these neurons are required for sexual receptivity to male mounts as well as social touch behaviors between females. Even in social isolation, optogenetic stimulation of Mrgprb4-lineage neurons through the back skin is sufficient to induce dopamine release, a conditioned place preference, and a dorsiflexion posture. This dorsiflexion resembles the natural behavioral response to social touch to the back, which is either a lordotic copulatory posture to male mounts, or a crawling posture from cagemate female contact. In the absence of Mrgprb4-lineage neurons, female mice no longer find male mounts rewarding: sexual receptivity is supplanted by aggression and a coincident decline in dopamine release. Together, these findings establish that Mrgprb4-lineage neurons are the first neurons of a skin-to-brain circuit encoding the rewarding quality of social touch. Using the same transdermal optogenetic approach, we also reveal (1) the possibility that these neurons may activate pain pathways in the context of inflammation, potentially implicating them in an allodynia phenotype, and (2) a related population of DRG neurons may provide insight into sex-differences in pain perception, yet further experimentation is necessary
City Mutable: The United States Census Bureau\u27s Quest To Define The City, 1850-1930
No full textThe idea that the population of the United States first became majority urban in 1920 has been repeated so often that it has become “fact,” uncritically reprinted in high school textbooks, academic works, reports of major research organizations, popular urbanist nonfiction, and more. However, this widely accepted “fact” warrants a reevaluation. What does the word urban mean and who defined it? Which characteristics distinguish urban space and who devised these criteria? When and why did urban become one of the most fundamental demographic and spatial categories by which data on people and places are collected and reported?
City Mutable excavates the intellectual origin story of the urban concept by examining the efforts of the United States Census Bureau to define the city for statistical analysis between 1850 and 1930. It argues that the Census Bureau did not merely observe American urbanization but also shaped it by creating the predominant techniques and methodologies for tracking urban growth in the United States. The agency enshrined urban greatness as a measure of national development in the eyes of the American public and its emphasis on the unit of the incorporated municipality incited the late nineteenth- and early twentieth century municipal annexation movement. By highlighting how pro-business organizations like chambers of commerce participated in drafting the census’s metropolitan definitions, it contends that turn-of-the-twentieth-century political, commercial, and industrial interests left an indelible imprint on the census’s urban-rural classification scheme.
The Census Bureau’s urban definition continues to guide state and federal funding formulas, inform scholarship and public policy, and direct narratives of American progress—or decay. By unearthing the evolution of this powerful idea, City Mutable prompts readers to question accepted demographic “turning points,” such as the United States population becoming majority urban in 1920 and the world population becoming majority urban in 2007. It encourages academics and policy makers to engage more critically with the constructs employed to study urbanization and opens space for radical and creative reimaginings of the meanings of the word urban