cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Blocked Elements in 1-D and 2-D Arrays—Part I: Detection and Basic Compensation on Simulated and In Vivo Targets
Creators: name: Jakovljevic, Marko
name: Trahey, Gregg E.
name: Dahl, Jeremy J.
name: Pinton, Gianmarco F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: During a transcostal ultrasound scan, ribs and other highly attenuating and/or reflective tissue structures can block parts of the array. Blocked elements tend to limit the acoustic window and impede visualization of structures of interest. Here, we demonstrate a method to detect blocked elements and we measure the loss of image quality they introduce in simulation and in vivo. We utilize a fullwave simulation tool and a clinical ultrasound scanner to obtain element signals from fully sampled matrix arrays during simulated and in vivo transcostal liver scans, respectively. The elements that were blocked by a rib showed lower average signal amplitude and lower average nearest-neighbor cross correlation than the elements in the remainder of the 2-D aperture. The growing receive-aperture B-mode images created from the element data indicate that the signals on blocked elements are dominated by noise and that turning them OFF has a potential to improve visibility of liver vasculature. Adding blocked elements to the growing receive apertures for five in vivo transcostal acquisitions resulted in average decrease in vessel contrast and contrast to noise ratio of 19% and 10%, respectively.
Acceptable loss: Fitness consequences of salinity-induced cell death in a halotolerant microalga
Creators: name: Zeballos, Nathalie
name: Grulois, Daphné
name: Leung, Christelle
name: Chevin, Luis-Miguel
Publisher: name: Zenodo
Year: 2023
Subjects: Dunaliella salina
Flow cytometry
population dynamics
programmed cell death
environmental stress
population decline
natural selection
fluorescence

description: Environmentally induced reductions in fitness components (survival, fecundity) are generally considered as passive, maladaptive responses to stress. However, there is also mounting evidence for active, programmed forms of environmentally induced cell death in unicellular organisms. While conceptual work has questioned how such programmed cell death (PCD) might be maintained by natural selection, few experimental studies have investigated how PCD influences genetic differences in longer-term fitness across environments. Here, we tracked the population dynamics of two closely related strains of the halotolerant microalga Dunaliella salina, following transfers across salinities. We showed that after a salinity rise, only one of these strains displayed a massive population decline (-69% in one hour), largely attenuated by exposure to a PCD inhibitor. However, this decline was followed by a rapid demographic rebound, characterized by faster growth than the non-declining strain, such that sharper decline was correlated with faster subsequent growth across experiments and conditions. Strikingly, the decline was more pronounced in conditions more favourable to growth (more light, more nutrients, less competition), further suggesting that it was not simply passive. We explored several hypotheses that could explain this decline-rebound pattern, which suggests that successive stresses could select for higher environmentally induced death in this system.
description: Raw data are .fcs files opened in the software Incyte (version 3.2), from where we extracted the population densities. Whole-well fluorescence spectrometer raw data (.RUC files) were opened in the software Mars (version 3.32).
All statistical analyses were performed on Rstudio (R version 3.6) using MASS version 7.3.53, tidyverse 1.3.1 and lubridate 1.8.0 packages.Funding provided by: European Research Council
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100010663
Award Number:
description: We tracked the population dynamics of two closely related strains of the halotolerant microalga Dunaliella salina, following transfers across salinities, using a cytometer and/or a spectrometer.
Cosmic Shear Results from the Deep Lens Survey - II: Full Cosmological Parameter Constraints from Tomography
Creators: name: Jee, M. James
name: Tyson, J. Anthony
name: Hilbert, Stefan
name: Schneider, Michael D.
name: Schmidt, Samuel
name: Wittman, David
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present a tomographic cosmic shear study from the Deep Lens Survey (DLS), which, providing a limiting magnitude r_{lim}~27 (5 sigma), is designed as a pre-cursor Large Synoptic Survey Telescope (LSST) survey with an emphasis on depth. Using five tomographic redshift bins, we study their auto- and cross-correlations to constrain cosmological parameters. We use a luminosity-dependent nonlinear model to account for the astrophysical systematics originating from intrinsic alignments of galaxy shapes. We find that the cosmological leverage of the DLS is among the highest among existing >10 sq. deg cosmic shear surveys. Combining the DLS tomography with the 9-year results of the Wilkinson Microwave Anisotropy Probe (WMAP9) gives Omega_m=0.293_{-0.014}^{+0.012}, sigma_8=0.833_{-0.018}^{+0.011}, H_0=68.6_{-1.2}^{+1.4} km/s/Mpc, and Omega_b=0.0475+-0.0012 for LCDM, reducing the uncertainties of the WMAP9-only constraints by ~50%. When we do not assume flatness for LCDM, we obtain the curvature constraint Omega_k=-0.010_{-0.015}^{+0.013} from the DLS+WMAP9 combination, which however is not well constrained when WMAP9 is used alone. The dark energy equation of state parameter w is tightly constrained when Baryonic Acoustic Oscillation (BAO) data are added, yielding w=-1.02_{-0.09}^{+0.10} with the DLS+WMAP9+BAO joint probe. The addition of supernova constraints further tightens the parameter to w=-1.03+-0.03. Our joint constraints are fully consistent with the final Planck results and also the predictions of a LCDM universe.
description: Accepted for publication in ApJ
A new version of fermion coupled coherent states method: Theory and applications in simulation of two-electron systems
Creators: name: Eidi, Mohammadreza
name: Vafaee, Mohsen
name: Niknam, Ali Reza
name: Morshedian, Nader
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We report a new version of fermion coupled coherent states method (FCCS-II) to simulate two-electron systems based on a self-symmetrized six-dimensional (6D) coherent states grid. Unlike the older fermion coupled coherent states method (FCCS-I), FCCS-II does not need any new equations in comparison with the coupled coherent states method. FCCS-II uses a simpler and more efficient approach for symmetrizing the spatial wave function in the simulation of fermionic systems. This method, has significantly increased the speed of computations and give us the capability to simulate the quantum systems with the larger CS grids. We apply FCCS-II to simulate the Helium atom and the Hydrogen molecule based on grids with a large numbers of coherent states. FCCS-II with a relatively low number of CS gives a potential energy curve for H2 that is very close to the exact potential curve. Moreover, we have re-derived all the important equations of the FCCS-I method.
description: 22 pages, 6 figures
Contrast Enhanced Superharmonic Imaging for Acoustic Angiography Using Reduced Form-Factor Lateral Mode Transmitters for Intravascular and Intracavity Applications
Creators: name: Huang, Wenbin
name: Dayton, Paul A.
name: Martin, K. Heath
name: Jiang, Xiaoning
name: Wang, Zhuochen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Techniques to image the microvasculature may play an important role in imaging tumor-related angiogenesis and vasa vasorum associated with vulnerable atherosclerotic plaques. However, the microvasculature associated with these pathologies is difficult to detect using traditional B-mode ultrasound or even harmonic imaging due to small vessel size and poor differentiation from surrounding tissue. Acoustic angiography, a microvascular imaging technique which utilizes superharmonic imaging (detection of higher order harmonics of microbubble response), can yield a much higher contrast to tissue ratio (CTR) than second harmonic imaging methods. In this work, two dual-frequency transducers using lateral mode transmitters were developed for superharmonic detection and acoustic angiography imaging in intracavity applications. A single element dual-frequency IVUS transducer was developed for concept validation, which achieved larger signal amplitude, better contrast to noise ratio (CNR) and pulse length compared to the previous work. A dual-frequency PMN-PT array transducer was then developed for superharmonic imaging with dynamic focusing. The axial and lateral size of the microbubbles in a 200 μm tube were measured to be 269 μm and 200 μm, respectively. The maximum CNR was calculated to be 22 dB. These results show that superharmonic imaging with a low frequency lateral mode transmitter is a feasible alternative to thickness mode transmitters when final transducer size requirements dictate design choices.
Methods of Generating Submicrometer Phase-Shift Perfluorocarbon Droplets for Applications in Medical Ultrasonography
Creators: name: Borden, Mark A.
name: Burns, Peter N.
name: Dayton, Paul A.
name: Matsunaga, Terry O.
name: Matsuura, Naomi
name: Sheeran, Paul S.
name: Williams, Ross
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Continued advances in the field of ultrasound and ultrasound contrast agents have created new approaches to imaging and medical intervention. Phase-shift perfluorocarbon droplets, which can be vaporized by ultrasound energy to transition from the liquid to the vapor state, are one of the most highly researched alternatives to clinical ultrasound contrast agents (i.e., microbubbles). In this paper, part of a special issue on methods in biomedical ultrasonics, we survey current techniques to prepare ultrasound-activated nanoscale phase-shift perfluorocarbon droplets, including sonication, extrusion, homogenization, microfluidics, and microbubble condensation. We provide example protocols and discuss advantages and limitations of each approach. Finally, we discuss best practice in characterization of this class of contrast agents with respect to size distribution and ultrasound activation.
Optimizing Acoustic Activation of Phase Change Contrast Agents With the Activation Pressure Matching Method: A Review
Creators: name: Dayton, Paul A.
name: Rojas, Juan D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Sub-micron phase-change contrast agents consist of a liquid perfluo ocarbon core that can be vaporized by ultrasound (acoustic droplet vaporization) to generate contrast with excellent spatial and temporal control. When these agents, commonly referred to as nanodroplets, are formulated with cores of low boiling-point perfluo ocarbons such as decaflu orobutane and octafluo opropane, they can be activated with low-mechanical index imaging pulses for diagnostic applications. Since the utilization of minimum mechanical index is often desirable to avoid unnecessary biological effects, enabling consistent activation of these agents in an acoustic fiel is a challenge because the energy that must be delivered to achieve the vaporization threshold increases with depth due to attenuation. A novel vaporization approach called Activation Pressure Matching has been developed to deliver the same pressure throughout a fiel of view in order to produce uniform nanodroplet vaporization and to limit the amount of energy that is delivered. In this manuscript, we discuss the application of this method with a Versasonics V1 Research Ultrasound System to modulate the output pressure from an ATL L11–5 transducer. Vaporization-pulse spacing optimization can be used in addition to matching the activation pressure through depth, and we demonstrate the feasibility of this approach both in vivo and in vitro. The use of optimized vaporization parameters increases the amount of time a single bolus of nanodroplets can generate useful contrast and provides consistent image enhancement in vivo. Therefore, APM is a useful technique for those wishing to maximize the efficac of phase change contrast agent while minimizing delivered acoustic energy.
Subresolution Displacements in Finite Difference Simulations of Ultrasound Propagation and Imaging
Creators: name: Pinton, Gianmarco F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Time domain finite difference simulations are used extensively to simulate wave propagation. They approximate the wave field on a discrete domain with a grid spacing that is typically on the order of a tenth of a wavelength. The smallest displacements that can be modeled by this type of simulation are thus limited to discrete values that are integer multiples of the grid spacing. This paper presents a method to represent continuous and subresolution displacements by varying the impedance of individual elements in a multi-element scatterer. It is demonstrated that this method removes the limitations imposed by the discrete grid spacing by generating a continuum of displacements as measured by the backscattered signal. The method is first validated on an ideal perfect correlation case with a single scatterer. It is subsequently applied to a more complex case with a field of scatterers that model an acoustic radiation force induced displacement used in ultrasound elasticity imaging. A custom finite difference simulation tool is used to simulate propagation from ultrasound imaging pulses in the scatterer field. These simulated transmit-receive events are then beamformed into images which are tracked with a correlation based algorithm to determine the displacement. A linear predictive model is developed to analytically describe the relationship between element impedance and backscattered phase shift. The error between model and simulation is λ/1364, where λ is the acoustical wavelength. An iterative method is also presented that reduces the simulation error to λ/5556 over one iteration. The proposed technique therefore offers a computationally efficient method to model continuous subresolution displacements of a scattering medium in ultrasound imaging. This method has applications that include ultrasound elastography, blood flow, and motion tracking. This method also extends generally to finite difference simulations of wave propagation, such as electromagnetic or seismic waves.
Compressed Coverage Masks for Path Rendering on Mobile GPUs
Creators: name: Manocha, Dinesh
name: Krajcevski, Pavel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: We present an algorithm to accelerate resolution independent curve rendering on mobile GPUs. Recent trends in graphics hardware have created a plethora of compressed texture formats specific to GPU manufacturers. However, certain implementations of platform independent path rendering require generating grayscale textures on the CPU containing the extent that each pixel is covered by the curve. In this paper, we demonstrate that generating a compressed grayscale texture prior to uploading it to the GPU creates faster rendering times in addition to the memory savings. We implement a real-time compression technique for coverage masks and compare our results against the GPU-based implementation of the highly optimized Skia rendering library. We also analyze the worst case properties of our compression algorithms. We observe up to a 2 × speed improvement over the existing GPU-based methods in addition to up to a 9:1 improvement in GPU memory gains. We demonstrate the performance on multiple mobile platforms.
Novel applications of complex analysis to effective parameter quantification in transport theory
Creators: name: Miyoshi, Hiroyuki
Publisher: name: Imperial College London
Year: 2023

description: This thesis proposes the application of complex analysis to the calculation of effective parameters of transport problems in multiply connected domains. This can be done by using special functions called Schottky-Klein prime functions. The effective parameters focused on in this thesis are electrical resistivity, electrical capacity, and slip lengths of channels. The prime function is a powerful mathematical function invented by Crowdy for solving problems in multiply connected domains including transport problems governed by Laplace’s equation and Poisson’s equation in domains with multiple boundaries. The functional properties of the prime function make it possible to analyse effective parameters in multiply connected domains. First, a new method for solving a new class of boundary value problems in multiply connected domains is explained. An explicit solution can be derived by multiplying of the boundary data with a radial slit map written in terms of the prime functions. We then focus on two electrical transport problems called “the van der Pauw method” and “electrical capacity”. For the van der Pauw method, the prime function allows us to derive new formulas for calculating the resistivity of holey samples. A new method for the electrical capacity of multiply connected domains is formulated by coupling the prime function with asymptotic matching. We next construct explicit solutions for flows through superhydrophobic surfaces in periodic channels and calculate the slip length of these channels. We end the thesis by mentioning that the new methodology gives accurate estimates for so-called “accessory parameter problems” associated with conformal maps of multiply connected domains.
Developments and applications of the aluminium-[18F]fluoride method for biomolecule radiolabelling
Creators: name: Teh, Jin Hui
Publisher: name: Imperial College London
Year: 2023

description: The development of novel methods to efficiently synthesise new radiotracers is an active area of research in nuclear medicine. One major advancement is the development of the aluminium-[18F]fluoride ([18F]AlF) method, which has enabled facile and efficient radiofluorination reactions. The [18F]AlF2+ complex, described as a pseudo-radiometal, combines the convenience of radiometal-based synthetic approaches with the favourable decay characteristics of fluorine-18. These advantages have led to the widespread implementation of the [18F]AlF method for producing new radiotracers, with an array of clinical trials already being reported. This thesis aims to further expand on the applications of the [18F]AlF method and develop new approaches to allow its incorporation into biomolecules. Firstly, the utility of the [18F]AlF method in enabling facile 18F-labelling of microbubbles was developed to enable their whole-body distributions to be tracked. An [18F]AlF-labelled tetrazine was synthesised in excellent radiochemical yield and used to radiolabel trans-cyclooctene-functionalised microbubbles via the efficient inverse-electron-demand Diels-Alder (IEDDA) reaction. To further improve the accessibility of 18F-labelled microbubbles, a kit-based approach was successfully developed. This approach allows microbubbles to be radiolabelled with minimal radiochemical expertise, which potentially facilitates the development of new lipid-based microbubble formulations. In addition, the [18F]AlF-labelled microbubbles were also successfully applied for evaluating the effects ultrasound-mediated microbubble destruction and sonoporation in enhancing the delivery of radioactivity to tumours, further demonstrating the utility of the [18F]AlF method in enabling different biological phenomena to be studied. This thesis also investigated the potential to improve on the current [18F]AlF-labelling methodologies. To facilitate [18F]AlF-labelling under milder conditions, the development of new chelators was undertaken. Whilst initial studies using aluminium-salen complexes showed their potential for 18F-labelling, conclusive evidence on the formation of an Al-F bond was not obtained, necessitating further optimisation of the ligand structure and fluorination conditions. Finally, the ability to site-selectively radiolabel biomolecules by [18F]AlF was explored using the π-clamp-mediated cysteine conjugation method. Two approaches were developed: (i) a prosthetic group approach, and (ii) a direct [18F]AlF-labelling approach. Both approaches demonstrated the utility of the [18F]AlF method to be used for site-selectively radiolabelling octreotate as the model peptide, providing the potential for translation to larger biomolecules. In summary, the work presented herein provides an extension to the current toolkit of radiolabelling microbubbles and biomolecules using the [18F]AlF method, which ultimately seeks to expand on the available strategies for producing new radiotracers.
Molecular modelling and statistical thermodynamics of semi-crystalline polymers: network constraints, fluid sorption and surface melting
Creators: name: Valsecchi, Michele
Publisher: name: Imperial College London
Year: 2023

description: Accurately predicting gas and liquid solubility in semi-crystalline polymers is crucial for optimizing their production, performance, and degradation behaviour. In this work a novel statistical-mechanical model for semi-crystalline polymers is showcased. The amorphous domains are divided into two portions: the semi-rigid inter-lamellar domains and the melt-like ``free" amorphous domains. Solubility in the inter-lamellar domains is reduced due to the presence of tie-molecules, which are polymer chains connecting different crystals. By incorporating reversible mass exchange at the crystal/amorphous interface, the model predicts variations in lamellar thickness and solubility with temperature. According to our model, the equilibrium solubility in each polymer sample is determined by its crystallinity, the fraction of tie-molecules at the crystal/amorphous interface, and the fraction of free amorphous domains. While crystallinity can be easily measured, the other two parameters are adjusted to minimize differences between the model's predictions (made in conjunction with the SAFT-γ Mie equation of state) and experimental sorption isotherms of pure fluids in polyethylene (PE), polypropylene (PP), and polyethylene glycol (PEG) samples. The model accurately reproduces the solubility of all solutes considered after the assignment of unique sample-specific parameters to each sample. A meta-analysis of literature data reveals that in PE, the fraction of free amorphous domains decreases with crystallinity whereas the fraction of tie-molecules lies in the range 0.2 – 0.4. The model's predictions of solubility of binary mixtures of short hydrocarbons in PE are in good agreement with experimental data. The model also accurately captures the temperature dependence of solubility in most of the polymer samples considered, except for those with low crystallinity where changes in the free amorphous domains with temperature may need consideration. Additionally, the model is applied to study the moisture uptake by PEG. By employing simple thermodynamic considerations, the model qualitatively predicts the humidity at which deliquescence occurs and describes the moisture uptake at each relative humidity after adjusting the fraction of tie-molecules.
Hadronic origin of multi-TeV gamma rays and neutrinos from low-luminosity active galactic nuclei: implications of past activities of the Galactic center
Creators: name: Fujita, Yutaka
name: Kimura, Shigeo S.
name: Murase, Kohta
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Radiatively inefficient accretion flows (RIAFs) in low-luminosity active galactic nuclei (LLAGNs) have been suggested as cosmic-ray and neutrino sources that may largely contribute to the observed diffuse neutrino intensity. We show that this scenario naturally predicts hadronic multi-TeV gamma-ray excesses around Galactic centers. The protons accelerated in the RIAF in Sagittarius A$^*$ (Sgr A$^*$) escape and interact with dense molecular gas surrounding Sgr A$^*$, which is known as the central molecular zone (CMZ), and produce gamma rays as well as neutrinos. Based on a theoretical model that is compatible with the IceCube data, we calculate gamma-ray spectra of the CMZ and find that the gamma rays with $\gtrsim 1$ TeV may have already been detected with the High Energy Stereoscopic System, if Sgr A$^*$ was more active in the past than it is today as indicated by various observations. Our model predicts that neutrinos should come from the CMZ with a spectrum similar to the gamma-ray spectrum. We also show that such a gamma-ray excess is expected for some nearby galaxies hosting LLAGNs.
description: Published in Phys. Rev. D
A FOWL version of ChEBI
Creators: name: Glauer, Martin
name: Neuhaus, Fabian
name: Hastings, Janna
Publisher: name: Zenodo
Year: 2022

description: This is a version of chebi with additional annotations that contain formalisations of a majority of the molecular classes using firtst order logic.
description: {"references": ["Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. (2016). ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res."]}
Functional impact of inactivating mutations in epigenetic regulators in cancer
Creators: name: Loukas, Ioannis
Publisher: name: Imperial College London
Year: 2023

description: Cancer evolution is driven by selection acting on genetic and epigenetic diversity to promote the propagation of the fittest subpopulations. This phenomenon is shaped by the tumor microenvironment which is often characterized by stressful conditions. Epigenetic regulators are frequently mutated during the later stages of tumorigenesis, but the functional impact of their inactivation is poorly understood. In this thesis, I hypothesize that the disruption of the epigenetic regulatory network increases cell fitness in unfavorable environments and thus is selected over time. Through large-scale fitness assays in various cancer models, I demonstrate that epigenetic deregulation leads to a widespread stress-specific survival advantage. This effect is mediated by mutations in all layers of epigenetic regulation, is shared across different stress conditions and is cancer type independent. Then, I explore various cellular mechanisms that can underlie this stress-specific fitness advantage. Genetic diversity, transcriptional heterogeneity or phenotypic plasticity cannot explain the increased survival under stress, as revealed by a combination of reversible epigenetic inhibition, live-cell imaging and single-cell transcriptomics. On the contrary, epigenetically deregulated cells remain phenotypically inert (less responsive) under stress. Transcriptional profiling of cancer populations in hostile conditions, revealed significant alterations in fitness and growth-related signatures. Disruption of the epigenetic machinery results in a defective stress response, thus decreasing the probability of such cells to surpass a stressed threshold and ultimately die. This defective transcriptional rewiring underpins the inert phenotype that emerges upon epigenetic deregulation. Collectively, by investigating the effect of inactivating mutations in epigenetic regulators on cell fitness under environmental stress, I propose that phenotypic inertia is the favorable cellular trait that is selected over time. My findings provide a potential explanation for the widespread subclonal mutations affecting epigenetic regulators and have significant implications for cancer evolution.
A cognitive perspective on learning, decision-making, and technology evaluations in organisations
Creators: name: Benigni, Stefano
Publisher: name: Imperial College London
Year: 2023

description: This dissertation examines how firms’ selection of technological and R&D opportunities shape the performance of their innovation efforts. Managers select R&D investments in complex and uncertain environments where it is difficult to learn from past decisions. I examine this challenge using empirical and agent-based modelling methods and by focusing on three interrelated aspects: managers’ individual learning processes, the adaptation of mental representations in complex environments, and the role of distributed expertise in group evaluations. In the first chapter, I propose an alternative explanation to how managers learn from experience that does not involve feedback and that is thus applicable to contexts where learning from feedback is difficult. I test this novel learning mechanism, termed ‘representation learning’, by analysing a large proprietary dataset of patent evaluations and termination decisions made by managers at a Fortune 500 firm. The second chapter explores further implications for performance of representation learning by means of an agent-based model of representation and policy search in rugged landscapes. This study examines how different representation search strategies affect decision-makers’ adaptation in complex environments. Finally, the third chapter explores the performance of group evaluation processes when evaluators differ in the depth and breadth of their knowledge of the technologies being evaluated. This research contributes to management literature by shedding light on the cognitive processes underlying learning and decision-making in uncertain and complex environments. These findings also have practical implications for strategy research and practice concerning the management of uncertain R&D and technology investments.
Tracing Analytic Ray Curves for Light and Sound Propagation in Non-Linear Media
Creators: name: Mo, Qi
name: Manocha, Dinesh
name: Yeh, Hengchin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The physical world consists of spatially varying media, such as the atmosphere and the ocean, in which light and sound propagates along non-linear trajectories. This presents a challenge to existing ray-tracing based methods, which are widely adopted to simulate propagation due to their efficiency and flexibility, but assume linear rays. We present a novel algorithm that traces analytic ray curves computed from local media gradients, and utilizes the closed-form solutions of both the intersections of the ray curves with planar surfaces, and the travel distance. By constructing an adaptive unstructured mesh, our algorithm is able to model general media profiles that vary in three dimensions with complex boundaries consisting of terrains and other scene objects such as buildings. Our analytic ray curve tracer with the adaptive mesh improves the efficiency considerably over prior methods. We highlight the algorithm's application on simulation of visual and sound propagation in outdoor scenes.
Pump Linewidth Requirements for Processing Dispersion-Altered DQPSK Signals using FWM
Creators: name: Dúill, Séan Ó
name: Naimi, Sepideh T.
name: Barry, Liam P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report on a potentially deleterious issue regarding the four-wave mixing based processing of dispersion-altered signals. We estimate the baudrate-dependent pump linewidth tolerances by calculating the extra optical signal to noise ratio (OSNR) penalty with respect to the propagation distance. We find that the issue is not important for 10 Gbaud differential quadrature phase shift keying (DQPSK) signals, though for 28 Gbaud (and 56 Gbaud) DQPSK signals we find that the pump linewidth requirements to implement FWM based optical signal processing needs to be in the sub-MHz range in order to avoid excessive OSNR penalties for the case of dispersion-altered signals. These results are pertinent for systems employing FWM, which could be all-optical wavelength converters for packet switching or mid-span spectral inversion techniques.
“We don’t want to be the bad guys”: Exploring the future of international oil companies in a ‘well below 2 degrees’ world
Creators: name: Halttunen, Krista
Publisher: name: Imperial College London
Year: 2023

description: Meeting the temperature goals of the Paris Agreement necessitates large reductions in greenhouse gas emissions. The emissions of the global oil industry contribute significantly to global warming, and the traditional business models of oil companies are incompatible with a sustainable energy transition. International oil companies (IOCs), which include some of the largest and most powerful corporations in the world, continue to generate enormous profits from fossil fuels while facing growing public criticism and pressure to change in response to the climate crisis. There is no clear pathway to a more sustainable future. To address this issue, this thesis explores from several angles what meeting the goals of the Paris Agreement might mean for IOCs. The thesis first examines how professionals working in the oil industry make sense of the contradiction between the IOC business model and the urgency of climate change mitigation. A novel framework of employee responses to the oil-climate tension is developed based on in-depth interviews with 12 professionals. Against this background, the thesis explores potential outcomes for IOCs’ business models and geopolitical and market positions. Insights from industry interviews are combined with literature to produce comprehensive typologies of the strategy and diversification options available for IOCs in a sustainable energy transition. The options are discussed in the context of their business potential, ability to reduce carbon emissions, and strategic fit to oil industry skills and assets. The geopolitical positions of IOCs in the energy transition are researched through 12 further expert interviews. Potential changes in IOC market positions in the energy transition are explored with a novel proof-of-concept model of the upstream oil market and an original data set constructed from publicly available sources. This thesis makes clear that while IOCs can contribute to the energy transition through diversification, changes to the core fossil fuel business are also needed for alignment with the Paris Agreement goals. IOCs stand to lose out in the energy transition, as a sustained decrease in oil demand would lead them to lose both market share and geopolitical influence relative to national oil companies. Overall, the oil industry is not on track to meet the goals of the Paris Agreement and needs to prepare better for the scenarios studied in this thesis.
Efficient Measurement of Multiparticle Entanglement with Embedding Quantum Simulator
Creators: name: Chen, Ming-Cheng
name: Wu, Dian
name: Su, Zu-En
name: Cai, Xin-Dong
name: Wang, Xi-Lin
name: Yang, Tao
name: Li, Li
name: Liu, Nai-Le
name: Lu, Chao-Yang
name: Pan, Jan-Wei
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We reports direct and scalable measurement of multiparticle entanglement concurrence and three-tangle with embedding photonic quantum simulators. In this embedding framework [Phys. Rev. Lett. 111, 240502 (2013)], $N$-qubit entanglement monotone, which associates with non-Hermitian operators, can be efficiently measured with only 2 (for even $N$) and 6 (for odd $N$) local measurement settings. Our experiment uses a multiphoton quantum simulator to mimic the dynamical entanglement evolution and track its concurrence and three-tangle.
description: Fig.4 was updated
Pairwise Force SPH Model for Real-Time Multi-Interaction Applications
Creators: name: Yang, Tao
name: Lin, Ming C.
name: Martin, Ralph R.
name: Hu, Shi-Min
name: Chang, Jian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: In this paper, we present a novel pairwise-force smoothed particle hydrodynamics (PF-SPH) model to allow modeling of various interactions at interfaces in real time. Realistic capture of interactions at interfaces is a challenging problem for SPH-based simulations, especially for scenarios involving multiple interactions at different interfaces. Our PF-SPH model can readily handle multiple kinds of interactions simultaneously in a single simulation; its basis is to use a larger support radius than that used in standard SPH. We adopt a novel anisotropic filtering term to further improve the performance of interaction forces. The proposed model is stable; furthermore, it avoids the particle clustering problem which commonly occurs at the free surface. We show how our model can be used to capture various interactions. We also consider the close connection between droplets and bubbles, and show how to animate bubbles rising in liquid as well as bubbles in air. Our method is versatile, physically plausible and easy-to-implement. Examples are provided to demonstrate the capabilities and effectiveness of our approach.
Representation of the grand partition function of the cell model: The state equation in the mean-field approximation
Creators: name: Kozlovskii, Mikhailo
name: Dobush, Oksana
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The method to calculate the grand partition function of a particle system, in which constituents interact with each other via potential, that include repulsive and attractive components, is proposed. The cell model, which was introduced to describe critical phenomena and phase transitions, is used to provide calculations. The exact procedure of integration over particle coordinates and summation over number of particles is proposed. As a result, an evident expression for the grand partition function of the fluid cell model is obtained in the form of multiple integral over collective variables. As it can be seen directly from the structure of the transition jacobian, the present multiparticle model appeared to be different from the Ising model, which is widely used to describe fluid systems. The state equation, which is valid for wide temperature ranges both above and below the critical one, is derived in mean-field approximation. The pressure calculated for the cell model at temperatures above the critical one is found to be continuously increasing function of temperature and density. The isotherms of pressure as a function of density have horizontal parts at temperatures below the critical one.
description: 20 pages, 10 figures
Multiscale optimisation of dynamic properties for additively manufactured lattice structures
Creators: name: Nightingale, Morgan
Publisher: name: Imperial College London
Year: 2023

description: A framework for tailoring the dynamic properties of functionally graded lattice structures through the use of multiscale optimisation is presented in this thesis. The multiscale optimisation utilises a two scale approach to allow for complex lattice structures to be simulated in real time at a similar computational expense to traditional finite element problems. The micro and macro scales are linked by a surrogate model that predicts the homogenised material properties of the underlying lattice geometry based on the lattice design parameters. Optimisation constraints on the resonant frequencies and the Modal Assurance Criteria are implemented that can induce the structure to resonate at specific frequencies whilst simultaneously tracking and ensuring the correct mode shapes are maintained. This is where the novelty of the work lies, as dynamic properties have not previously been optimised for in a multiscale, functionally graded lattice structure. Multiscale methods offer numerous benefits and increased design freedom when generating optimal structures for dynamic environments. These benefits are showcased in a series of optimised cantilever structures. The results show a significant improvement in dynamic behavior when compared to the unoptimised case as well as when compared to a single scale topology optimised structure. The validation of the resonant properties for the lattice structures is performed through a series of mechanical tests on additive manufactured lattices. These tests address both the micro and the macro scale of the multiscale method. The homogeneous and surrogate model assumptions of the micro scale are investigated through both compression and tensile tests of uniform lattice samples. The resonant frequency predictions of the macro scale optimisation are verified through mechanical shaker testing and computed tomography scans of the lattice structure. Sources of discrepancy between the predicted and observed behavior are also investigated and explained.
The Pentaquark Candidates in the Dynamical Diquark Picture
Creators: name: Lebed, Richard F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Starting with the dynamical picture of the exotic $c\bar c$-containing states $XY \! Z$ as the confinement-induced hadronization of a rapidly separating pair of a compact diquark and antidiquark, we describe the pentaquark candidates $P_c^+(4380)$ and $P_c^+(4450)$ in terms of a confined but rapidly separating color-antitriplet diquark $cu$ and color-triplet "triquark" $\bar c (ud)$. This separation explains the relatively small $P_c^+$ widths, despite these 5-quark systems lying far above both the $J/ψ\, p$ and $Λ_c \bar D^{(*)0}$ thresholds. The $P_c^+$ states are predicted to form isospin doublets with neutral partners $P_c^0$.
description: 5 pages, 1 pdf figure, pdflatex. Version accepted by Phys. Lett. B
The Chimpanzee Model of Viral Hepatitis: Advances in Understanding the Immune Response and Treatment of Viral Hepatitis
Creators: name: Lemon, Stanley M.
name: Walker, Christopher M.
name: Lanford, Robert E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Chimpanzees (Pan troglodytes) have contributed to diverse fields of biomedical research due to their close genetic relationship to humans and in many instances due to the lack of any other animal model. This review focuses on the contributions of the chimpanzee model to research on hepatitis viruses where chimpanzees represented the only animal model (hepatitis B and C) or the most appropriate animal model (hepatitis A). Research with chimpanzees led to the development of vaccines for HAV and HBV that are used worldwide to protect hundreds of millions from these diseases and, where fully implemented, have provided immunity for entire generations. More recently, chimpanzee research was instrumental in the development of curative therapies for hepatitis C virus infections. Over a span of 40 years, this research would identify the causative agent of NonA,NonB hepatitis, validate the molecular tools for drug discovery, and provide safety and efficacy data on the therapies that now provide a rapid and complete cure of HCV chronic infections. Several cocktails of antivirals are FDA approved that eliminate the virus following 12 weeks of once-per-day oral therapy. This represents the first cure of a chronic viral disease and, once broadly implemented, will dramatically reduce the occurrence of cirrhosis and liver cancer. The recent contributions of chimpanzees to our current understanding of T cell immunity for HCV, development of novel therapeutics for HBV, and the biology of HAV are reviewed. Finally, a perspective is provided on the events leading to the cessation of the use of chimpanzees in research and the future of the chimpanzees previously used to bring about these amazing breakthroughs in human healthcare.
Lattice vibrations boost demagnetization entropy in shape memory alloy
Creators: name: Stonaha, Paul
name: Manley, Mike
name: Bruno, Nick
name: Karaman, Ibrahim
name: Arroyave, Raymundo
name: Singh, Navdeep
name: Abernathy, Douglas
name: Chi, Songxue
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Magnetocaloric (MC) materials present an avenue for chemical-free, solid state refrigeration through cooling via adiabatic demagnetization. We have used inelastic neutron scattering to measure the lattice dynamics in the MC material Ni45Co5Mn36.6In13.4. Upon heating across the Curie Temperature (TC), the material exhibits an anomalous increase in phonon entropy of 0.22 +/- 0.04 kB/atom, which is ten times larger than expected from conventional thermal expansion. This transition is accompanied by an abrupt softening of the transverse optic phonon. We present first-principle calculations showing a strong coupling between lattice distortions and magnetic excitations.
Airway Memory CD4 +  T Cells Mediate Protective Immunity against Emerging Respiratory Coronaviruses
Creators: name: David, Chella S.
name: Zhao, Jingxian
name: Channappanavar, Rudragouda
name: Perlman, Stanley
name: Meyerholz, David K.
name: Baric, Ralph S.
name: Zhao, Jincun
name: Mangalam, Ashutosh K.
name: Fett, Craig
name: Agnihothram, Sudhakar
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Two zoonotic coronaviruses (CoV), SARS-CoV and MERS-CoV have crossed species to cause severe human respiratory disease. Here, we showed that induction of airway memory CD4+ T cells specific for a conserved epitope shared by SARS-CoV and MERS-CoV is a potential strategy for developing pan-coronavirus vaccines. Airway memory CD4+ T cells differed phenotypically and functionally from lung-derived cells and were crucial for protection against both CoVs in mice. Protection was interferon-γ-dependent and required early induction of robust innate and virus-specific CD8+ T cell responses. The conserved epitope was also recognized in SARS-CoV and MERS-CoV-infected human leukocyte antigen DR2 and DR3 transgenic mice, indicating potential relevance in human populations. Additionally, this epitope was cross-protective between human and bat CoVs, the progenitors for many human CoVs. Vaccine strategies that induce airway memory CD4+ T cells targeting conserved epitopes may have broad applicability in the context of new CoV and other respiratory virus outbreaks.
Intestinal Interleukin-17 Receptor Signaling Mediates Reciprocal Control of the Gut Microbiota and Autoimmune Inflammation
Creators: name: Metzger, Dennis W.
name: Vikram, Amit
name: Montelaro, Ronald C.
name: Good, Misty
name: Schoenborn, Alexi A.
name: Kumar, Pawan
name: Kolls, Jay K.
name: Eddens, Taylor
name: Bibby, Kyle
name: Castillo, Patricia
name: Gulati, Ajay S.
name: Horne, William
name: Monin, Leticia
name: Elsegeiny, Waleed
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Interleukin-17 (IL-17) and IL-17 receptor (IL-17R) signaling are essential for regulating mucosal host defense against many invading pathogens. Commensal bacteria, especially segmented filamentous bacteria (SFB), are a crucial factor that drives T helper 17 (Th17) cell development in the gastrointestinal tract. In this study, we demonstrate that Th17 cells controlled SFB burden. Disruption of IL-17R signaling in the enteric epithelium resulted in SFB dysbiosis due to reduced expression of α-defensins, Pigr and Nox1. When subjected to experimental autoimmune encephalomyelitis, IL-17R signaling deficient mice demonstrated earlier disease onset and worsened severity that was associated with increased intestinal Csf2 expression and elevated systemic GM-CSF cytokine concentrations. Conditional deletion of IL-17R in the enteric epithelium demonstrated that there was a reciprocal relationship between the gut microbiota and enteric IL-17R signaling that controlled dysbiosis, constrained Th17 development, and regulated the susceptibility to autoimmune inflammation.