cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
PDGF Signaling in Sertoli Cell Cilia and Seminiferous Tubule Morphogenesis
Creators: name: Ahmadi Jeyhoonabadi, Maryam
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Veterinary Science

description: Immature porcine testicular Sertoli cells possess primary cilia, organelles that transmit extracellular signals into the cell. A yet unidentified ciliary signal in Sertoli cells has been found necessary for in vitro morphogenesis of tubules and testicular organoids. Herein, we hypothesized that platelet-derived growth factor receptor alpha (PDGFRα) signaling through the cilia of the Sertoli cells modifies cell migration and extracellular matrix (ECM) production, consequently altering in vitro formation of testicular organoids and seminiferous tubules. Immunocytochemistry revealed PDGFRα was present on Sertoli cell cilia as well as the rest of the cell membrane and cytoplasm. Inhibiting PDGFRα signaling did not prevent organoid and tubule formation. However, it appeared to correlate with ablation of cytoplasmic extensions from the surface of the in vitro formed tubules. Inhibition of PDGFRα signaling resulted in reduction in cell area, increase in the percentage of cells with prominent peripheral paxillin expression, and increase in the number of ciliated cells and cilia length. Immunohistochemistry revealed that cilia, which colocalized with PDGFRα, were positioned away from the basement membrane of the seminiferous tubules, close to the Sertoli cell nuclei, in an area that was occupied with Sertoli cell cytoplasm. When observed via transmission electron microscopy, Sertoli cell cilia exhibited ciliary pockets around their axoneme. These results demonstrate that PDGFRα activity in Sertoli cells can influence in vitro tubule morphogenesis, possibly by altering cell cytoskeleton, cell-ECM interaction, and cilia. However, the role of cilia-specific signaling remains to be determined.
Optimal Control of a Soft CyberOctopus Arm
Creators: name: Wang, Tixian
name: Halder, Udit
name: Chang, Heng-Sheng
name: Gazzola, Mattia
name: Mehta, Prashant G.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optimization and Control (math.OC)
subject: Robotics (cs.RO)
subject: Systems and Control (eess.SY)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In this paper, we use the optimal control methodology to control a flexible, elastic Cosserat rod. An inspiration comes from stereotypical movement patterns in octopus arms, which are observed in a variety of manipulation tasks, such as reaching or fetching. To help uncover the mechanisms underlying these observed morphologies, we outline an optimal control-based framework. A single octopus arm is modeled as a Hamiltonian control system, where the continuum mechanics of the arm is modeled after the Cosserat rod theory, and internal, distributed muscle forces and couples are considered as controls. First order necessary optimality conditions are derived for an optimal control problem formulated for this infinite dimensional system. Solutions to this problem are obtained numerically by an iterative forward-backward algorithm. The state and adjoint equations are solved in a dynamic simulation environment, setting the stage for studying a broader class of optimal control problems. Trajectories that minimize control effort are demonstrated and qualitatively compared with observed behaviors.
Controlling a CyberOctopus Soft Arm with Muscle-like Actuation
Creators: name: Chang, Heng-Sheng
name: Halder, Udit
name: Gribkova, Ekaterina
name: Tekinalp, Arman
name: Naughton, Noel
name: Gazzola, Mattia
name: Mehta, Prashant G.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Robotics (cs.RO)
subject: Systems and Control (eess.SY)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This paper presents an application of the energy shaping methodology to control a flexible, elastic Cosserat rod model of a single octopus arm. The novel contributions of this work are two-fold: (i) a control-oriented modeling of the anatomically realistic internal muscular architecture of an octopus arm; and (ii) the integration of these muscle models into the energy shaping control methodology. The control-oriented modeling takes inspiration in equal parts from theories of nonlinear elasticity and energy shaping control. By introducing a stored energy function for muscles, the difficulties associated with explicitly solving the matching conditions of the energy shaping methodology are avoided. The overall control design problem is posed as a bilevel optimization problem. Its solution is obtained through iterative algorithms. The methodology is numerically implemented and demonstrated in a full-scale dynamic simulation environment Elastica. Two bio-inspired numerical experiments involving the control of octopus arms are reported.
Molecular and cellular mechanisms of inhibitory synapse formation in developing rat hippocampal neurons
Creators: name: Dobie, Frederick Andrew
Publisher: name: University of British Columbia
Year: 2012

description: The proper functioning of the brain and central nervous system (CNS) requires the precise formation of synapses between neurons. The two main neurotransmitter systems for fast synaptic communication in the CNS are excitatory glutamate and inhibitory gamma-aminobutyric acid. A growing body of evidence has begun to uncover several shared and divergent rules for the establishment of each of these two types of synapses. At the molecular level, a number of key proteins have been shown to be involved in the initial formation and subsequent development of synaptic connection, including cell adhesion molecules (CAMs). Among the CAMs, neurexins and neuroligins are important synaptogenic proteins that act trans-synaptically to organize synapses: binding of axonal beta-neurexins by neuroligins is sufficient to cause development of a presynaptic specialization at that site, while binding of dendritic neuroligin-1 or neuroligin-2 by beta-neurexins is sufficient to cause development of postsynaptic excitatory or inhibitory specializations, respectively. In Chapter 2, we explore the role of alpha-neurexins in synapse organization. We find alpha-neurexins are able to specifically induce the formation of inhibitory synapses, presumably through clustering of postsynaptic neuroligin-2. Moreover, we find that the expression of various splice variants of alpha- and beta-neurexins is regulated both during development and by activity, suggesting a physiological role for alternative splicing in the modulation of synapse assembly. At the cellular level, it is now clear from live imaging studies that synapses and their formation are highly dynamic processes. A number of studies have established the temporal recruitment of pre- and postsynaptic components to nascent synapses and how synapse formation can influence neuron growth. However, these studies have focused on excitatory synapses. In Chapter 3, we explore the cellular mechanisms of inhibitory synapse formation and modulation. We find that entire synapses are highly mobile and can undergo dynamic structural modulation. New synapses are formed by gradual accumulation of components from diffuse cytoplasmic pools, with a significant contribution of presynaptic vesicles from previously recycling sites. These results provide new insights into the mechanisms of inhibitory synapse formation and how it is both similar and different from excitatory synapse formation.
From Bipolar to Elliptical: Simulating the Morphological Evolution of Planetary Nebulae
Creators: name: Huarte-Espinosa, Martín
name: Frank, Adam
name: Balick, Bruce
name: Blackman, Eric G.
name: De Marco, Orsola
name: Kastner, Joel H.
name: Sahai, Raghvendra
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The majority of Proto-planetary nebulae (PPN) are observed to have bipolar morphologies. The majority of mature PN are observed to have elliptical shapes. In this paper we address the evolution of PPN/PN morphologies attempting to understand if a transition from strongly bipolar to elliptical shape can be driven by changes in the parameters of the mass loss process. To this end we present 2.5D hydrodynamical simulations of mass loss at the end stages of stellar evolution for intermediate mass stars. We track changes in wind velocity, mass loss rate and mass loss geometry. In particular we focus on the transition from mass loss dominated by a short duration jet flow (driven during the PPN phase) to mass loss driven by a spherical fast wind (produced by the central star of the PN). We address how such changes in outflow characteristics can change the nebula from a bipolar to an elliptical morphology. Our results show that including a period of jet formation in the temporal sequence of PPN to PN produces realistic nebular synthetic emission geometries. More importantly such a sequence provides insight, in principle, into the apparent difference in morphology statistics characterizing PPN and PN systems. In particular we find that while jet driven PPN can be expected to be dominated by bipolar morphologies, systems that begin with a jet but are followed by a spherical fast wind will evolve into elliptical nebulae. Furthermore, we find that spherical nebulae are highly unlikely to ever derive from either bipolar PPN or elliptical PN.
description: Accepted for publication in the MNRAS, 15 pages, 7 figures
On the connectedness principle and dual complexes for generalized pairs
Creators: name: Filipazzi, Stefano
name: Svaldi, Roberto
Publisher: name: arXiv
Year: 2020
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: Let $(X,B)$ be a pair, and let $f \colon X \rightarrow S$ be a contraction with $-(K_X + B)$ nef over $S$. A conjecture, known as the Shokurov-Kollár connectedness principle, predicts that $f^{-1} (s) \cap \mathrm{Nklt}(X,B)$ has at most two connected components, where $s \in S$ is an arbitrary schematic point and $\mathrm{Nklt}(X,B)$ denotes the non-klt locus of $(X,B)$. In this work, we prove this conjecture, characterizing those cases in which $\mathrm{Nklt}(X,B)$ fails to be connected, and we extend these same results also to the category of generalized pairs. Finally, we apply these results and the techniques to the study of the dual complex for generalized log Calabi-Yau pairs, generalizing results of Kollár-Xu and Nakamura.
description: Final version, to appear in "Forum of Mathematics, Sigma"
Kupffer Cells In Action: Understanding The Mechanisms Of Hepadnaviral Persistence
Creators: name: Al-Yasiri, Layla
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Woodchuck Hepatitis Virus (WHV)
subject: Hepatitis B Virus (HBV)
subject: Hepadnavirus
subject: Kupffer Cells
subject: Innate Immunity
subject: Intravital Microscopy (IVM)
subject: Microbiology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine

description: Hepatitis B virus (HBV) is the prototypical member of Hepadnaviridae family, and a causative agent of liver disease. Despite the availability of a vaccine, an estimated 1.5 million new individuals become infected each year. HBV can establish persistent infection in hepatocytes, which can disrupt hepatic homeostasis. Kupffer cells (KCs) are liver-resident macrophages that act as the first of line of defense against infectious agents. Woodchuck hepatitis virus (WHV) is a member of Hepadnaviridae. North American woodchucks (Marmota monax) infected with WHV present a natural immunocompetent model and demonstrate comparable infection outcomes and progression to hepatocellular carcinoma. We hypothesized that KC absence in acute viral hepatitis leads to chronicity by impacting virus processing and immune responses. To investigate this, we sought to uncover the early host-virus interactions in acute WHV infection. We designed and optimized in-house WHV and woodchuck-specific assays to assess intrahepatic and systemic virus presence following WHV challenge (<24 hours) and infection (6 weeks). An intravital imaging protocol was developed to capture real-time events in a living woodchuck using purified and fluorescently labelled WHV. Clodronate liposome-mediated depletion of KCs in woodchucks was performed to evaluate pre-acute challenge and acute infection in either the presence or absence of KCs. Intravital imaging of woodchucks challenged with WHV showed first appearance of virus in the liver within 30 seconds and capture by KCs within 5-10 minutes. In addition, depletion of KCs did not impact the localization of WHV during the initial hour or 24 hours of challenge. Assessment of WHV markers, serology and liver histology revealed differences in viral and biochemical markers between the KC-depleted and non-depleted animals over the initial 6 weeks. KC depletion, prior to acute WHV infection, resulted in faster onset of acute hepatitis (elevated liver enzymes) and greater suppression of WHV DNA (in circulation and intrahepatically). However, there was no difference in WHV DNA suppression between KC-depleted and non-depleted cohorts after 6 weeks p.i, as all assayed woodchucks achieved suppression of plasma WHV DNA. This may suggest that KCs normally operate under tolerogenic conditions to prevent hepatocyte damage and hepatitis, allowing for greater viral replication and immune evasion.
Coulomb drag in graphene near the Dirac point
Creators: name: Schütt, M.
name: Ostrovsky, P. M.
name: Titov, M.
name: Gornyi, I. V.
name: Narozhny, B. N.
name: Mirlin, A. D.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We study Coulomb drag in double-layer graphene near the Dirac point. A particular emphasis is put on the case of clean graphene, with transport properties dominated by the electron-electron interaction. Using the quantum kinetic equation framework, we show that the drag becomes $T$-independent in the clean limit, $Tτ\to \infty$, where $T$ is temperature and $1/τ$ impurity scattering rate. For stronger disorder (or lower temperature), $Tτ\ll 1/α^2$, where $α$ is the interaction strength, the kinetic equation agrees with the leading-order ($α^2$) perturbative result. At still lower temperatures, $Tτ\ll 1$ (diffusive regime) this contribution gets suppressed, while the next-order ($α^3$) contribution becomes important; it yields a peak centered at the Dirac point with a magnitude that grows with lowering $Tτ$.
description: 3 figures, with expanded Supplemental Material attached as an appendix
Computing motivic Donaldson-Thomas invariants
Creators: name: Morrison, Andrew James
Publisher: name: University of British Columbia
Year: 2012

description: This thesis develops a method (dimensional reduction) to compute motivic Donaldson--Thomas invariants. The method is then employed to compute these invariants in several different cases. Given a moduli scheme with a symmetric obstruction theory a Donaldson--Thomas type invariant can be defined by integrating Behrend's function over the scheme. Motivic Donaldson--Thomas theory aims to provide a more refined invariant associated to each such moduli space - a virtual motive. From the modern point of view motivic Donaldson-Thomas invariants should be defined for a three dimensional Calabi--Yau category. These categories often arise in a geometric context as the derived category of representations of a quiver with potential. Provided the potential has a linear factor we are able to reduce the problem of computing the corresponding virtual motives to a much simpler one. This includes geometric examples coming from local curves which we compute explicitly.
Much Ado About a Design Process
Creators: name: Raschke, Jared
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: set design
subject: lighting design
subject: Theater

description: The intention of this artist’s statement is to showcase proficiency in scenic and lighting design for the theatre. The following paper outlines the design process through early conception, research, full realisation of the set and lighting designs for William Shakespeare’s Much Ado About Nothing, directed by Cali Sproule and presented in the University Theatre at the University of Calgary from Nov 25th – Dec 5th, 2022.
A heuristic guide to evaluating triple-sums
Creators: name: Mortenson, Eric T.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: Using a heuristic that relates Appell--Lerch functions to divergent partial theta functions one can expand Hecke-type double-sums in terms of Appell--Lerch functions. We give examples where the heuristic can be used as a guide to evaluate analogous triple-sums in terms of Appell--Lerch functions or false theta functions.
description: 26 pages. Submitted to Hardy Ramanujan Journal for special volume in honour of Ramanujan
Computing Nash equilibria for integer programming games
Creators: name: Carvalho, Margarida
name: Lodi, Andrea
name: Pedroso, João Pedro
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: FOS: Computer and information sciences

description: The recently defined class of integer programming games (IPG) models situations where multiple self-interested decision makers interact, with their strategy sets represented by a finite set of linear constraints together with integer requirements. Many real-world problems can suitably be fit in this class, and hence anticipating IPG outcomes is of crucial value for policy makers and regulators. Nash equilibria have been widely accepted as the solution concept of a game. Consequently, their computation provides a reasonable prediction of the games outcome. In this paper, we start by showing the computational complexity of deciding the existence of a Nash equilibrium for an IPG. Then, using sufficient conditions for their existence, we develop two general algorithmic approaches that are guaranteed to approximate an equilibrium under mild conditions. We also showcase how our methodology can be changed to determine other equilibria definitions. The performance of our methods is analyzed through computational experiments in a knapsack game, a competitive lot-sizing game, and a kidney exchange game. To the best of our knowledge, this is the first time that equilibria computation methods for general integer programming games have been designed and computationally tested.
Sphenomerides trapezioides
Creators: name: Ng, Peter K. L.
name: Ahyong, Shane T.
name: Castro, Peter
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Decapoda
Trapeziidae
Sphenomerides
Sphenomerides trapezioides

description: Sphenomerides trapezioides (Wood-Mason in Wood-Mason & Alcock, 1891)
(Figs. 5C, 6D, 7E, 8D, J, 9I, J, 10E, 12)
 Sphenomerus trapezioides Wood-Mason & Alcock, 1891: 263 (type locality: Andaman Sea); Wood-Mason, 1892: pl. 5, fig. 2; Alcock, 1898: 228.
 Sphenomerides trapezioides — Serène, 1973: 207, figs. 6, 27, 28, pl. 5, 1984: 289, fig. 196, pl. 42, fig. D; Castro et al., 2004: 34 (in key), 60, pl. 4 fig. E; Ng et al., 2008: 185; Castro, 2013: 461, figs. 2F–H; Silambarasan et al., 2023: 550, fig. 4C.
 Diagnosis. As for subfamily.
 Remarks. See remarks for genus.
description: Published as part of Ng, Peter K. L., Ahyong, Shane T. & Castro, Peter, 2023, Re-appraisal of the families and subfamilies of Trapezioidea Miers, 1886, with establishment of a new family, Ectaesthesiidae (Crustacea: Decapoda: Brachyura), pp. 606-631 in Raffles Bulletin of Zoology 71 on page 622, DOI: 10.26107/RBZ-2023-0047, http://zenodo.org/record/10271307
Higgs production via gluon fusion in the POWHEG approach in the SM and in the MSSM
Creators: name: Bagnaschi, E.
name: Degrassi, G.
name: Slavich, P.
name: Vicini, A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We consider the gluon fusion production cross section of a scalar Higgs boson at NLO QCD in the SM and in the MSSM. We implement the calculation in the POWHEG approach, and match the NLO-QCD results with the PYTHIA and HERWIG QCD parton showers. We discuss a few representative scenarios in the SM and MSSM parameter spaces, with emphasis on the fermion and squark mass effects on the Higgs boson distributions.
description: 27 pages, 36 eps figures; v2: 2 eps figures added, section 3.2 expanded, version published in JHEP
Quantum walk processes in quantum devices
Creators: name: Madhu, Anandu Kalleri
name: Melnikov, Alexey A.
name: Fedichkin, Leonid E.
name: Alodjants, Alexander
name: Lee, Ray-Kuang
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Simulation and programming of current quantum computers as Noisy Intermediate-Scale Quantum (NISQ) devices represent a hot topic at the border of current physical and information sciences. The quantum walk process represents a basic subroutine in many quantum algorithms and plays an important role in studying physical phenomena. Simulating quantum walk processes is computationally challenging for classical processors. With an increasing improvement in qubits fidelity and qubits number in a single register, there is a potential to improve quantum walks simulations substantially. However, efficient ways to simulate quantum walks in qubit registers still have to be explored. Here, we explore the relationship between quantum walk on graphs and quantum circuits. Firstly, we discuss ways to obtain graphs provided quantum circuit. We then explore techniques to represent quantum walk on a graph as a quantum circuit. Specifically, we study hypercube graphs and arbitrary graphs. Our approach to studying the relationship between graphs and quantum circuits paves way for the efficient implementation of quantum walks algorithms on quantum computers.
description: 11 pages, 5 figures, 3 tables
Contributions of Modularity and Integration to Phenotypic Variation and Complexity in the C. eos-neogaeus Hybridization Complex
Creators: name: Duclos, Kevin Karl
Publisher: name: Cumming School of Medicine
Year: 2023
Subjects: subject: Chrosomus eso-neogaeus
subject: evo-devo
subject: Cypriniformes
subject: Evolution
subject: Geometric morphometrics
subject: Hybridization
subject: Education--Sciences
subject: Biology
subject: Anatomy
subject: Zoology
subject: FOS: Biological sciences

description: Evolutionary developmental biology links the key ideas of evolution, such as the study of evolvability, into the study of developmental properties and mechanisms. Biological complexity is recognized as key component of evolvability and the emergence of novel traits. However, the study of complexity and how it factors into evolvability has been mired in inconsistent definitions and the lack of a clear framework including the fact that phenotype is an end result of developmental processes. Complex phenotypes are the result of interactions between intrinsic factors, such as developmental processes and constraints, and extrinsic factors, including selective pressures and environmental stimuli. As such, complexity is tightly regulated and structured through ontogeny. In this thesis, I address the links between complexity, evolvability and the emergence of novelty using the C. eos-neogaeus hybridization complex as a study system. I first explore how the conceptual and methodological frameworks of modularity and integration allow explicit studies of the links between complexity and evolvability. I subsequently contextualize complexity in the framework of epigenetics sensu Waddington and identify hybridization, and hybrid organisms as pertinent models for the study of biological complexity. Using geometric morphometrics, I assess phenotypic integration and modularity in the cranial and postcranial skeleton of the C. eos-neogaeus hybridization complex. I show that hybridization results in varying patterns of modularity and phenotypic integration between parental species and hybrid lineages of the C. eos-neogaeus complex. I show that shared pairwise phenotypic integration between traits result in different effects on the directionality of shape variation across lineages. The modification of the directionality of shape variation, promotes phenotypic transgression and phenotypic novelty in hybrids. Finally, I explored topological variation and integration in the pectoral girdle across hybrid lineages and parental species of the C eos-neogaeus complex. I identify conserved patterns of modularity in the pectoral girdle within the C. eos-neogaeus complex despite lineage-specific variation in structure and the shape of individual bones within the pectoral girdle. While the factors promoting increases and decreases in complexity through evolution require further attention, my thesis illustrates how modularity and integration are crucial in organizing and maintaining complexity within and between species.
Spatial, temporal, and circuit-specific activation patterns of basolateral amygdala projection neurons during stress
Creators: name: Aukema, Robert
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Education--Sciences

description: In humans and rodents, the amygdala is rapidly activated by stress and hyperactivated in conditions of pathological stress or trauma. However, there is a striking lack of information of the anatomical specificity of amygdala subregions and circuits explicitly activated by stress, and of its role in governing typical responses to stress such as hypothalamic-pituitary-adrenal (HPA) axis activation. The overarching aim of this thesis was to conduct a systematic investigation of the spatial, temporal, and circuit-specific activation patterns of basolateral amygdala (BLA) projection neurons during exposure to acute stress. Additionally, we explicitly tested the role of the BLA in activation of the HPA axis, as this remains a poorly understood process. Chapter 1 describes how the BLA is anatomically well-situated for cognitive evaluation of emotional stimuli and describes the role of the BLA in diverse behavioural and physiological processes via efferent projections to many different brain structures. Chapter 2 identifies a common BLA subregion that is responsive to stressful stimuli, albeit with distinct temporal activation patterns, and which bidirectionally influences HPA axis activity. Chapter 3 maps the topographical distribution of six different populations of projection neurons throughout the BLA, and demonstrates that, although widely activated by stress exposure, inhibition of isolated populations does not influence HPA axis activity. Chapter 4 investigates the topographical distribution and stress-induced activation of BLA neurons expressing corticotropin-releasing hormone receptor type I (CRHR1), which, just like discrete circuits, does not influence HPA axis activity on its own. Together, this emphasizes the heterogeneity of BLA projection populations, while providing evidence that a large, diverse population of BLA projection neurons are activated by exposure to acute psychological stress.
The electromagnetic model of short GRBs, the nature of prompt tails, supernova-less long GRBs and highly efficient episodic accretion
Creators: name: Lyutikov, Maxim
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Many short GRBs show prompt tails lasting up to hundreds of seconds that can be energetically dominant over the initial sub-second spike. In this paper we develop an electromagnetic model of short GRBs that explains the two stages of the energy release, the prompt spike and the prompt tail. The key ingredient of the model is the recent discovery that an isolated black hole can keep its open magnetic flux for times much longer than the collapse time and, thus, can spin-down electromagnetically, driving the relativistic wind. First, the merger is preceded by an electromagnetic precursor wind. If a fraction of the wind power is converted into pulsar-like coherent radio emission, this may produce an observable radio burst of few milliseconds. At the active stage of the merger, two neutron stars produces a black hole surrounded by an accretion torus in which the amplified magnetic field extracts the rotational energy of the black hole and drives an axially-collimated electromagnetic wind. For observers nearly aligned with the orbital normal this is seen as a classical short GRB. After the accretion of the torus, the isolated black hole keeps the open magnetic flux and drives the equatorially (not axially) collimated outflow, which is seen by an observer at intermediate polar angles as a prompt tail. The tail carries more energy than the prompt spike, but its emission is de-boosted for observers along the orbital normal. Observers in the equatorial plane miss the prompt spike and interpret the prompt tail as an energetic supernova-less long GRB. We also demonstrate that episodic accretion onto the BH of magnetized clouds that carry non-zero magnetic flux can be highly efficient in extracting the spin energy of the BH, producing the outflows with the power exceeding the average accretion power.
Exploring Intensive Care Unit Nurses’ Decision Making in Alarm Management
Creators: name: Krakova, Nikola
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: intensive care unit
subject: alarm management
subject: decision making
subject: Nursing
subject: FOS: Health sciences

description: Alarm fatigue, which occurs when the exposure to an increased amount of false or nonactionable alarms leads to alarm desensitization and reduced clinical response by the healthcare provider, can pose a significant risk to patient safety. With the increasing advances in technology and frequency of alarms in our healthcare system, alarm fatigue is an important and growing safety concern that needs to be addressed. Exploring alarm-related decision making is key to reducing alarm fatigue, as it is important to the development of alarm management related initiatives, education, and policies. To examine this, I used Interpretive Description methodology to explore factors that influence Intensive Care Unit nurses’ decision making regarding alarm management, specifically how they triage and respond to various alarms. This study included 12 participants, comprised of nurses with varying levels of experience, working at three different Intensive Care Units. The results of the interviews suggest that the nurses’ decision making consists of three steps that capture their alarm management response: awareness, triage, and response. Based on these results, a positive alarm management culture, standardized alarm-related education, and mentorship should be evaluated to implement an effective alarm management response and reduce alarm fatigue.
Products and Intersections of Prime-Power Ideals in Leavitt Path Algebras
Creators: name: Mesyan, Zachary
name: Rangaswamy, Kulumani M.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 16W10, 16D25, 16D70

description: We continue a very fruitful line of inquiry into the multiplicative ideal theory of an arbitrary Leavitt path algebra L. Specifically, we show that factorizations of an ideal in L into irredundant products or intersections of finitely many prime-power ideals are unique, provided that the ideals involved are powers of distinct prime ideals. We also characterize the completely irreducible ideals in L, which turn out to be prime-power ideals of a special type, as well as ideals that can be factored into products or intersections of finitely many completely irreducible ideals.
description: 24 pages. arXiv admin note: text overlap with arXiv:1908.05805
Quasilinear elliptic equations and weighted Sobolev-Poincaré inequalities with distributional weights
Creators: name: Jaye, Benjamin J.
name: Maz'ya, Vladimir G.
name: Verbitsky, Igor E.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Analysis of PDEs (math.AP)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: We introduce a class of weak solutions to the quasilinear equation $-Δ_p u = σ|u|^{p-2}u$ in an open set $Ω\subset\mathbf{R}^n$. Here $p>1$, and $Δ_p u$ is the $p$-Laplacian operator. Our notion of solution is tailored to general distributional coefficients $σ$ satisfying a certain weighted Sobolev-Poincare inequality. We also study weak solutions of the closely related equation $-Δ_p v = (p-1)|\nabla v|^p + σ$, under the same conditions on $σ$. Our results for this latter equation will allow us to characterize the class of distributions $σ$ which satisfy the Sobolev-Poincare inequality, thereby extending earlier results on the form boundedness problem for the Schrödinger operator to $p\neq 2$.
description: 36 pages
Anaglyphula whitteni Vermeulen 1996
Creators: name: Chen, Zhe-Yu
name: Páll-Gergely, Barna
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Littorinimorpha
Assimineidae
Anaglyphula
Anaglyphula whitteni

description: Anaglyphula whitteni Vermeulen, 1996
(Figs. 2B–C, 4C)
 Anaglyphula whitteni Vermeulen, 1996: 150, fig. 1.
 Type material. NHMUK 20000247 (paratype), Indonesia, Bali, above Danau Buyen, at c. 1400 m asl, forest on volcanic soil, leg. A.J. Whitten, 1993.
 Remarks. A constriction formed by a thin radial palatal fold is internally present at ½ whorl away from the aperture and is visible from the aperture. The sculpture of this species is characterised by converging, wavy ribs, similar to the type species of Acmella (see Das et al., 2021). However, its shell outline and umbilicus are consistent with those of Anaglyphula cancellata, so we retain this arrangement. The converging ribs can also be considered as a tendency to form the rib-mesh present in the type species.
description: Published as part of Chen, Zhe-Yu & Páll-Gergely, Barna, 2023, A new species of Anaglyphula Rensch, 1932 from an island off the coast of West Indonesia, with redescription of the type species (Gastropoda: Caenogastropoda: Assimineidae), pp. 597-605 in Raffles Bulletin of Zoology 71 on page 604, DOI: 10.26107/RBZ-2023-0046, http://zenodo.org/record/10271430
Quantifying and Visualizing Regional Bone Changes in the Knee following an ACL Tear
Creators: name: Morrison, Alida Claire
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Engineering--Biomedical

description: ACL tears are a common type of injury that often happens during sports activities. While some people may regain knee function after healing, the development of post-traumatic osteoarthritis (PTOA) is a possible long-term outcome of a knee injury. The integrity of many tissues is affected by the injury including bone, which typically experiences density loss. Sub-regional analysis of bone density using medical imaging provides more detailed insight into bone status after an acute knee injury, however these spatial positions may overlook areas with significant local change. This work examined patterns of bone change through the distal femur and proximal tibia following an ACL tear using computed tomography (CT) images of 10 participants. Clinical CT and high resolution peripheral quantitative CT (HR-pQCT) scans of injured knees were measured at baseline and 1-year follow-up time points. The longitudinal data were registered, and the voxel-wise differences were visualized to identify regions of significant bone changes and compare the two modalities. Patterns of bone density changes were assessed in the context of individual patient locations of bone contusions, fractures, and osteochondral injuries, as described in baseline magnetic resonance imaging (MRI) reports. In the femur, bone loss was observed at both condyles and, for 90% of participants, bone loss was also observed at the site of insertion of the ACL. Posterior horn meniscus injury typically corresponded to bone loss on the associated femoral condyle, and on the posterior tibial plateau. Widespread changes to bone density in the injured knee are influenced not only by ACL tear, but by concurrent injuries such as meniscal damage. These significant changes within the first year post injury may play an important role in the long term health of the knee.
Investigation of the effect gut microbiota have on the calcium isotopic composition in different calcium reservoirs of mice
Creators: name: Walls, Dorothy Mae
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: DGA Resin
subject: Double-spike
subject: Calcium isotopes
subject: δ(44Ca/40Ca)
subject: δ(44Ca/42Ca)
subject: Gut microbiota
subject: Mice
subject: Physics

description: The determination of the isotopic composition of calcium (Ca) in the body has gained increasing recognition as a powerful tool to monitor Ca metabolism, and bone metabolism in biological systems. Calcium is an essential mineral in the body and is critical for building and maintaining strong teeth and bones. Mishandling of this metal is associated with several diseases and disorders within the body. Therefore, understanding calcium metabolism is necessary to address the significance of this mineral, and the role it plays in the health of an individual. This thesis describes the development of an analytical technique to measure calcium isotope amount ratios in biological samples from as little as 670 ng, which is a two-fold decrease in the amount of Ca required compared to recent studies using MC TIMS. The technique was used to determine how the distribution of calcium isotopes changes in mice where calcium metabolism has been impacted by an altered composition of gut microbiota in the gastrointestinal tract of the mice. This technique developed in this thesis was applied to biological standard reference materials, and the δ(44/40Ca) isotope amount ratio of the reference materials NIST SRM 1400, NIST SRM 1486, and IAPSO were in good agreement and within uncertainty of literature data. Others were measured for Ca isotopic composition for the first time. The technique was then applied to the analysis of the calcium isotopic fractionation for three mouse groups with different gut bacterial compositions in four different tissue pools (diet, kidney, bone, and feces). Two cohorts of mice differentiated by age were investigated, where the first cohort was 91 days old, and the second was approximately 85 days old. There were no observed trends in the Ca isotopic compositions in the Ca reservoirs of the mice for given gut bacteria groups across the two cohorts. Therefore, we conclude that changes in gut microbiota do not produce a significant change in the redistribution of the isotopes of Ca in the different Ca pools in mice.
Efficient Extension of a Software Analysis Framework to Additional Languages
Creators: name: Soltanpour, Shahryar
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: Software Engineering
subject: Computer Science
subject: Software Analysis
subject: Embedded Language Identification
subject: Education--Technology

description: In the current era of software development, multi-language codebases are common, and change propagation in these codebases is challenging. The existing change propagation tool ModCP is a solution that can assist software developers with propagating changes across several languages, but only one at a time. However, ModCP has some architectural problems in that make supporting new languages hard to develop and maintain for a long time. In addition, supporting change propagation across code snippets consisting of a programming language embedded inside a different programming language would be a useful feature for ModCP. To achieve this, we must detect the embedded code snippets in a code being analyzed by ModCP. In this thesis, we develop a new, more efficient architecture for ModCP, involving a single abstract model that each language extends for its usage, resulting in complete isolation between language results. We compare our approach with a baseline version that uses the same, concrete model for all languages and adds new models when necessary. Our approach reduces code complexity and development time and makes code more compatible with best practices of development compared to the baseline. Moreover, we design a system for ModCP to guess and validate the programming language used in code snippets, based on the initial detection of keywords, as input to execute change propagation for multi-language codes embedded inside each other. We compare our keyword detection approach with existing deep learning and brute force approaches and show that our method is the best choice if accuracy, performance, and scalability are needed simultaneously.
Allogeneic Adipose-Derived Mesenchymal Stem Cells as an Adjunct to Endovascular Treatment of Intracranial Aneurysms
Creators: name: Belanger, Brooke Lynnae
Publisher: name: Graduate Studies
Year: 2023
Subjects: subject: aneurysm
subject: stem cells
subject: Neuroscience

description: Intracranial aneurysms are a condition characterized by the weakening of blood vessels in the brain, affecting approximately 1 in 5 individuals. Rupture of these fragile blood vessels can result significant brain bleeding, also known as subarachnoid hemorrhage, leading to a stroke that can cause severe neurological deficits or death. Current treatment approaches involve either endovascular or open surgery. One of the most common treatments is endovascular surgery, a minimally invasive procedure that entails inserting a small catheter through the femoral or radial artery and navigating it to the location of the aneurysm in the brain. Depending on the anatomical features, the aneurysm sac is filled with small platinum coils, or a mesh metal stent which is placed to cover the aneurysm opening. The objective in both cases is to redirect blood flow and eliminate the risk of stroke. However, recurrent aneurysms occur in up to 30% of these procedures, necessitating multiple surgeries. Recent advancements have introduced novel endovascular devices such as bioresorbable stents to enhance the outcomes of aneurysm treatment. Additionally, allogeneic adult mesenchymal stem cells have shown promise in improving healing processes. This dissertation aims to expand our understanding of the impact of stem cells on aneurysm healing and how they can be effectively utilized to improve the outcomes of brain aneurysm treatments, including endovascular coiling and stenting.
One-dimensional interacting electrons beyond the Dzyaloshinskii-Larkin theorem
Creators: name: Teber, S.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We consider one-dimensional (1D) interacting electrons beyond the Dzyaloshinskii-Larkin theorem, i.e., keeping forward scattering interactions among the electrons but adding a non-linear correction to the electron dispersion relation. The latter generates multi-loop corrections to the polarization operator and electron self-energy thereby providing a variety of inelastic processes affecting equilibrium as well as non-equilibrium properties of the 1D system. We first review the computation of equilibrium properties, e.g., the high frequency part of the dynamical structure factor and corrections to the electron-electron scattering rate. On this basis, microscopic equilibration processes are identified and a qualitative estimate of the relaxation rate of thermal carriers is given.
description: 4 pages, 5 figures
Additional file 1 of Long-term effects of cemented and cementless fixations of total knee arthroplasty: a meta-analysis and systematic review of randomized controlled trials
Creators: name: Chen, Cheng
name: Shi, Yanyan
name: Wu, Zhanpo
name: Gao, Zengxin
name: Chen, Youmin
name: Guo, Changzheng
name: Bao, Xianguo
Publisher: name: figshare
Year: 2021
Subjects: Medicine
Biotechnology
Science Policy

description: Additional file 1. Table S1: MEDLINE search strategy. Figure S1: Egger's test survivorship. Figure S2: Egger's test KS knee score. Figure S3: Egger's test KS function score. Figure S4: Egger's test WAMAC score. Figure S5: Egger's test HSS score. Figure S6: Egger's test Range of motion. Figure S7: Egger's test radiolucent line. Figure S8: Egger's test MTPM.
Four tops and the t tbar forward-backward asymmetry
Creators: name: Aguilar-Saavedra, J. A.
name: Santiago, Jose
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: New colour octet vectors below the TeV scale could explain the anomalous t tbar forward-backward asymmetry observed at the Tevatron experiments, while being consistent with the current LHC data. These models generally lead to four-top final states at the LHC at observable levels. We compute the four-top production cross section at the LHC in a model with a massive colour octet vector as a function its mass, its width and its coupling to the top quark. Octet masses in the vicinity of the t tbar threshold are generally excluded by present limits on the production of same-sign dileptons and trileptons. Masses above 650 GeV are allowed, quite independently of the couplings, but they can be probed with the luminosity of 5 fb^-1 already collected at the LHC, up to around 800 GeV. The four-top production cross section is increased by a factor ~ 2 with sqrt{s}=8 TeV and by up to almost two orders of magnitude with sqrt{s}=14 TeV, thus greatly increasing the reach for massive gluons after the LHC energy upgrade.
description: LaTeX 5 pages. Added results for 14 TeV. Final version to appear in PRD
Doctor Imitator: Hand-Radiography-based Bone Age Assessment by Imitating Scoring Methods
Creators: name: Chen, Jintai
name: Yu, Bohan
name: Lei, Biwen
name: Feng, Ruiwei
name: Chen, Danny Z.
name: Wu, Jian
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Bone age assessment is challenging in clinical practice due to the complicated bone age assessment process. Current automatic bone age assessment methods were designed with rare consideration of the diagnostic logistics and thus may yield certain uninterpretable hidden states and outputs. Consequently, doctors can find it hard to cooperate with such models harmoniously because it is difficult to check the correctness of the model predictions. In this work, we propose a new graph-based deep learning framework for bone age assessment with hand radiographs, called Doctor Imitator (DI). The architecture of DI is designed to learn the diagnostic logistics of doctors using the scoring methods (e.g., the Tanner-Whitehouse method) for bone age assessment. Specifically, the convolutions of DI capture the local features of the anatomical regions of interest (ROIs) on hand radiographs and predict the ROI scores by our proposed Anatomy-based Group Convolution, summing up for bone age prediction. Besides, we develop a novel Dual Graph-based Attention module to compute patient-specific attention for ROI features and context attention for ROI scores. As far as we know, DI is the first automatic bone age assessment framework following the scoring methods without fully supervised hand radiographs. Experiments on hand radiographs with only bone age supervision verify that DI can achieve excellent performance with sparse parameters and provide more interpretability.
description: Original Title: "Doctor Imitator: A Graph-based Bone Age Assessment Framework Using Hand Radiographs" @inproceedings{chen2020doctor, title={Doctor imitator: A graph-based bone age assessment framework using hand radiographs}, author={Chen, Jintai and Yu, Bohan and Lei, Biwen and Feng, Ruiwei and Chen, Danny Z and Wu, Jian}, booktitle={MICCAI}, year={2020} }